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.

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

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

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.

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.

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.

Coulomb interaction rules timescales in potassium ion channel tunneling

NASA Astrophysics Data System (ADS)

De March, N.; Prado, S. D.; Brunnet, L. G.

2018-06-01

Assuming the selectivity filter of KcsA potassium ion channel may exhibit quantum coherence, we extend a previous model by Vaziri and Plenio (2010 New J. Phys. 12 085001) to take into account Coulomb repulsion between potassium ions. We show that typical ion transit timescales are determined by this interaction, which imposes optimal input/output parameter ranges. Also, as observed in other examples of quantum tunneling in biological systems, the addition of moderate noise helps coherent ion transport.

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.

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.

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.

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

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.

Partial Model of Insulator/Insulator Contact Charging

NASA Technical Reports Server (NTRS)

Hogue, Michael; Calle, C. I.; Buhler, C. R.; Mucciolo, E. R.

2005-01-01

Two papers present a two-phase equilibrium model that partly explains insulator/ insulator contact charging. In this model, a vapor of ions within a gas is in equilibrium with a submonolayer of ions of the same species that have been adsorbed on the surface of an insulator. The surface is modeled as having localized states, each with a certain energy of adsorption for an ion. In an earlier version of the model described in the first paper, the ions do not interact with each other. Using the grand canonical ensemble, the chemical potentials of both vapor and absorbed phases are derived and equated to determine the vapor pressure. If a charge is assigned to the vapor particles (in particular, if single ionization is assumed), then the surface charge density associated with adsorbed ions can be calculated as a function of pressure. In a later version of the model presented in the second paper, the submodel of the vapor phase is extended to include electrostatic interactions between vapor ions and adsorbed ones as well as the screening effect, at a given distance from the surface, of ions closer to the surface. Theoretical values of this model closely match preliminary experimental data on the discharge of insulators as a function of pressure.

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

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.

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.

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.

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.

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

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.

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.

Competition among Li+, Na+, K+ and Rb+ Monovalent Ions for DNA in Molecular Dynamics Simulations using the Additive CHARMM36 and Drude Polarizable Force Fields

PubMed Central

Savelyev, Alexey; MacKerell, Alexander D.

2015-01-01

In the present study we report on interactions of and competition between monovalent ions for two DNA sequences in MD simulations. Efforts included the development and validation of parameters for interactions among the first-group monovalent cations, Li+, Na+, K+ and Rb+, and DNA in the Drude polarizable and additive CHARMM36 force fields (FF). The optimization process targeted gas-phase QM interaction energies of various model compounds with ions and osmotic pressures of bulk electrolyte solutions of chemically relevant ions. The optimized ionic parameters are validated against counterion condensation theory and buffer exchange-atomic emission spectroscopy measurements providing quantitative data on the competitive association of different monovalent ions with DNA. Comparison between experimental and MD simulation results demonstrates that, compared to the additive CHARMM36 model, the Drude FF provides an improved description of the general features of the ionic atmosphere around DNA and leads to closer agreement with experiment on the ionic competition within the ion atmosphere. Results indicate the importance of extended simulation systems on the order of 25 Å beyond the DNA surface to obtain proper convergence of ion distributions. PMID:25751286

Does Cation Size Affect Occupancy and Electrostatic Screening of the Nucleic Acid Ion Atmosphere?

PubMed Central

2016-01-01

Electrostatics are central to all aspects of nucleic acid behavior, including their folding, condensation, and binding to other molecules, and the energetics of these processes are profoundly influenced by the ion atmosphere that surrounds nucleic acids. Given the highly complex and dynamic nature of the ion atmosphere, understanding its properties and effects will require synergy between computational modeling and experiment. Prior computational models and experiments suggest that cation occupancy in the ion atmosphere depends on the size of the cation. However, the computational models have not been independently tested, and the experimentally observed effects were small. Here, we evaluate a computational model of ion size effects by experimentally testing a blind prediction made from that model, and we present additional experimental results that extend our understanding of the ion atmosphere. Giambasu et al. developed and implemented a three-dimensional reference interaction site (3D-RISM) model for monovalent cations surrounding DNA and RNA helices, and this model predicts that Na+ would outcompete Cs+ by 1.8–2.1-fold; i.e., with Cs+ in 2-fold excess of Na+ the ion atmosphere would contain an equal number of each cation (Nucleic Acids Res.2015, 43, 8405). However, our ion counting experiments indicate that there is no significant preference for Na+ over Cs+. There is an ∼25% preferential occupancy of Li+ over larger cations in the ion atmosphere but, counter to general expectations from existing models, no size dependence for the other alkali metal ions. Further, we followed the folding of the P4–P6 RNA and showed that differences in folding with different alkali metal ions observed at high concentration arise from cation–anion interactions and not cation size effects. Overall, our results provide a critical test of a computational prediction, fundamental information about ion atmosphere properties, and parameters that will aid in the development of next-generation nucleic acid computational models. PMID:27479701

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

Pickup ion processes associated with spacecraft thrusters: Implications for solar probe plus

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

Clemens, Adam, E-mail: a.j.clemens@qmul.ac.uk; Burgess, David

2016-03-15

Chemical thrusters are widely used in spacecraft for attitude control and orbital manoeuvres. They create an exhaust plume of neutral gas which produces ions via photoionization and charge exchange. Measurements of local plasma properties will be affected by perturbations caused by the coupling between the newborn ions and the plasma. A model of neutral expansion has been used in conjunction with a fully three-dimensional hybrid code to study the evolution and ionization over time of the neutral cloud produced by the firing of a mono-propellant hydrazine thruster as well as the interactions of the resulting ion cloud with the ambientmore » solar wind. Results are presented which show that the plasma in the region near to the spacecraft will be perturbed for an extended period of time with the formation of an interaction region around the spacecraft, a moderate amplitude density bow wave bounding the interaction region and evidence of an instability at the forefront of the interaction region which causes clumps of ions to be ejected from the main ion cloud quasi-periodically.« less

Development of Monopole Interaction Models for Ionic Compounds. Part I: Estimation of Aqueous Henry's Law Constants for Ions and Gas Phase pKa Values for Acidic Compounds.

PubMed

Hilal, S H; Saravanaraj, A N; Carreira, L A

2014-02-01

The SPARC (SPARC Performs Automated Reasoning in Chemistry) physicochemical mechanistic models for neutral compounds have been extended to estimate Henry's Law Constant (HLC) for charged species by incorporating ionic electrostatic interaction models. Combinations of absolute aqueous pKa values, relative pKa values in the gas phase, and aqueous HLC for neutral compounds have been used to develop monopole interaction models that quantify the energy differences upon moving an ionic solute molecule from the gas phase to the liquid phase. Inter-molecular interaction energies were factored into mechanistic contributions of monopoles with polarizability, dipole, H-bonding, and resonance. The monopole ionic models were validated by a wide range of measured gas phase pKa data for 450 acidic compounds. The RMS deviation error and R(2) for the OH, SH, CO2 H, CH3 and NR2 acidic reaction centers (C) were 16.9 kcal/mol and 0.87, respectively. The calculated HLCs of ions were compared to the HLCs of 142 ions calculated by quantum mechanics. Effects of inter-molecular interaction of the monopoles with polarizability, dipole, H-bonding, and resonance on acidity of the solutes in the gas phase are discussed. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

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.

Extension to Higher Mass Numbers of an Improved Knockout-Ablation-Coalescence Model for Secondary Neutron and Light Ion Production in Cosmic Ray Interactions

NASA Astrophysics Data System (ADS)

Indi Sriprisan, Sirikul; Townsend, Lawrence; Cucinotta, Francis A.; Miller, Thomas M.

Purpose: An analytical knockout-ablation-coalescence model capable of making quantitative predictions of the neutron spectra from high-energy nucleon-nucleus and nucleus-nucleus collisions is being developed for use in space radiation protection studies. The FORTRAN computer code that implements this model is called UBERNSPEC. The knockout or abrasion stage of the model is based on Glauber multiple scattering theory. The ablation part of the model uses the classical evaporation model of Weisskopf-Ewing. In earlier work, the knockout-ablation model has been extended to incorporate important coalescence effects into the formalism. Recently, alpha coalescence has been incorporated, and the ability to predict light ion spectra with the coalescence model added. The earlier versions were limited to nuclei with mass numbers less than 69. In this work, the UBERNSPEC code has been extended to make predictions of secondary neutrons and light ion production from the interactions of heavy charged particles with higher mass numbers (as large as 238). The predictions are compared with published measurements of neutron spectra and light ion energy for a variety of collision pairs. Furthermore, the predicted spectra from this work are compared with the predictions from the recently-developed heavy ion event generator incorporated in the Monte Carlo radiation transport code HETC-HEDS.

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

HZEFRG1: An energy-dependent semiempirical nuclear fragmentation model

NASA Technical Reports Server (NTRS)

Townsend, Lawrence W.; Wilson, John W.; Tripathi, Ram K.; Norbury, John W.; Badavi, Francis F.; Khan, Ferdous

1993-01-01

Methods for calculating cross sections for the breakup of high-energy heavy ions by the combined nuclear and coulomb fields of the interacting nuclei are presented. The nuclear breakup contributions are estimated with an abrasion-ablation model of heavy ion fragmentation that includes an energy-dependent, mean free path. The electromagnetic dissociation contributions arising from the interacting coulomb fields are estimated by using Weizsacker-Williams theory extended to include electric dipole and electric quadrupole contributions. The complete computer code that implements the model is included as an appendix. Extensive comparisons of cross section predictions with available experimental data are made.

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

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.

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.

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.

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.

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.

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.

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.

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.

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

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

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+).

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.

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.

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

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

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.

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.

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.

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.

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.

Dynamics of the Rydberg state population of slow highly charged ions impinging a solid surface at arbitrary collision geometry

NASA Astrophysics Data System (ADS)

Nedeljković, N. N.; Majkić, M. D.; Božanić, D. K.; Dojčilović, R. J.

2016-06-01

We consider the population dynamics of the intermediate Rydberg states of highly charged ions (core charge Z\\gg 1, principal quantum number {n}{{A}}\\gg 1) interacting with solid surfaces at arbitrary collision geometry. The recently developed resonant two-state vector model for the grazing incidence (2012 J. Phys. B: At. Mol. Opt. Phys. 45 215202) is extended to the quasi-resonant case and arbitrary angle of incidence. According to the model, the population probabilities depend both on the projectile parallel and perpendicular velocity components, in a complementary way. A cascade neutralization process for {{{Xe}}}Z+ ions, for Z=15{--}45, interacting with a conductive-surface is considered by taking into account the population dynamics. For an arbitrary collision geometry and given range of ionic velocities, a micro-staircase model for the simultaneous calculation of the kinetic energy gain and the charge state of the ion in front of the surface is proposed. The relevance of the obtained results for the explanation of the formation of nanostructures on solid surfaces by slow highly charged ions for normal incidence geometry is briefly discussed.

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.

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

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.

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.

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.

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.

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.

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.

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.

Charge-exchange plasma environment for an ion drive spacecraft. [a model for describing mercury ion engines and its effect on spacecraft subsystems

NASA Technical Reports Server (NTRS)

Kaufman, H. R.; Carruth, M. R., Jr.

1979-01-01

The charge exchange plasma environment around a spacecraft that uses mercury ion thrusters for propulsion is described. The interactions between the plasma environment and the spacecraft are determined and a model which describes the propagation of the mercury charge exchange plasma is discussed. The model is extended to describe the flow of the molybdenum component of the charge exchange plasma. The uncertainties in the models for various conditions are discussed and current drain to the solar array, charge exchange plasma material deposition, and the effects of space plasma on the charge exchange plasma propagation are addressed.

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.

Development of Monopole Interaction Models for Ionic Compounds. Part I: Estimation of Aqueous Henry’s Law Constants for Ions and Gas Phase pKa Values for Acidic Compounds

EPA Science Inventory

The SPARC (SPARC Performs Automated Reasoning in Chemistry) physicochemical mechanistic models for neutral compounds have been extended to estimate Henry’s Law Constant (HLC) for charged species by incorporating ionic electrostatic interaction models. Combinations of absolute aq...

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).

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

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.

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.

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.

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.

Long-pore Electrostatics in Inward-rectifier Potassium Channels

PubMed Central

Robertson, Janice L.; Palmer, Lawrence G.; Roux, Benoît

2008-01-01

Inward-rectifier potassium (Kir) channels differ from the canonical K+ channel structure in that they possess a long extended pore (∼85 Å) for ion conduction that reaches deeply into the cytoplasm. This unique structural feature is presumably involved in regulating functional properties specific to Kir channels, such as conductance, rectification block, and ligand-dependent gating. To elucidate the underpinnings of these functional roles, we examine the electrostatics of an ion along this extended pore. Homology models are constructed based on the open-state model of KirBac1.1 for four mammalian Kir channels: Kir1.1/ROMK, Kir2.1/IRK, Kir3.1/GIRK, and Kir6.2/KATP. By solving the Poisson-Boltzmann equation, the electrostatic free energy of a K+ ion is determined along each pore, revealing that mammalian Kir channels provide a favorable environment for cations and suggesting the existence of high-density regions in the cytoplasmic domain and cavity. The contribution from the reaction field (the self-energy arising from the dielectric polarization induced by the ion's charge in the complex geometry of the pore) is unfavorable inside the long pore. However, this is well compensated by the electrostatic interaction with the static field arising from the protein charges and shielded by the dielectric surrounding. Decomposition of the static field provides a list of residues that display remarkable correspondence with existing mutagenesis data identifying amino acids that affect conduction and rectification. Many of these residues demonstrate interactions with the ion over long distances, up to 40 Å, suggesting that mutations potentially affect ion or blocker energetics over the entire pore. These results provide a foundation for understanding ion interactions in Kir channels and extend to the study of ion permeation, block, and gating in long, cation-specific pores. PMID:19001143

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

Divalent Ion Parameterization Strongly Affects Conformation and Interactions of an Anionic Biomimetic Polymer.

PubMed

Daily, Michael D; Baer, Marcel D; Mundy, Christopher J

2016-03-10

The description of peptides and the use of molecular dynamics simulations to refine structures and investigate the dynamics on an atomistic scale are well developed. Through a consensus in this community over multiple decades, parameters were developed for molecular interactions that only require the sequence of amino-acids and an initial guess for the three-dimensional structure. The recent discovery of peptoids will require a retooling of the currently available interaction potentials in order to have the same level of confidence in the predicted structures and pathways as there is presently in the peptide counterparts. Here we present modeling of peptoids using a combination of ab initio molecular dynamics (AIMD) and atomistic resolution classical force field (FF) to span the relevant time and length scales. To properly account for the dominant forces that stabilize ordered structures of peptoids, namely steric-, electrostatic, and hydrophobic interactions mediated through side chain-side chain interactions in the FF model, those have to be first mapped out using high fidelity atomistic representations. A key feature here is not only to use gas phase quantum chemistry tools, but also account for solvation effects in the condensed phase through AIMD. One major challenge is to elucidate ion binding to charged or polar regions of the peptoid and its concomitant role in the creation of local order. Here, similar to proteins, a specific ion effect is observed suggesting that both the net charge and the precise chemical nature of the ion will need to be described.

Synergistically-enhanced ion track formation in pre-damaged strontium titanate by energetic heavy ions

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

Xue, Haizhou; Zarkadoula, Eva; Sachan, Ritesh

Latent ion tracks created by energetic heavy ions (12 MeV Ti to 946 MeV Au) in single crystal SrTiO 3 are investigated in this paper using Rutherford backscattering spectrometry and scanning transmission electron microscopy. The results demonstrate that pre-existing irradiation damage, introduced via elastic collision processes, interacts synergistically with the electronic energy deposition from energetic heavy ions to enhance formation of latent ion tracks. The average amorphous cross-section increases with the level of pre-damage and is linearly proportional to the electronic energy loss of the ions, with a slope dependent on the pre-damage level. For the highest energy ions (629more » MeV Xe and 946 MeV Au), the tracks are continuous over the pre-damaged depth, but become discontinuous beyond the pre-damaged region. Finally, this work provides new understanding and insights on ion-solid interactions that significantly impact the interpretation of latent track formation processes, models of amorphization, and the fabrication of electro-ceramic devices.« less

Synergistically-enhanced ion track formation in pre-damaged strontium titanate by energetic heavy ions

DOE PAGES

Xue, Haizhou; Zarkadoula, Eva; Sachan, Ritesh; ...

2018-03-20

Latent ion tracks created by energetic heavy ions (12 MeV Ti to 946 MeV Au) in single crystal SrTiO 3 are investigated in this paper using Rutherford backscattering spectrometry and scanning transmission electron microscopy. The results demonstrate that pre-existing irradiation damage, introduced via elastic collision processes, interacts synergistically with the electronic energy deposition from energetic heavy ions to enhance formation of latent ion tracks. The average amorphous cross-section increases with the level of pre-damage and is linearly proportional to the electronic energy loss of the ions, with a slope dependent on the pre-damage level. For the highest energy ions (629more » MeV Xe and 946 MeV Au), the tracks are continuous over the pre-damaged depth, but become discontinuous beyond the pre-damaged region. Finally, this work provides new understanding and insights on ion-solid interactions that significantly impact the interpretation of latent track formation processes, models of amorphization, and the fabrication of electro-ceramic devices.« less

An approach to the ionic cholinergic interaction. Theoretical treatment of the interaction between tetramethylammonium and acetate ions

NASA Astrophysics Data System (ADS)

Zuccarello, Felice; Raudino, Antonio; Buemi, Giuseppe

1980-03-01

The interaction between the anionic site of cholinesterase and the cationic end of acetylcholine is estimated by considering a simplified model. The effect of the aqueous environment on the stability of the aggregate is considered.

Kinetic modeling of streamer penetration into de-ionized water

NASA Astrophysics Data System (ADS)

Levko, Dmitry; Sharma, Ashish; Raja, Laxminarayan L.

2018-03-01

Interest in plasma-liquid interaction phenomena has grown in recent years due to applications in plasma medicine, water purification, and plasma-hydrocarbon reforming. The plasma in contact with liquid is generated, for example, using the plasma jets or streamer discharges. The interaction between the streamer and water can cause both physical and chemical modifications of the liquid. In this paper, the interaction between an anode-directed streamer and the de-ionized water is studied using one-dimensional particle-in-cell Monte Carlo collisions model. In this model, plasma species in both gas and liquid phase are considered as the macro-particles. We find that the penetration of the streamer head into the liquid causes ionization of water molecules by electron impact, a process which is usually ignored in the fluid models. The main charge carriers in the liquid phase are negative water ions which agree with earlier experimental and computational modeling studies. Additionally, we observe an ion-rich sheath in the vicinity of the water surface on the gas side.

Balancing the Interactions of Ions, Water, and DNA in the Drude Polarizable Force Field

PubMed Central

2015-01-01

Recently we presented a first-generation all-atom Drude polarizable force field for DNA based on the classical Drude oscillator model, focusing on optimization of key dihedral angles followed by extensive validation of the force field parameters. Presently, we describe the procedure for balancing the electrostatic interactions between ions, water, and DNA as required for development of the Drude force field for DNA. The proper balance of these interactions is shown to impact DNA stability and subtler conformational properties, including the conformational equilibrium between the BI and BII states, and the A and B forms of DNA. The parametrization efforts were simultaneously guided by gas-phase quantum mechanics (QM) data on small model compounds and condensed-phase experimental data on the hydration and osmotic properties of biologically relevant ions and their solutions, as well as theoretical predictions for ionic distribution around DNA oligomer. In addition, fine-tuning of the internal base parameters was performed to obtain the final DNA model. Notably, the Drude model is shown to more accurately reproduce counterion condensation theory predictions of DNA charge neutralization by the condensed ions as compared to the CHARMM36 additive DNA force field, indicating an improved physical description of the forces dictating the ionic solvation of DNA due to the explicit treatment of electronic polarizability. In combination with the polarizable DNA force field, the availability of Drude polarizable parameters for proteins, lipids, and carbohydrates will allow for simulation studies of heterogeneous biological systems. PMID:24874104

ATP4A gene regulatory network for fine-tuning of proton pump and ion channels.

PubMed

Singh, Vijai; Mani, Indra; Chaudhary, Dharmendra Kumar

2013-06-01

The ATP4A encodes α subunit of H(+), K(+)-ATPase that contains catalytic sites of the enzyme forming pores through cell membrane which allows the ion transport. H(+), K(+)-ATPase is a membrane bound P-type ATPase enzyme which is found on the surface of parietal cells and uses the energy derived from each cycle of ATP hydrolysis that can help in exchanging ions (H(+), K(+) and Cl(-)) across the cell membrane secreting acid into the gastric lumen. The 3-D model of α-subunit of H(+), K(+)-ATPase was generated by homology modeling. It was evaluated and validated on the basis of free energies and amino acid residues. The inhibitor binding amino acid active pockets were identified in the 3-D model by molecular docking. The two drugs Omeprazole and Rabeprazole were found more potent interactions with generated model of α-subunit of H(+), K(+)-ATPase on the basis of their affinity between drug-protein interactions. We have generated ATP4A gene regulatory networks for interactions with other proteins which involved in regulation that can help in fine-tuning of proton pump and ion channels. These findings provide a new dimension for discovery and development of proton pump inhibitors and gene regulation of the ATPase. It can be helpful in better understanding of human physiology and also using synthetic biology strategy for reprogramming of parietal cells for control of gastric ulcers.

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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 (MX2), where M = Mg2+, Ca2+, Sr2+, Ba2+ 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.

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.

Sensing of heavy metal ions by intrinsic TMV coat protein fluorescence.

PubMed

Bayram, Serene S; Green, Philippe; Blum, Amy Szuchmacher

2018-04-15

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, Cd 2+ , Pb 2+ , Zn 2+ and Ni 2+ 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. Copyright © 2018 Elsevier B.V. All rights reserved.

Ion Selectivity in the KcsA Potassium Channel from the Perspective of the Ion Binding Site

PubMed Central

Dixit, Purushottam D.; Merchant, Safir; Asthagiri, D.

2009-01-01

To understand the thermodynamic exclusion of Na+ relative to K+ from the S2 site of the selectivity filter, the distribution PX(ɛ) (X = K+ or Na+) of the binding energy (ɛ) of the ion with the channel is analyzed using the potential distribution theorem. By expressing the excess chemical potential of the ion as a sum of mean-field 〈ɛ〉 and fluctuation μexflux,X contributions, we find that selectivity arises from a higher value of μflux,Na+ex relative to μflux,K+ex. To understand the role of site-site interactions on μexflux,X, we decompose PX(ɛ) into n-dependent distributions, where n is the number of ion-coordinating ligands within a distance λ from the ion. For λ comparable to typical ion-oxygen bond distances, investigations building on this multistate model reveal an inverse correlation between favorable ion-site and site-site interactions: the ion-coordination states that most influence the thermodynamics of the ion are also those for which the binding site is energetically less strained and vice versa. This correlation motivates understanding entropic effects in ion binding to the site and leads to the finding that μexflux,X is directly proportional to the average site-site interaction energy, a quantity that is sensitive to the chemical type of the ligand coordinating the ion. Increasing the coordination number around Na+ only partially accounts for the observed magnitude of selectivity; acknowledging the chemical type of the ion-coordinating ligand is essential. PMID:19289040

Ion beam microtexturing and enhanced surface diffusion

NASA Technical Reports Server (NTRS)

Robinson, R. S.

1982-01-01

Ion beam interactions with solid surfaces are discussed with particular emphasis on microtexturing induced by the deliberate deposition of controllable amounts of an impurity material onto a solid surface while simultaneously sputtering the surface with an ion beam. Experimental study of the optical properties of microtextured surfaces is described. Measurements of both absorptance as a function of wavelength and emissivity are presented. A computer code is described that models the sputtering and ion reflection processes involved in microtexture formation.

Non-covalent and coordination interactions in Cu(II) systems with uridine, uridine 5'-monophosphate and triamine or tetramine as biogenic amine analogues in aqueous solutions.

PubMed

Łomozik, Lechosław; Jastrzab, Renata

2003-10-01

Reactions of metallation and non-covalent interactions have been studied in ternary systems of Cu(II) ions with uridine, uridine 5'-monophosphate and diamines or triamines. It has been found that in metal-free systems the reaction centres of the nucleoside with the polyamine are the donor nitrogen atoms N(3) and protonated -NH(x) groups of the amines. In comparison to systems with adenosine or cytidine, the pH range of complex formation is shifted towards higher values. It is a consequence of significantly higher basicity of uridine and in agreement with the ion-ion, ion-dipole interaction model assumed. Formation of molecular complexes of uridine 5'-monophosphate with polyamines at a low pH is the result of activity of the phosphate group which plays the role of a negatively charged reaction site. Non-covalent interactions interfere in processes of bioligand metallation. Centres of weak interactions are simultaneously binding sites of metal ions. In protonated Cu(Urd)(PA)H(x) complexes, coordination has been found to involve the N(3) atom from the nucleoside and two donor nitrogen atoms from the polyamine (PA). In the heteroligand species Cu(Urd)(PA), despite deprotonation of all amine groups, one of these groups is located outside the inner coordination sphere. In complexes with uridine-5'-monophosphate, the phosphate group is active in metallation. Moreover, in certain coordination compounds this group is engaged in non-covalent interactions with PA molecules, despite binding Cu ions, as has been shown on the basis of equilibrium and spectral studies.

van der Waals Interactions in Hadron Resonance Gas: From Nuclear Matter to Lattice QCD.

PubMed

Vovchenko, Volodymyr; Gorenstein, Mark I; Stoecker, Horst

2017-05-05

An extension of the ideal hadron resonance gas (HRG) model is constructed which includes the attractive and repulsive van der Waals (VDW) interactions between baryons. This VDW-HRG model yields the nuclear liquid-gas transition at low temperatures and high baryon densities. The VDW parameters a and b are fixed by the ground state properties of nuclear matter, and the temperature dependence of various thermodynamic observables at zero chemical potential are calculated within the VDW-HRG model. Compared to the ideal HRG model, the inclusion of VDW interactions between baryons leads to a qualitatively different behavior of second and higher moments of fluctuations of conserved charges, in particular in the so-called crossover region T∼140-190  MeV. For many observables this behavior resembles closely the results obtained from lattice QCD simulations. This hadronic model also predicts nontrivial behavior of net-baryon fluctuations in the region of phase diagram probed by heavy-ion collision experiments. These results imply that VDW interactions play a crucial role in the thermodynamics of hadron gas. Thus, the commonly performed comparisons of the ideal HRG model with the lattice and heavy-ion data may lead to misconceptions and misleading conclusions.

The dynamo of the diurnal tide and its effect on the thermospheric circulation

NASA Technical Reports Server (NTRS)

Mayr, H. G.; Harris, I.; Herrero, F. A.

1990-01-01

A theoretical multiconstituent model (including O, N2, and O2) which describes the interactions between neutral winds, dynamo electric fields, and ion drifts is used to interpret observations that revealed a dominance of the fundamental diurnal tide in the upper thermosphere and at equatorial latitudes, and its effect on the thermospheric circulation. The model is shown to reproduce reasonably well the magnitudes of the neutral winds, ion drift velocities, and the ratio between the two. A solution for the neutral winds in which the dynamo electric field is forced to zero shows that the dynamo-induced ion drift is very important in accelerating the neutral atmosphere at higher altitudes. The dynamo interaction primarily affects the curl component of the field; its effect on the temperature and density perturbations is small.

Lieb-Robinson bounds for spin-boson lattice models and trapped ions.

PubMed

Jünemann, J; Cadarso, A; Pérez-García, D; Bermudez, A; García-Ripoll, J J

2013-12-06

We derive a Lieb-Robinson bound for the propagation of spin correlations in a model of spins interacting through a bosonic lattice field, which satisfies a Lieb-Robinson bound in the absence of spin-boson couplings. We apply these bounds to a system of trapped ions and find that the propagation of spin correlations, as mediated by the phonons of the ion crystal, can be faster than the regimes currently explored in experiments. We propose a scheme to test the bounds by measuring retarded correlation functions via the crystal fluorescence.

A comparative study of the magnetization in transition metal ion doped CeO2, TiO2 and SnO2 nanoparticles

NASA Astrophysics Data System (ADS)

Apostolov, A. T.; Apostolova, I. N.; Wesselinowa, J. M.

2018-05-01

Using the microscopic s-d model taking into account anharmonic spin-phonon interactions we have studied the magnetic properties of Co and Cu ion doped CeO2 and TiO2 nanoparticles and compared them with those of SnO2. By Co-doping there is a maximum in the magnetization M(x) curve for all nanoparticles observed in the most transition metal doped ones. The s-d interaction plays an important role by the decrease of M at higher dopant concentration. We have discussed the magnetization in dependence of different model parameters. By small Cu-ion doping there are some differences. In CeO2M decreases with the Cu-concentration, whereas in TiO2 and SnO2M increases. For higher Cu dopant concentrations M(X) decreases in TiO2 nanoparticles. We obtain room temperature ferromagnetism also in Zn doped CeO2, TiO2 and SnO2 nanoparticles, i.e. in non-transition metal ion doped ones. The different behavior of M in Co and Cu doped nanoparticles is due to a combination effect of multivalent metal ions, oxygen vacancies, different radius of cation dopants, connection between lattice and magnetism, as well as competition between the s-d and d-d ferromagnetic or antiferromagnetic interactions.

Separation of aromatic carboxylic acids using quaternary ammonium salts on reversed-phase HPLC. 1. Separation behavior of aromatic carboxylic acids

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

Kawamura, K.; Okuwaki, A.; Verheyen, T.

In order to develop separation processes and analytical methods for aromatic carboxylic acids for the coal oxidation products, the separation behavior of aromatic carboxylic acids on a reversed-phase HPLC using eluent containing quaternary ammonium salt has been investigated. The retention mechanism of aromatic carboxylic acids was discussed on the basis of both ion-pair partition model and ion-exchange model. The retention behavior of aromatic carboxylic acids possessing one (or two) carboxylic acid group(s) followed the ion-pair partition model, where linear free energy relationship was observed between the capacity factor and the extraction equilibrium constants of benzoic acid and naphthalene carboxylic acid.more » Besides, the retention behavior followed ion-exchange model with increasing the number of carboxylic acids, where the capacity factor of benzene polycarboxylic acids is proportional to the association constants between aromatic acids and quaternary ammonium ions calculated on the basis of an electrostatic interaction model.« less

Saturation of conductance in single ion channels: the blocking effect of the near reaction field.

PubMed

Nadler, Boaz; Schuss, Zeev; Hollerbach, Uwe; Eisenberg, R S

2004-11-01

The ionic current flowing through a protein channel in the membrane of a biological cell depends on the concentration of the permeant ion, as well as on many other variables. As the concentration increases, the rate of arrival of bath ions to the channel's entrance increases, and typically so does the net current. This concentration dependence is part of traditional diffusion and rate models that predict Michaelis-Menten current-concentration relations for a single ion channel. Such models, however, neglect other effects of bath concentrations on the net current. The net current depends not only on the entrance rate of ions into the channel, but also on forces acting on ions inside the channel. These forces, in turn, depend not only on the applied potential and charge distribution of the channel, but also on the long-range Coulombic interactions with the surrounding bath ions. In this paper, we study the effects of bath concentrations on the average force on an ion in a single ion channel. We show that the force of the reaction field on a discrete ion inside a channel embedded in an uncharged lipid membrane contains a blocking (shielding) term that is proportional to the square root of the ionic bath concentration. We then show that different blocking strengths yield different behavior of the current-concentration and conductance-concentration curves. Our theory shows that at low concentrations, when the blocking force is weak, conductance grows linearly with concentration, as in traditional models, e.g., Michaelis-Menten formulations. As the concentration increases to a range of moderate shielding, conductance grows as the square root of concentration, whereas at high concentrations, with high shielding, conductance may actually decrease with increasing concentrations: the conductance-concentration curve can invert. Therefore, electrostatic interactions between bath ions and the single ion inside the channel can explain the different regimes of conductance-concentration relations observed in experiments.

Equilibrium swelling properties of polyampholytic hydrogels

NASA Astrophysics Data System (ADS)

English, Anthony E.; Mafé, Salvador; Manzanares, José A.; Yu, Xiahong; Grosberg, Alexander Yu.; Tanaka, Toyoichi

1996-06-01

The role of counter ions and ion dissociation in establishing the equilibrium swelling of balanced and unbalanced polyampholytic hydrogels has been investigated experimentally and theoretically. The swelling dependence on both the net charge offset and the external bath salt concentration has been examined using an acrylamide based polyampholytic hydrogels. By careful consideration of the swelling kinetics, we illustrate the effects of ion dissociation equilibria and counter ion shielding in polyampholytic hydrogels near their balance point where both polyelectrolyte and polyampholyte effects are present. The theory considers a Flory type swelling model where the Coulombic interactions between fixed ions in the hydrogel resemble those of an ionic solid with a Debye screening factor. Theoretical predictions from this model are in qualitative agreement with our experimental results.

Stochastic Ion Heating by the Lower-Hybrid Waves

NASA Technical Reports Server (NTRS)

Khazanov, G.; Tel'nikhin, A.; Krotov, A.

2011-01-01

The resonance lower-hybrid wave-ion interaction is described by a group (differentiable map) of transformations of phase space of the system. All solutions to the map belong to a strange attractor, and chaotic motion of the attractor manifests itself in a number of macroscopic effects, such as the energy spectrum and particle heating. The applicability of the model to the problem of ion heating by waves at the front of collisionless shock as well as ion acceleration by a spectrum of waves is discussed. Keywords: plasma; ion-cyclotron heating; shocks; beat-wave accelerator.

Inhibition of ferric ion to oxalate oxidase shed light on the substrate binding site.

PubMed

Pang, Yu; Lan, Wanjun; Huang, Xuelei; Zuo, Guanke; Liu, Hui; Zhang, Jingyan

2015-10-01

Oxalate oxidase (OxOx), a well known enzyme catalyzes the cleavage of oxalate to carbon dioxide with reduction of dioxygen to hydrogen peroxide, however its catalytic process is not well understood. To define the substrate binding site, interaction of Fe(3+) ions with OxOx was systemically investigated using biochemical method, circular dichrosim spectroscopy, microscale thermophoresis, and computer modeling. We demonstrated that Fe(3+) is a non-competitive inhibitor with a milder binding affinity to OxOx, and the secondary structure of the OxOx was slightly altered upon its binding. On the basis of the structural properties of the OxOx and its interaction with Fe(3+) ions, two residue clusters of OxOx were assigned as potential Fe(3+) binding sites, the mechanism of the inhibition of Fe(3+) was delineated. Importantly, the residues that interact with Fe(3+) ions are involved in the substrate orienting based on computer docking. Consequently, the interaction of OxOx with Fe(3+) highlights insight into substrate binding site in OxOx.

3D Hybrid Simulations of Interactions of High-Velocity Plasmoids with Obstacles

NASA Astrophysics Data System (ADS)

Omelchenko, Y. A.; Weber, T. E.; Smith, R. J.

2015-11-01

Interactions of fast plasma streams and objects with magnetic obstacles (dipoles, mirrors, etc) lie at the core of many space and laboratory plasma phenomena ranging from magnetoshells and solar wind interactions with planetary magnetospheres to compact fusion plasmas (spheromaks and FRCs) to astrophysics-in-lab experiments. Properly modeling ion kinetic, finite-Larmor radius and Hall effects is essential for describing large-scale plasma dynamics, turbulence and heating in complex magnetic field geometries. Using an asynchronous parallel hybrid code, HYPERS, we conduct 3D hybrid (particle-in-cell ion, fluid electron) simulations of such interactions under realistic conditions that include magnetic flux coils, ion-ion collisions and the Chodura resistivity. HYPERS does not step simulation variables synchronously in time but instead performs time integration by executing asynchronous discrete events: updates of particles and fields carried out as frequently as dictated by local physical time scales. Simulations are compared with data from the MSX experiment which studies the physics of magnetized collisionless shocks through the acceleration and subsequent stagnation of FRC plasmoids against a strong magnetic mirror and flux-conserving boundary.

Multi-Species Test of Ion Cyclotron Resonance Heating at High Altitudes

NASA Technical Reports Server (NTRS)

Persoon, A. M.; Peterson, W. K.; Andre, M.; Chang, T.; Gurnett, D. A.; Retterer, J. M.; Crew, G. B.

1997-01-01

Observations of ion distributions and plasma waves obtained by the Dynamics Explorer 1 satellite in the high-altitude, nightside auroral zone are used to study ion energization for three ion species. A number of theoretical models have been proposed to account for the transverse heating of these ion populations. One of these, the ion cyclotron resonance heating (ICRH) mechanism, explains ion conic formation through ion cyclotron resonance with broadband electromagnetic wave turbulence in the vicinity of the characteristic ion cyclotron frequency. The cyclotron resonant heating of the ions by low- frequency electromagnetic waves is an important energy source for the transport of ions from the ionosphere to the magnetosphere. In this paper we test the applicability of the ICRH mechanism to three simultaneously heated and accelerated ion species by modelling the ion conic formation in terms of a resonant wave-particle interaction in which the ions extract energy from the portion of the broadband electromagnetic wave spectrum which includes the ion cyclotron frequency. Using a Monte Carlo technique we evaluate the ion heating produced by the electromagnetic turbulence at low frequencies and find that the wave amplitudes near the ion cyclotron frequencies are sufficient to explain the observed ion energies.

Multi-Species Test of Ion Cyclotron Resonance Heating at High Altitudes

NASA Technical Reports Server (NTRS)

Persoon, A. M.; Peterson, W. K.; Andre, M.; Chang, T.; Gurnett, D. A.; Retterer, J. M.; Crew, G. B.

1997-01-01

Observations of ion distributions and plasma waves obtained by the Dynamics Explorer 1 satellite in the high-altitude, nightside auroral zone are used to study ion energization for three ion species. A number of theoretical models have been proposed to account for the transverse heating of these ion populations. One of these, the ion cyclotron resonance heating (ICRH) mechanism, explains ion conic formation through ion cyclotron resonance with broadband electromagnetic wave turbulence in the vicinity of the characteristic ion cyclotron frequency. The cyclotron resonant heating of the ions by low-frequency electromagnetic waves is an important energy source for the transport of ions from the ionosphere to the magnetosphere. In this paper we test the applicability of the ICRH mechanism to three simultaneously heated and accelerated ion species by modelling the ion conic formation in terms of a resonant wave-particle interaction in which the ions extract energy from the portion of the broadband electromagnetic wave spectrum which includes the ion cyclotron frequency. Using a Monte Carlo technique we evaluate the ion heating produced by the electromagnetic turbulence at low frequencies and find that the wave amplitudes near the ion cyclotron frequencies are sufficient to explain the observed ion energies.

Modeling interactions in major ion toxicity to Ceriodaphnia dubia

EPA Science Inventory

Various anthopogenic activities can cause exposures of freshwater systems to greatly elevated concentrations of major ions (Na, K, Ca, Mg, Cl, SO4, HCO3) with widely-varying compositions. A data set on the acute toxicity of single salts and binary salt mixtures to Ceriodaphnia d...

Overview of the Graphical User Interface for the GERM Code (GCR Event-Based Risk Model

NASA Technical Reports Server (NTRS)

Kim, Myung-Hee; Cucinotta, Francis A.

2010-01-01

The descriptions of biophysical events from heavy ions are of interest in radiobiology, cancer therapy, and space exploration. The biophysical description of the passage of heavy ions in tissue and shielding materials is best described by a stochastic approach that includes both ion track structure and nuclear interactions. A new computer model called the GCR Event-based Risk Model (GERM) code was developed for the description of biophysical events from heavy ion beams at the NASA Space Radiation Laboratory (NSRL). The GERM code calculates basic physical and biophysical quantities of high-energy protons and heavy ions that have been studied at NSRL for the purpose of simulating space radiobiological effects. For mono-energetic beams, the code evaluates the linear-energy transfer (LET), range (R), and absorption in tissue equivalent material for a given Charge (Z), Mass Number (A) and kinetic energy (E) of an ion. In addition, a set of biophysical properties are evaluated such as the Poisson distribution of ion or delta-ray hits for a specified cellular area, cell survival curves, and mutation and tumor probabilities. The GERM code also calculates the radiation transport of the beam line for either a fixed number of user-specified depths or at multiple positions along the Bragg curve of the particle. The contributions from primary ion and nuclear secondaries are evaluated. The GERM code 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. The QMSFRG model has been shown to be in excellent agreement with available experimental data for nuclear fragmentation cross sections, and has been used by the GERM code for application to thick target experiments. The GERM code provides scientists participating in NSRL experiments with the data needed for the interpretation of their experiments, including the ability to model the beam line, the shielding of samples and sample holders, and the estimates of basic physical and biological outputs of the designed experiments. We present an overview of the GERM code GUI, as well as providing training applications.

Overview of the Graphical User Interface for the GERMcode (GCR Event-Based Risk Model)

NASA Technical Reports Server (NTRS)

Kim, Myung-Hee Y.; Cucinotta, Francis A.

2010-01-01

The descriptions of biophysical events from heavy ions are of interest in radiobiology, cancer therapy, and space exploration. The biophysical description of the passage of heavy ions in tissue and shielding materials is best described by a stochastic approach that includes both ion track structure and nuclear interactions. A new computer model called the GCR Event-based Risk Model (GERM) code was developed for the description of biophysical events from heavy ion beams at the NASA Space Radiation Laboratory (NSRL). The GERMcode calculates basic physical and biophysical quantities of high-energy protons and heavy ions that have been studied at NSRL for the purpose of simulating space radiobiological effects. For mono-energetic beams, the code evaluates the linear-energy transfer (LET), range (R), and absorption in tissue equivalent material for a given Charge (Z), Mass Number (A) and kinetic energy (E) of an ion. In addition, a set of biophysical properties are evaluated such as the Poisson distribution of ion or delta-ray hits for a specified cellular area, cell survival curves, and mutation and tumor probabilities. The GERMcode also calculates the radiation transport of the beam line for either a fixed number of user-specified depths or at multiple positions along the Bragg curve of the particle. The contributions from primary ion and nuclear secondaries are evaluated. 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. The QMSFRG model has been shown to be in excellent agreement with available experimental data for nuclear fragmentation cross sections, and has been used by the GERMcode for application to thick target experiments. The GERMcode provides scientists participating in NSRL experiments with the data needed for the interpretation of their experiments, including the ability to model the beam line, the shielding of samples and sample holders, and the estimates of basic physical and biological outputs of the designed experiments. We present an overview of the GERMcode GUI, as well as providing training applications.

The Importance of the Cathode Plume and Its Interactions with the Ion Beam in Numerical Simulations of Hall Thrusters

NASA Technical Reports Server (NTRS)

Lopez Ortega, Alejandro; Mikellides, Ioannis G.

2015-01-01

Hall2De is a first-principles, 2-D axisymmetric code that solves the equations of motion for ions, electrons, and neutrals on a magnetic-field-aligned grid. The computational domain downstream of the acceleration channel exit plane is large enough to include self-consistently the cathode boundary. In this paper, we present results from numerical simulations of the H6 laboratory thruster with an internally mounted cathode, with the aim of highlighting the importance of properly accounting for the interactions between the ion beam and cathode plume. The anomalous transport of electrons across magnetic field lines in Hall2De is modelled using an anomalous collision frequency, ?anom, yielding ?anom approximately equal to omega ce (i.e., the electron cyclotron frequency) in the plume. We first show that restricting the anomalous collision frequency to only regions where the current density of ions is large does not alter the plasma discharge in the Hall thruster as long as the interaction between the ion beam and the cathode plume is captured properly in the computational domain. This implies that the boundary conditions must be placed sufficiently far as to not interfere with the electron transport in this region. These simulation results suggest that electron transport across magnetic field lines occurs largely inside the beam and may be driven by the interactions between beam ions and electrons. A second finding that puts in relevance the importance of including the cathode plume in numerical simulations is on the significance of accounting for the ion acoustic turbulence (IAT), now known to occur in the vicinity of the cathode exit. We have included in the Hall2De simulations a model of the IAT-driven anomalous collision frequency based on Sagdeev's model for saturation of the ion-acoustic instability. This implementation has allowed us to achieve excellent agreement with experimental measurements in the near plume obtained during the operation of the H6 thruster at nominal conditions (300V, 20A) and chamber background pressure of approximately 1.5 x 10(exp -5) Torr. In addition, the numerical results obtained with the latter approach exhibit less sensitivity to background pressure than previous attempts at explaining the features of the plasma properties in the near plume.

The Electric Propulsion Interactions Code (EPIC): A Member of the NASA Space Environment and Effects Program (SEE) Toolset

NASA Technical Reports Server (NTRS)

Mikellides, Ioannis G.; Mandell, Myron J.; Kuharski, Robert A.; Davis, D. A.; Gardner, Barbara M.; Minor, Jody

2003-01-01

Science Applications International Corporation is currently developing the Electric Propulsion Interactions Code, EPIC, as part of a project sponsored by the Space Environments and Effects Program at NASA Marshall Space Flight Center. Now in its second year of development, EPIC is an interactive computer toolset that allows the construction of a 3-D spacecraft model, and the assessment of a variety of interactions between its subsystems and the plume from an electric thruster. This paper reports on the progress of EPZC including the recently added ability to exchange results the NASA Charging Analyzer Program, Nascap-2k. The capability greatly enhances EPIC's range of applicability. Expansion of the toolset's various physics models proceeds in parallel with the overall development of the software. Also presented are recent upgrades of the elastic scattering algorithm in the electric propulsion Plume Tool. These upgrades are motivated by the need to assess the effects of elastically scattered ions on the SIC for ion beam energies that exceed loo0 eV. Such energy levels are expected in future high-power (>10 kW) ion propulsion systems empowered by nuclear sources.

Deconstructing Free Energies in the Law of Matching Water Affinities.

PubMed

Shi, Yu; Beck, Thomas

2017-03-09

The law of matching water affinities (LMWA) is explored in classical molecular dynamics simulations of several alkali halide ion pairs, spanning the size range from small kosmotropes to large chaotropes. The ion-ion potentials of mean force (PMFs) are computed using three methods: the local molecular field theory (LMFT), the weighted histogram analysis method (WHAM), and integration of the average force. All three methods produce the same total PMF for a given ion pair. In addition, LMFT-based partitioning into van der Waals and local and far-field electrostatic free energies and assessment of the enthalpic, entropic, and ion-water components yield insights into the origins of the observed free energy profiles in water. The results highlight the importance of local electrostatic interactions in determining the shape of the PMFs, while longer-ranged interactions enhance the overall ion-ion attraction, as expected in a dielectric continuum model. The association equilibrium constants are estimated from the smooth WHAM curves and compared to available experimental conductance data. By examining the variations in the average hydration numbers of ions with ion-ion distance, a correlation of the water structure in the hydration shells with the free energy features is found.

Surface-plasmon--ion interaction in laser ablation of ions from a surface

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

Ritchie, R.H.; Manson, J.R.; Echenique, P.M.

1994-01-15

Experimental work by Shea and Compton suggests that Ag[sup +] ions emitted from a roughened Ag surface irradiated by a nanosecond or picosecond laser beam may absorb the full energy of the Ag surface plasmon (SP). We have modeled this process as an inverse bremsstrahlung-type absorption of the SP quantum by an Ag[sup +] ion which undergoes a collision with the surface. We estimate the absorption probability and find it to be consistent with the Shea-Compton results.

Modeling interactions in major ion toxicity to Ceriodaphnia dubia (presentation)

EPA Science Inventory

Various anthropogenic activities can cause exposures of freshwater systems to greatly elevated concentrations of major ions (Na, K, Ca, Mg, Cl, SO4, HCO3) with widely-varying compositions. A data set on the acute toxicity of single salts and binary salt mixtures to Ceriodaphnia d...

Protein-ion binding process on finite macromolecular concentration. A Poisson-Boltzmann and Monte Carlo study.

PubMed

de Carvalho, Sidney Jurado; Fenley, Márcia O; da Silva, Fernando Luís Barroso

2008-12-25

Electrostatic interactions are one of the key driving forces for protein-ligands complexation. Different levels for the theoretical modeling of such processes are available on the literature. Most of the studies on the Molecular Biology field are performed within numerical solutions of the Poisson-Boltzmann Equation and the dielectric continuum models framework. In such dielectric continuum models, there are two pivotal questions: (a) how the protein dielectric medium should be modeled, and (b) what protocol should be used when solving this effective Hamiltonian. By means of Monte Carlo (MC) and Poisson-Boltzmann (PB) calculations, we define the applicability of the PB approach with linear and nonlinear responses for macromolecular electrostatic interactions in electrolyte solution, revealing some physical mechanisms and limitations behind it especially due the raise of both macromolecular charge and concentration out of the strong coupling regime. A discrepancy between PB and MC for binding constant shifts is shown and explained in terms of the manner PB approximates the excess chemical potentials of the ligand, and not as a consequence of the nonlinear thermal treatment and/or explicit ion-ion interactions as it could be argued. Our findings also show that the nonlinear PB predictions with a low dielectric response well reproduce the pK shifts calculations carried out with an uniform dielectric model. This confirms and completes previous results obtained by both MC and linear PB calculations.

Numerical Methods of Computational Electromagnetics for Complex Inhomogeneous Systems

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

Cai, Wei

Understanding electromagnetic phenomena is the key in many scientific investigation and engineering designs such as solar cell designs, studying biological ion channels for diseases, and creating clean fusion energies, among other things. The objectives of the project are to develop high order numerical methods to simulate evanescent electromagnetic waves occurring in plasmon solar cells and biological ion-channels, where local field enhancement within random media in the former and long range electrostatic interactions in the latter are of major challenges for accurate and efficient numerical computations. We have accomplished these objectives by developing high order numerical methods for solving Maxwell equationsmore » such as high order finite element basis for discontinuous Galerkin methods, well-conditioned Nedelec edge element method, divergence free finite element basis for MHD, and fast integral equation methods for layered media. These methods can be used to model the complex local field enhancement in plasmon solar cells. On the other hand, to treat long range electrostatic interaction in ion channels, we have developed image charge based method for a hybrid model in combining atomistic electrostatics and continuum Poisson-Boltzmann electrostatics. Such a hybrid model will speed up the molecular dynamics simulation of transport in biological ion-channels.« less

Image charge effects on electron capture by dust grains in dusty plasmas.

PubMed

Jung, Y D; Tawara, H

2001-07-01

Electron-capture processes by negatively charged dust grains from hydrogenic ions in dusty plasmas are investigated in accordance with the classical Bohr-Lindhard model. The attractive interaction between the electron in a hydrogenic ion and its own image charge inside the dust grain is included to obtain the total interaction energy between the electron and the dust grain. The electron-capture radius is determined by the total interaction energy and the kinetic energy of the released electron in the frame of the projectile dust grain. The classical straight-line trajectory approximation is applied to the motion of the ion in order to visualize the electron-capture cross section as a function of the impact parameter, kinetic energy of the projectile ion, and dust charge. It is found that the image charge inside the dust grain plays a significant role in the electron-capture process near the surface of the dust grain. The electron-capture cross section is found to be quite sensitive to the collision energy and dust charge.

Interactions between copper(II) and DOM in the urban stormwater runoff: modeling and characterizations.

PubMed

Zhao, Chen; Wang, Chong-Chen; Li, Jun-Qi; Wang, Peng; Ou, Jia-Qi; Cui, Jing-Rui

2018-01-01

Dissolved organic matter (DOM) can strongly interact with both organic and inorganic contaminants to influence their transportation, transformation, bioavailability, toxicity and even their ultimate fate. Within this work, DOM was extracted from urban stormwater runoff samples collected from a regular sampling site of a typical residential area in Beijing, China. Copper(II) ions were selected as model to investigate the interactions between DOM and typical heavy metals. Both ultraviolet (UV) absorbance and fluorescence titration methods were introduced to determine the complex capacities (C L ) and conditional stability constants (log K M ) of bonding between DOM and copper (II) ions, which revealed that the values of C L were 85.62 and 87.23 μmol mg -1 and the log K M values were 5.37 and 5.48, respectively. The results suggested the successful complexation between DOM and copper(II) ions. Furthermore, morphology of the DOM binding to copper(II) ions was confirmed by both energy-dispersive X-ray spectroscopy (EDX) and X-ray photoelectron spectroscopy (XPS), which can facilitate to clarify the corresponding mechanism. The Cu 2p 3/2 peak at 933.7 eV and the characteristic shake-up peaks of Cu-O were found in the XPS spectra, implying that copper(II) ions might coordinate with hydroxyl (aliphatic or phenolic) or carboxyl groups. With these profitable results, it can be concluded that DOM in urban stormwater runoff has a strong binding affinity with copper(II) ions, which may further lead to potentially significant influence on their migration and transformation.

Characteristics of cometary picked-up ions in a global model of Giacobini-Zinner

NASA Astrophysics Data System (ADS)

Kimmel, C. D.; Luhmann, J. G.; Phillips, J. L.; Fedder, J. A.

1987-08-01

Energetic ions observed during the International Cometary Explorer (ICE) spacecraft flyby of comet Giacobini-Zinner provide information about both the constitution of comets and the plasma physical processes associated with their interaction with the solar wind. In this investigation the details of ion 'pickup,' in the limit where small-scale fluctuations in the plasma and magnetic field are neglected, are modeled by following the motion of a large number of initially cold, heavy (mass 18) ions in a global magnetohydrodynamic model of the local plasma and magnetic field. The results indicate how the background or macroscopic velocity and magnetic field structure of the comet can affect the average spatial and spectral characteristics of the observed cometary ions. These effects, which occur by virtue of forces associated with the compression and the curvature of the magnetic field in the presence of the stagnating plasma flow, can explain the double maxima in the time series of the energetic ion flux observed along the ICE trajectory.

Characteristics of cometary picked-up ions in a global model of Giacobini-Zinner

NASA Technical Reports Server (NTRS)

Kimmel, C. D.; Luhmann, J. G.; Phillips, J. L.; Fedder, J. A.

1987-01-01

Energetic ions observed during the International Cometary Explorer (ICE) spacecraft flyby of comet Giacobini-Zinner provide information about both the constitution of comets and the plasma physical processes associated with their interaction with the solar wind. In this investigation the details of ion 'pickup,' in the limit where small-scale fluctuations in the plasma and magnetic field are neglected, are modeled by following the motion of a large number of initially cold, heavy (mass 18) ions in a global magnetohydrodynamic model of the local plasma and magnetic field. The results indicate how the background or macroscopic velocity and magnetic field structure of the comet can affect the average spatial and spectral characteristics of the observed cometary ions. These effects, which occur by virtue of forces associated with the compression and the curvature of the magnetic field in the presence of the stagnating plasma flow, can explain the double maxima in the time series of the energetic ion flux observed along the ICE trajectory.

Energy gain calculations in Penning fusion systems using a bounce-averaged Fokker-Planck model

NASA Astrophysics Data System (ADS)

Chacón, L.; Miley, G. H.; Barnes, D. C.; Knoll, D. A.

2000-11-01

In spherical Penning fusion devices, a spherical cloud of electrons, confined in a Penning-like trap, creates the ion-confining electrostatic well. Fusion energy gains for these systems have been calculated in optimistic conditions (i.e., spherically uniform electrostatic well, no collisional ion-electron interactions, single ion species) using a bounce-averaged Fokker-Planck (BAFP) model. Results show that steady-state distributions in which the Maxwellian ion population is dominant correspond to lowest ion recirculation powers (and hence highest fusion energy gains). It is also shown that realistic parabolic-like wells result in better energy gains than square wells, particularly at large well depths (>100 kV). Operating regimes with fusion power to ion input power ratios (Q-value) >100 have been identified. The effect of electron losses on the Q-value has been addressed heuristically using a semianalytic model, indicating that large Q-values are still possible provided that electron particle losses are kept small and well depths are large.

Clarification of the binding model of lead(II) with a highly sensitive and selective fluoroionophore sensor by spectroscopic and structural study

NASA Astrophysics Data System (ADS)

Ma, Lijun; Li, Yue; Li, Lei; Wu, Yuqing; Buchet, Rene; Ding, Yihong

2009-03-01

The detection of lead ion is very important both in environment and in biological systems because of its toxicity. A fluoroionophore sensor, N-[4(1-pyrene)-butyroyl]- L-tryptophan (PLT), distinguishing Pb 2+ from other 12 metal ions and exhibiting a very high sensitivity (0.15 μM) in aqueous solution, has been reported. The present study describes the spectroscopic clarification of the intrinsic differences of the binding model between PLT with Pb 2+ and with other ions. The fluorescent property of solid metal carboxylates reflects a character of the metal complex in solution, which results in a facility to solve problems by using solid sample of complex and vibrational spectroscopy. Both FT-infrared and Raman spectroscopy are employed to clarify the binding model between lead ion and its high sensitive and selective fluoroionophore sensor PLT, and essentially to explain why the metal ions other than Pb 2+ cannot response to PLT. The IR spectral data clearly show that a bridging bidentate coordination occurs when PLT is coordinated with Cu 2+ and Zn 2+; while a chelating bidentate coordination between the carboxyl anion and Pb 2+ exists in PLT-Pb, which is a new information beyond the NMR results in previous report. Meanwhile, the present study also indicates a characteristic interaction of lead ion and indole ring as well as the hydrogen bonding between amide groups. Furthermore, the quantum chemical calculations at the DFT level confirm the spectral and structural information of PLT-Pb 2+ proposed by experiments. Thus, the type of coordination, the interaction of the indole ring with the metal ion, and the hydrogen bonding between amide groups in PLT-Pb are likely responsible for the high selectivity of PLT to the lead(II) ion.

Clarification of the binding model of lead(II) with a highly sensitive and selective fluoroionophore sensor by spectroscopic and structural study.

PubMed

Ma, Lijun; Li, Yue; Li, Lei; Wu, Yuqing; Buchet, Rene; Ding, Yihong

2009-03-01

The detection of lead ion is very important both in environment and in biological systems because of its toxicity. A fluoroionophore sensor, N-[4(1-pyrene)-butyroyl]-l-tryptophan (PLT), distinguishing Pb(2+) from other 12 metal ions and exhibiting a very high sensitivity (0.15microM) in aqueous solution, has been reported. The present study describes the spectroscopic clarification of the intrinsic differences of the binding model between PLT with Pb(2+) and with other ions. The fluorescent property of solid metal carboxylates reflects a character of the metal complex in solution, which results in a facility to solve problems by using solid sample of complex and vibrational spectroscopy. Both FT-infrared and Raman spectroscopy are employed to clarify the binding model between lead ion and its high sensitive and selective fluoroionophore sensor PLT, and essentially to explain why the metal ions other than Pb(2+) cannot response to PLT. The IR spectral data clearly show that a bridging bidentate coordination occurs when PLT is coordinated with Cu(2+) and Zn(2+); while a chelating bidentate coordination between the carboxyl anion and Pb(2+) exists in PLT-Pb, which is a new information beyond the NMR results in previous report. Meanwhile, the present study also indicates a characteristic interaction of lead ion and indole ring as well as the hydrogen bonding between amide groups. Furthermore, the quantum chemical calculations at the DFT level confirm the spectral and structural information of PLT-Pb(2+) proposed by experiments. Thus, the type of coordination, the interaction of the indole ring with the metal ion, and the hydrogen bonding between amide groups in PLT-Pb are likely responsible for the high selectivity of PLT to the lead(II) ion.

Cooperativity and complexity in the binding of anions and cations to a tetratopic ion-pair host.

PubMed

Howe, Ethan N W; Bhadbhade, Mohan; Thordarson, Pall

2014-05-21

Cooperative interactions play a very important role in both natural and synthetic supramolecular systems. We report here on the cooperative binding properties of a tetratopic ion-pair host 1. This host combines two isophthalamide anion recognition sites with two unusual "half-crown/two carbonyl" cation recognition sites as revealed by the combination of single-crystal X-ray analysis of the free host and the 1:2 host:calcium cation complex, together with two-dimensional NMR and computational studies. By systematically comparing all of the binding data to several possible binding models and focusing on four different variants of the 1:2 binding model, it was in most cases possible to quantify these complex cooperative interactions. The data showed strong negative cooperativity (α = 0.01-0.05) of 1 toward chloride and acetate anions, while for cations the results were more variable. Interestingly, in the competitive (CDCl3/CD3OD (9:1, v/v)) solvent, the addition of calcium cations to the tetratopic ion-pair host 1 allosterically switched "on" chloride binding that is otherwise not present in this solvent system. The insight into the complexity of cooperative interactions revealed in this study of the tetratopic ion-pair host 1 can be used to design better cooperative supramolecular systems for information transfer and catalysis.

Charge exchange in solar wind-cometary interactions

NASA Technical Reports Server (NTRS)

Gombosi, T. I.; Horanyi, M.; Kecskemety, K.; Cravens, T. E.; Nagy, A. F.

1983-01-01

A simple model of a cometary spherically symmetrical atmosphere and ionosphere is considered. An analytic solution of the governing equations describing the radial distribution of the neutral and ion densities is found. The new solution is compared to the well-known solution of the equations containing only ionization terms. Neglecting recombination causes a significant overestimate of the ion density in the vicinity of the comet. An axisymmetric model of the solar wind-cometary interaction is considered, taking into account the loss of solar wind ions due to charge exchange. The calculations predict that for active comets, solar wind absorption due to charge exchange becomes important at a few thousand kilometers from the nucleus, and a surface separating the shocked solar wind from the cometary ionosphere develops in this region. These calculations are in reasonable agreement with the few observations available for the ionopause location at comets.

Electrostatic solvation free energies of charged hard spheres using molecular dynamics with density functional theory interactions

DOE PAGES

Duignan, Timothy T.; Baer, Marcel D.; Schenter, Gregory K.; ...

2017-07-26

Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into simple and intuitive contributions will have important implications for models of electrolyte solution. In this paper, we provide definitions of the various types of single ion solvation free energies based on different simulation protocols. We calculate solvation free energies of charged hard spheres using density functional theory interaction potentials with molecular dynamics simulation and isolate the effects of charge and cavitation, comparing tomore » the Born (linear response) model. We show that using uncorrected Ewald summation leads to unphysical values for the single ion solvation free energy and that charging free energies for cations are approximately linear as a function of charge but that there is a small non-linearity for small anions. The charge hydration asymmetry for hard spheres, determined with quantum mechanics, is much larger than for the analogous real ions. Finally, this suggests that real ions, particularly anions, are significantly more complex than simple charged hard spheres, a commonly employed representation.« less

Electrostatic solvation free energies of charged hard spheres using molecular dynamics with density functional theory interactions

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

Duignan, Timothy T.; Baer, Marcel D.; Schenter, Gregory K.

Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into simple and intuitive contributions will have important implications for models of electrolyte solution. In this paper, we provide definitions of the various types of single ion solvation free energies based on different simulation protocols. We calculate solvation free energies of charged hard spheres using density functional theory interaction potentials with molecular dynamics simulation and isolate the effects of charge and cavitation, comparing tomore » the Born (linear response) model. We show that using uncorrected Ewald summation leads to unphysical values for the single ion solvation free energy and that charging free energies for cations are approximately linear as a function of charge but that there is a small non-linearity for small anions. The charge hydration asymmetry for hard spheres, determined with quantum mechanics, is much larger than for the analogous real ions. Finally, this suggests that real ions, particularly anions, are significantly more complex than simple charged hard spheres, a commonly employed representation.« less

Electrostatic solvation free energies of charged hard spheres using molecular dynamics with density functional theory interactions

NASA Astrophysics Data System (ADS)

Duignan, Timothy T.; Baer, Marcel D.; Schenter, Gregory K.; Mundy, Chistopher J.

2017-10-01

Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into simple and intuitive contributions will have important implications for models of electrolyte solution. Here, we provide definitions of the various types of single ion solvation free energies based on different simulation protocols. We calculate solvation free energies of charged hard spheres using density functional theory interaction potentials with molecular dynamics simulation and isolate the effects of charge and cavitation, comparing to the Born (linear response) model. We show that using uncorrected Ewald summation leads to unphysical values for the single ion solvation free energy and that charging free energies for cations are approximately linear as a function of charge but that there is a small non-linearity for small anions. The charge hydration asymmetry for hard spheres, determined with quantum mechanics, is much larger than for the analogous real ions. This suggests that real ions, particularly anions, are significantly more complex than simple charged hard spheres, a commonly employed representation.

Industrial ion source technology

NASA Technical Reports Server (NTRS)

Kaufman, H. R.; Robinson, R. S.

1978-01-01

An analytical model was developed to describe the development of a coned surface texture with ion bombardment and simultaneous deposition of an impurity. A mathematical model of sputter deposition rate from a beveled target was developed in conjuction with the texturing models to provide an important input to that model. The establishment of a general procedure that will allow the treatment of manay different sputtering configurations is outlined. Calculation of cross sections for energetic binary collisions was extened to Ar, Kr.. and Xe with total cross sections for viscosity and diffusion calculated for the interaction energy range from leV to 1000eV. Physical sputtering and reactive ion etching experiments provided experimental data on the operating limits of a broad beam ion source using CF4 as a working gas to produce reactive species in a sputtering beam. Magnetic clustering effects are observed when Al is seeded with Fe and sputtered with Ar(?) ions. Silicon was textured at a micron scale by using a substrate temperature of 600 C.

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.

Studies of Interstellar Pickup Ions in the Solar Wind

NASA Technical Reports Server (NTRS)

Isenberg, Philip A.; Lee, Martin A.; Mobius, Eberhard

1996-01-01

The work under this grant involves studies of the interaction of interstellar pickup ions with the solar wind, with the goal of a comprehensive model of the particle distributions and wave intensities to be expected throughout the heliosphere, as well as the interactions of those distributions with the solar wind termination shock. In the past year, we have completed a number of projects, including observations and modeling of the effects of a large scattering mean free path on the pickup He(+) seen at AMPTE, an analytical model of anisotropic pickup tons in a steady radial magnetic field, and a derivation of a reduced solar wind Mach number due to increased estimates on the inflowing hydrogen density allowing for a weak termination shock. In the next year, we plan to investigate in more detail the correspondence between our models of anisotropic pickup ions and the data on spectra, variations, and proton-He(+) correlation provided by AMPTE, Ulysses, and our instrument on SOHO. We will model the time-dependent pickup ion density resulting from finite periods of radial magnetic field. We will also incorporate the effects of a large mean free path into our analysis of the He(+) focusing cone, leading to more accurate parameter values for the interstellar helium gas. This progress report also includes a discussion of our Space Physics Educational Outreach activities in the past year and plans for the next year.

(In)validity of the constant field and constant currents assumptions in theories of ion transport.

PubMed Central

Syganow, A; von Kitzing, E

1999-01-01

Constant electric fields and constant ion currents are often considered in theories of ion transport. Therefore, it is important to understand the validity of these helpful concepts. The constant field assumption requires that the charge density of permeant ions and flexible polar groups is virtually voltage independent. We present analytic relations that indicate the conditions under which the constant field approximation applies. Barrier models are frequently fitted to experimental current-voltage curves to describe ion transport. These models are based on three fundamental characteristics: a constant electric field, negligible concerted motions of ions inside the channel (an ion can enter only an empty site), and concentration-independent energy profiles. An analysis of those fundamental assumptions of barrier models shows that those approximations require large barriers because the electrostatic interaction is strong and has a long range. In the constant currents assumption, the current of each permeating ion species is considered to be constant throughout the channel; thus ion pairing is explicitly ignored. In inhomogeneous steady-state systems, the association rate constant determines the strength of ion pairing. Among permeable ions, however, the ion association rate constants are not small, according to modern diffusion-limited reaction rate theories. A mathematical formulation of a constant currents condition indicates that ion pairing very likely has an effect but does not dominate ion transport. PMID:9929480

A unifying approach to lattice dynamical and electronic properties of solids

NASA Astrophysics Data System (ADS)

Falter, C.

1988-06-01

A unified analysis of lattice dynamical and electronic properties of solids with special emphasis on the interaction between electrons and phonons is presented. The article is roughly divided into two parts reflecting different points of view. The density response of the electrons provides the link between these parts. In the first part, the microscopic theory in terms of the density response in crystals is discussed. Relations are pointed out between the density response approach and the density functional theory. The latter is used for a representation of the exchange-correlation interaction and the microscopic force constants. Relevant methods, as recently proposed by various authors for the calculation of the density response in inhomogeneous solids are discussed. Particular attention is paid to the development of a renormalized response description. Applications of this method to lattice dynamical and electronic properties are presented. In the second part an alternative physical concept, the quasi-ion approach, is outlined. This concept is shown to provide a microscopic basis for electronic charge localization in crystals and proves the importance of the correlation between crystal symmetry and many-body effects. Is is derived that within linear response theory an appropriate decomposition of the valence charge density leads uniquely to a spatially localized density contribution at the individual ion which follows its motion rigidly. The composite consisting of this partial density and the ion core is taken to be an individual entity, denoted as quasi-ion, from which the crystal is built up. In a certain sense this is a generalization of Ziman's concept of neutral pseudo-atoms being approximately valid in simple metals. New insight into the bonding mechanism and charge relaxation processes is shown to follow from this concept. In particular, we discuss the covalent, ionic and metallic bonding mechanisms, using the localized picture provided by the partial densities, on the same basis. The quasi-ion approach is also applied to the calculation of phonon-induced charge density redistributions and to the construction of a simplified formulation of microscopic lattice dynamics. Investigations of the phonon dispersion for different bonding types are given within a rigid quasi-ion model and extensions of this model are outlined. Among other things, these calculations indicate that bonding dynamics of (covalent) molecules and crystals can be described by relative rotations of the quasi-ions under the condition of rotational invariance of the system. Finally, possible applications of the quasi-ion concept to an approximate formulation of anharmonic lattice dynamics and the interaction between electrons and phonons are discussed. A numerical investigation of this interaction is presented and compared with the results from the rigid-ion model. As a consequence of the quasi-ion concept a consistent calculation of the phonon dispersion, the electronic band structure and the electron-phonon interaction becomes possible.

A sorption model for alkalis in cement-based materials - Correlations with solubility and electrokinetic properties

NASA Astrophysics Data System (ADS)

Henocq, Pierre

2017-06-01

In cement-based materials, radionuclide uptake is mainly controlled by calcium silicate hydrates (C-S-H). This work presents an approach for defining a unique set of parameters of a surface complexation model describing the sorption behavior of alkali ions on the C-S-H surface. Alkali sorption processes are modeled using the CD-MUSIC function integrated in the Phreeqc V.3.0.6 geochemical code. Parameterization of the model was performed based on (1) retention, (2) zeta potential, and (3) solubility experimental data from the literature. This paper shows an application of this model to sodium ions. It was shown that retention, i.e. surface interactions, and solubility are closely related, and a consistent sorption model for radionuclides in cement-based materials requires a coupled surface interaction/chemical equilibrium model. In case of C-S-H with low calcium-to-silicon ratios, sorption of sodium ions on the C-S-H surface strongly influences the chemical equilibrium of the C-S-H + NaCl system by significantly increasing the aqueous calcium concentration. The close relationship between sorption and chemical equilibrium was successfully illustrated by modeling the effect of the solid-to-liquid ratio on the calcium content in solution in the case of C-S-H + NaCl systems.

Effects of nonadditive interactions on ion solvation at the water/vapor interface: a molecular dynamics study.

PubMed

Yagasaki, Takuma; Saito, Shinji; Ohmine, Iwao

2010-12-09

The solvation of halide ions at the water/vapor interface is investigated by using molecular dynamics simulations with nonpolarizable molecular mechanical (MM), polarizable MM, and quantum mechanical (QM)/MM methods. The free energy profile of the ion solvation is decomposed into the energy and the entropic contributions along the ion displacement from inside to the surface of water. It is found that the surface affinity of the ion, relative to the bulk value, is determined by a subtle balance between the energetic destabilization and the entropic stabilization with the ion displacement. The amount of energetic destabilization is found to be reduced when nonadditive interactions are included, as in the polarizable MM and QM/MM models. The structure of water around the ion at the interface is also largely modified when the higher order effects are considered. For example, the induced dipole effect enhances the solvation structure around the ion at the interface significantly and thus reduces the amount of entropic stabilization at the interface, relative to in the bulk. It is found that this induced dipole effect causes the slowing in the ion-water hydrogen bond dynamics at the interface. On the other hand, the higher order induced multipole effects in the QM/MM method suppress both the excessive enhancement of the solvation structure and the slowing of the ion-water hydrogen bond dynamics at the interface. The present study demonstrates that not only the induced dipole moment but also the higher order induced multipole moments, which are neglected in standard empirical models, are essential for the correct description of the ion solvation at the water/vapor interface.

Configuration interaction in charge exchange spectra of tin and xenon

NASA Astrophysics Data System (ADS)

D'Arcy, R.; Morris, O.; Ohashi, H.; Suda, S.; Tanuma, H.; Fujioka, S.; Nishimura, H.; Nishihara, K.; Suzuki, C.; Kato, T.; Koike, F.; O'Sullivan, G.

2011-06-01

Charge-state-specific extreme ultraviolet spectra from both tin ions and xenon ions have been recorded at Tokyo Metropolitan University. The electron cyclotron resonance source spectra were produced from charge exchange collisions between the ions and rare gas target atoms. To identify unknown spectral lines of tin and xenon, atomic structure calculations were performed for Sn14+-Sn17+ and Xe16+-Xe20+ using the Hartree-Fock configuration interaction code of Cowan (1981 The Theory of Atomic Structure and Spectra (Berkeley, CA: University of California Press)). The energies of the capture states involved in the single-electron process that occurs in these slow collisions were estimated using the classical over-barrier model.

Recent trends in precision measurements of atomic and nuclear properties with lasers and ion traps

NASA Astrophysics Data System (ADS)

Block, Michael

2017-11-01

The X. international workshop on "Application of Lasers and Storage Devices in Atomic Nuclei Research" took place in Poznan in May 2016. It addressed the latest experimental and theoretical achievements in laser and ion trap-based investigations of radionuclides, highly charged ions and antiprotons. The precise determination of atomic and nuclear properties provides a stringent benchmark for theoretical models and eventually leads to a better understanding of the underlying fundamental interactions and symmetries. This article addresses some general trends in this field and highlights select recent achievements presented at the workshop. Many of these are covered in more detail within the individual contributions to this special issue of Hyperfine Interactions.

Ionic force field optimization based on single-ion and ion-pair solvation properties: Going beyond standard mixing rules

NASA Astrophysics Data System (ADS)

Fyta, Maria; Netz, Roland R.

2012-03-01

Using molecular dynamics (MD) simulations in conjunction with the SPC/E water model, we optimize ionic force-field parameters for seven different halide and alkali ions, considering a total of eight ion-pairs. Our strategy is based on simultaneous optimizing single-ion and ion-pair properties, i.e., we first fix ion-water parameters based on single-ion solvation free energies, and in a second step determine the cation-anion interaction parameters (traditionally given by mixing or combination rules) based on the Kirkwood-Buff theory without modification of the ion-water interaction parameters. In doing so, we have introduced scaling factors for the cation-anion Lennard-Jones (LJ) interaction that quantify deviations from the standard mixing rules. For the rather size-symmetric salt solutions involving bromide and chloride ions, the standard mixing rules work fine. On the other hand, for the iodide and fluoride solutions, corresponding to the largest and smallest anion considered in this work, a rescaling of the mixing rules was necessary. For iodide, the experimental activities suggest more tightly bound ion pairing than given by the standard mixing rules, which is achieved in simulations by reducing the scaling factor of the cation-anion LJ energy. For fluoride, the situation is different and the simulations show too large attraction between fluoride and cations when compared with experimental data. For NaF, the situation can be rectified by increasing the cation-anion LJ energy. For KF, it proves necessary to increase the effective cation-anion Lennard-Jones diameter. The optimization strategy outlined in this work can be easily adapted to different kinds of ions.

Information technology in chemistry research and education: Part I. Ab initio studies on the hydrolysis of aromatic diazonium ions. Part II. Theoretical study and molecular modeling of non-covalent interactions. Part III. Applying information technology in chemistry education

NASA Astrophysics Data System (ADS)

Wu, Zhengyu

Part I of this dissertation studies the bonding in chemical reactions, while Part II studies the bonding related to inter- and intra-molecular interactions. Part III studies the application of IT technology in chemistry education. Part I of this dissertation (chapter 1 and chapter 2) focuses on the theoretical studies on the mechanism of the hydrolysis reactions of benzenediazonium ion and guaninediazonium ion. The major conclusion is that in hydrolysis reactions the "unimolecular mechanism" actually has to involve the reacting solvent molecule. Therefore, the unimolecular pathway can only serve as a conceptual model but will not happen in the reality. Chapter I concludes that the hydrolysis reaction of benzenediazonium ion takes the direct SN2Ar mechanism via a transition state but without going through a pre-coordination complex. Chapter 2 concludes that the formation of xanthine from the dediazoniation reaction of guaninediazonium ion in water takes the SN2Ar pathway without a transition state. And oxanine might come from an intermediate formed by the bimolecular deprotonation of the H atom on N3 of guaninediazonium ion synchronized with the pyrimidine ring opening reaction. Part II of this dissertation includes chapters 3, 4, and 5. Chapter 3 studies the quadrupole moment of benzene and quadrupole-quadrupole interactions. We concluded that the quadrupole-quadrupole interaction is important in the arene-arene interactions. Our study shows the most stable structure of benzene dimer is the point-to-face T-shaped structure. Chapter 4 studies the intermolecular interactions that result in the disorder of the crystal of 4-Chloroacetophenone-(4-methoxyphenylethylidene). We analyzed all the nearest neighbor interactions within that crystal and found that the crystal structure is determined by its thermo-dynamical properties. Our calculation perfectly reproduced the percentage of parallel-alignment of the crystal. Part III of this dissertation is focused on the application of database management system and computer technology on chemistry education. A database-supported webtool was developed to support the creation of news portfolio and peer reviews online. The responses to an in-class survey show that students embrace the use of this webtool for its conceptually clear design and its easiness of use.

Gas Flow and Ion Transfer in Heated ESI Capillary Interfaces

NASA Astrophysics Data System (ADS)

Bernier, Laurent; Pinfold, Harry; Pauly, Matthias; Rauschenbach, Stephan; Reiss, Julius

2018-02-01

Transfer capillaries are the preferred means to transport ions, generated by electrospray ionization, from ambient conditions to vacuum. During the transfer of ions through the narrow, long tubes into vacuum, substantial losses are typical. However, recently it was demonstrated that these losses can be avoided altogether. To understand the experimental observation and provide a general model for the ion transport, here, we investigate the ion transport through capillaries by numerical simulation of interacting ions. The simulation encompasses all relevant factors, such as space charge, diffusion, gas flow, and heating. Special attention is paid to the influence of the gas flow on the transmission and especially the change imposed by heating. The gas flow is modeled by a one-dimensional gas dynamics description. A large number of ions are treated as point particles in this gas flow. This allows to investigate the influence of the capillary heating on the gas flow and by this on the ion transport. The results are compared with experimental findings. [Figure not available: see fulltext.

Four-fluid MHD Simulations of the Plasma and Neutral Gas Environment of Comet Churyumov-Gerasimenko Near Perihelion

NASA Astrophysics Data System (ADS)

Huang, Z.; Toth, G.; Gombosi, T.; Jia, X.; Rubin, M.; Fougere, N.; Tenishev, V.; Combi, M.; Bieler, A.; Hansen, K.; Shou, Y.; Altwegg, K.

2015-10-01

We develop a 3-D four fluid model to study the plasma environment of comet Churyumov- Gerasimenko (CG), which is the target of the Rosetta mission. Our model is based on BATS-R-US within the SWMF (Space Weather Modeling Framework) that solves the governing multifluid MHD equations and 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 mass loading processes, including photo and electron impact ionization, furthermore taken into account are charge exchange, dissociative ion-electron recombination, as well as collisional interactions between different fluids. We simulate the near nucleus plasma and neutral gas environment with a realistic shape model of CG near perihelion and compare our simulation results with Rosetta observations.

Quantum simulation of interacting spin models with trapped ions

NASA Astrophysics Data System (ADS)

Islam, Kazi Rajibul

The quantum simulation of complex many body systems holds promise for understanding the origin of emergent properties of strongly correlated systems, such as high-Tc superconductors and spin liquids. Cold atomic systems provide an almost ideal platform for quantum simulation due to their excellent quantum coherence, initialization and readout properties, and their ability to support several forms of interactions. In this thesis, I present experiments on the quantum simulation of long range Ising models in the presence of transverse magnetic fields with a chain of up to sixteen ultracold 171Yb+ ions trapped in a linear radio frequency Paul trap. Two hyperfine levels in each of the 171Yb+ ions serve as the spin-1/2 systems. We detect the spin states of the individual ions by observing state-dependent fluorescence with single site resolution, and can directly measure any possible spin correlation function. The spin-spin interactions are engineered by applying dipole forces from precisely tuned lasers whose beatnotes induce stimulated Raman transitions that couple virtually to collective phonon modes of the ion motion. The Ising couplings are controlled, both in sign and strength with respect to the effective transverse field, and adiabatically manipulated to study various aspects of this spin model, such as the emergence of a quantum phase transition in the ground state and spin frustration due to competing antiferromagnetic interactions. Spin frustration often gives rise to a massive degeneracy in the ground state, which can lead to entanglement in the spin system. We detect and characterize this frustration induced entanglement in a system of three spins, demonstrating the first direct experimental connection between frustration and entanglement. With larger numbers of spins we also vary the range of the antiferromagnetic couplings through appropriate laser tunings and observe that longer range interactions reduce the excitation energy and thereby frustrate the ground state order. This system can potentially be scaled up to study a wide range of fully connected spin networks with a few dozens of spins, where the underlying theory becomes intractable on a classical computer.

Interaction of cadmium with phosphate on goethite

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

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

1997-08-01

Interactions between different ions are of importance in understanding chemical processes in natural systems. In this study simultaneous adsorption of phosphate and cadmium on goethite is studied in detail. The charge distribution (CD)-multisite complexation (MUSIC) model has been successful in describing extended data sets of cadmium adsorption and phosphate adsorption on goethite. In this study, the parameters of this model for these two data sets were combined to describe a new data set of simultaneous adsorption of cadmium and phosphate on goethite. Attention is focused on the surface speciation of cadmium. With the extra information that can be obtained frommore » the interaction experiments, the cadmium adsorption model is refined. For a perfect description of the data, the singly coordinated surface groups at the 110 face of goethite were assumed to form both monodentate and bidentate surface species with cadmium. The CD-MUSIC model is able to describe data sets of both simultaneous and single adsorption of cadmium and phosphate with the same parameters. The model calculations confirmed the idea that only singly coordinated surface groups are reactive for specific ion binding.« less

Carbon Mineralization Using Phosphate and Silicate Ions

NASA Astrophysics Data System (ADS)

Gokturk, H.

2013-12-01

Carbon dioxide (CO2) reduction from combustion of fossil fuels has become an urgent concern for the society due to marked increase in weather related natural disasters and other negative consequences of global warming. CO2 is a highly stable molecule which does not readily interact with other neutral molecules. However it is more responsive to ions due to charge versus quadrupole interaction [1-2]. Ions can be created by dissolving a salt in water and then aerosolizing the solution. This approach gives CO2 molecules a chance to interact with the hydrated salt ions over the large surface area of the aerosol. Ion containing aerosols exist in nature, an example being sea spray particles generated by breaking waves. Such particles contain singly and doubly charged salt ions including Na+, Cl-, Mg++ and SO4--. Depending on the proximity of CO2 to the ion, interaction energy can be significantly higher than the thermal energy of the aerosol. For example, an interaction energy of 0.6 eV is obtained with the sulfate (SO4--) ion when CO2 is the nearest neighbor [2]. In this research interaction between CO2 and ions which carry higher charges are investigated. The molecules selected for the study are triply charged phosphate (PO4---) ions and quadruply charged silicate (SiO4----) ions. Examples of salts which contain such molecules are potassium phosphate (K3PO4) and sodium orthosilicate (Na4SiO4). The research has been carried out with first principle quantum mechanical calculations using the Density Functional Theory method with B3LYP functional and Pople type basis sets augmented with polarization and diffuse functions. Atomic models consist of the selected ions surrounded by water and CO2 molecules. Similar to the results obtained with singly and doubly charged ions [1-2], phosphate and silicate ions attract CO2 molecules. Energy of interaction between the ion and CO2 is 1.6 eV for the phosphate ion and 3.3 eV for the silicate ion. Hence one can expect that the selected ions would enhance the absorption of CO2 into the aerosol even more than the singly or doubly charged ions. Ion containing aerosols also help to catalyze reactions between water and CO2. Hydrated phosphate and silicate ions tend to attract hydrogen atoms from neighboring water molecules to reduce the charged state. When there is CO2 in the vicinity of the ion, the remainder of the water molecule which loses the hydrogen(s) reacts with CO2 to form carbonates. (PO4---) + H2O + CO2 -> (HPO3--) + (HCO3-) (SiO4----) + H2O + CO2 -> (HSiO4---) + (HCO3-) (SiO4----) + H2O + CO2 -> (H2SiO4--) + (CO3--) In conclusion, highly charged phosphate and silicate ions dissolved in water and aerosolized into small droplets can facilitate both the capture and the mineralization of CO2. This method would be especially effective in a CO2 rich environment such as the exhaust gas of a combustion process. [1] H. Gokturk, "Geoengineering with Charged Droplets," AGU Fall Meeting, San Francisco 2011 [2] H. Gokturk, "Atomistic Simulation of Sea Spray Particles," AGU Fall Meeting, San Francisco 2012

Twisted-Light-Ion Interaction: The Role of Longitudinal Fields

NASA Astrophysics Data System (ADS)

Quinteiro, G. F.; Schmidt-Kaler, Ferdinand; Schmiegelow, Christian T.

2017-12-01

The propagation of light beams is well described using the paraxial approximation, where field components along the propagation direction are usually neglected. For strongly inhomogeneous or shaped light fields, however, this approximation may fail, leading to intriguing variations of the light-matter interaction. This is the case of twisted light having opposite orbital and spin angular momenta. We compare experimental data for the excitation of a quadrupole transition in a single trapped 40Ca+ ion from Schmiegelow et al. [Nat. Commun. 7, 12998 (2016), 10.1038/ncomms12998] with a complete model where longitudinal components of the electric field are taken into account. Our model matches the experimental data and excludes by 11 standard deviations the approximation of a complete transverse field. This demonstrates the relevance of all field components for the interaction of twisted light with matter.

Transverse eV Ion Heating by Random Electric Field Fluctuations in the Plasmasphere

NASA Technical Reports Server (NTRS)

Artemyev, A. V.; Mourenas, D.; Agapitov, O. V.; Blum, L.

2017-01-01

Charged particle acceleration in the Earth inner magnetosphere is believed to be mainly due to the local resonant wave-particle interaction or particle transport processes. However, the Van Allen Probes have recently provided interesting evidence of a relatively slow transverse heating of eV ions at distances about 2-3 Earth radii during quiet times. Waves that are able to resonantly interact with such very cold ions are generally rare in this region of space, called the plasmasphere. Thus, non-resonant wave-particle interactions are expected to play an important role in the observed ion heating. We demonstrate that stochastic heating by random transverse electric field fluctuations of whistler (and possibly electromagnetic ion cyclotron) waves could explain this weak and slow transverse heating of H+ and O+ ions in the inner magnetosphere. The essential element of the proposed model of ion heating is the presence of trains of random whistler (hiss) wave packets, with significant amplitude modulations produced by strong wave damping, rapid wave growth, or a superposition of wave packets of different frequencies, phases, and amplitudes. Such characteristics correspond to measured characteristics of hiss waves in this region. Using test particle simulations with typical wave and plasma parameters, we demonstrate that the corresponding stochastic transverse ion heating reaches 0.07-0.2 eV/h for protons and 0.007-0.015 eV/h for O+ ions. This global temperature increase of the Maxwellian ion population from an initial Ti approx. 0.3 eV could potentially explain the observations.

Interaction of elaiophylin with model bilayer membrane

NASA Astrophysics Data System (ADS)

Genova, J.; Dencheva-Zarkova, M.

2017-01-01

Elaiophylin is a new macrodiolide antibiotic, which is produced by the Streptomyces strains [1]. It displays biological activities against Gram-positive bacteria and fungi. The mode of action of this antibiotic has been attributed to an alteration of the membrane permeability. When this antibiotic is inserted into the bilayer membranes destabilization of the membrane and formation of ion-penetrable channels is observed. The macrodiolide antibiotic forms stable cation selective ion channels in synthetic lipid bilayer membranes. The aim of this work was to study the interactions of Elaiophylin with model bilayer membranes and to get information on the mechanical properties of lipid bilayers in presence of this antibiotic. Patch-clamp technique [2] were used in the study

Thermophysical Properties of Ionic Liquid, 1-Pentyl-3-methylimidazolium Chloride in Water at Different Temperatures

NASA Astrophysics Data System (ADS)

Shekaari, Hemayat; Mousavi, Sedighehnaz S.; Mansoori, Yagoub

2009-04-01

Osmotic coefficients, {φ}, electrical conductance data, Λ, and refractive indices, n D, of aqueous solutions of the ionic liquid, 1-pentyl-3-methylimidazolium chloride [PnMIm]Cl have been measured at T = (298.15, 308.15, 318.15, and 328.15) K. Measurements of osmotic coefficients were carried out by the vapor-pressure osmometry method (VPO). Osmotic coefficient values show that ion-solvent interactions are stronger at lower temperature. The osmotic coefficients were correlated to the Pitzer-ion interaction and modified NRTL (MNRTL) models. From these data, mean molal activity coefficients, γ±, and excess Gibbs free energies, G E, have been calculated. Electrical conductance data have been applied for determination of association constants, K a, and limiting molar conductances, Λ 0, using the low concentration chemical model (lcCM). Calculated ion-association constant, K a, values show that ion-association effects increase at high temperatures which is in agreement with osmotic coefficient results. Experimental results of refractive indices for the binary system are reported, and have been fitted by a polynomial expansion.

A study of quantum mechanical probabilities in the classical Hodgkin-Huxley model.

PubMed

Moradi, N; Scholkmann, F; Salari, V

2015-03-01

The Hodgkin-Huxley (HH) model is a powerful model to explain different aspects of spike generation in excitable cells. However, the HH model was proposed in 1952 when the real structure of the ion channel was unknown. It is now common knowledge that in many ion-channel proteins the flow of ions through the pore is governed by a gate, comprising a so-called "selectivity filter" inside the ion channel, which can be controlled by electrical interactions. The selectivity filter (SF) is believed to be responsible for the selection and fast conduction of particular ions across the membrane of an excitable cell. Other (generally larger) parts of the molecule such as the pore-domain gate control the access of ions to the channel protein. In fact, two types of gates are considered here for ion channels: the "external gate", which is the voltage sensitive gate, and the "internal gate" which is the selectivity filter gate (SFG). Some quantum effects are expected in the SFG due to its small dimensions, which may play an important role in the operation of an ion channel. Here, we examine parameters in a generalized model of HH to see whether any parameter affects the spike generation. Our results indicate that the previously suggested semi-quantum-classical equation proposed by Bernroider and Summhammer (BS) agrees strongly with the HH equation under different conditions and may even provide a better explanation in some cases. We conclude that the BS model can refine the classical HH model substantially.

Ion Move Brownian Dynamics (IMBD)--simulations of ion transport.

PubMed

Kurczynska, Monika; Kotulska, Malgorzata

2014-01-01

Comparison of the computed characteristics and physiological measurement of ion transport through transmembrane proteins could be a useful method to assess the quality of protein structures. Simulations of ion transport should be detailed but also timeefficient. The most accurate method could be Molecular Dynamics (MD), which is very time-consuming, hence is not used for this purpose. The model which includes ion-ion interactions and reduces the simulation time by excluding water, protein and lipid molecules is Brownian Dynamics (BD). In this paper a new computer program for BD simulation of the ion transport is presented. We evaluate two methods for calculating the pore accessibility (round and irregular shape) and two representations of ion sizes (van der Waals diameter and one voxel). Ion Move Brownian Dynamics (IMBD) was tested with two nanopores: alpha-hemolysin and potassium channel KcsA. In both cases during the simulation an ion passed through the pore in less than 32 ns. Although two types of ions were in solution (potassium and chloride), only ions which agreed with the selectivity properties of the channels passed through the pores. IMBD is a new tool for the ion transport modelling, which can be used in the simulations of wide and narrow pores.

Loss of ring current O+ ions due to interaction with Pc 5 waves

NASA Astrophysics Data System (ADS)

Hudson, Mary; Chan, Anthony; Roth, Ilan

1993-01-01

The behavior of ring current ions in low-frequency geomagnetic pulsations is investigated analytically and numerically. We focus primarily on ring current O+ ions, whose flux increases dramatically during geomagnetic storms and decays at a rate which is not fully explained by collisional processes. This paper presents a new loss mechanism for the O+ ions due to the combined effects of convection and corotation electric fields and interaction with Pc 5 waves (wave period: 150-600 s) via a magnetic drift-bounce resonance. A test particle code has been developed to calculate the motion of the ring current O+ ions in a time-independent dipole magnetic field, and convection and corotation electric fields, plus Pc 5 wave fields, for which a simple analytical model has been formulated based on spacecraft observations. For given fields, whether a particle gains or loses energy depends on its initial kinetic energy, pitch angle at the equatorial plane, and the position of its guiding center with respect to the azimuthal phase of the wave. The ring current O+ ions show a dispersion in energies and L values with decreasing local time across the dayside, and a bulk shift to lower energies and higher L values. The former is due to the wave-particle interaction causing the ion to gain or lose energy, while the latter is due to the convection electric field. Our simulations show that, due to the interaction with the Pc 5 waves, the particle's kinetic energy can drop below that required to overcome the convection potential and the particle will be lost to the dayside magnetopause by a sunward E×B drift. This may contribute to the loss of O+ ions at intermediate energies (tens of keV) observed during the recovery phase of geomagnetic storms.

Neutral-neutral and neutral-ion collision integrals for Y2O3-Ar plasma system

NASA Astrophysics Data System (ADS)

Dhamale, Gayatri D.; Nath, Swastik; Mathe, Vikas L.; Ghorui, Srikumar

2017-06-01

A detailed investigation on the neutral-neutral and neutral-ion collision integrals is reported for Y2O3-Ar plasma, an important system of functional material with unique properties having a wide range of processing applications. The calculated integrals are indispensible pre-requisite for the estimation of transport properties needed in CFD modelling of associated plasma processes. Polarizability plays an important role in determining the integral values. Ambiguity in selecting appropriate polarizability data available in the literature and calculating effective number of electrons in the ionized species contributing to the polarizability are addressed. The integrals are evaluated using Lennard-Jones like phenomenological potential up to (l,s) = (4,4). Used interaction potential is suitable for both neutral-neutral and neutral-ion interactions. For atom-parent ion interactions, contribution coming from the inelastic resonant charge transfer process has been accounted properly together with that coming from the elastic counterpart. A total of 14 interacting species and 60 different interactions are considered. Key contributing factors like basic electronic properties of the interacting species and associated polarizability values are accounted carefully. Adopted methodology is first benchmarked against data reported in the literature and then applied to the Y2O3-Ar plasma system for estimating the collision integrals. Results are presented in the temperature range of 100 K-100 000 K.

Comparison between Free and Immobilized Ion Effects on Hydrophobic Interactions: A Molecular Dynamics Study.

PubMed

Huang, Kai; Gast, Sebastian; Ma, C Derek; Abbott, Nicholas L; Szlufarska, Izabela

2015-10-15

Fundamental studies of the effect of specific ions on hydrophobic interactions are driven by the need to understand phenomena such as hydrophobically driven self-assembly or protein folding. Using β-peptide-inspired nanorods, we investigate the effects of both free ions (dissolved salts) and proximally immobilized ions on hydrophobic interactions. We find that the free ion effect is correlated with the water density fluctuation near a nonpolar molecular surface, showing that such fluctuation can be an indicator of hydrophobic interactions in the case of solution additives. In the case of immobilized ion, our results demonstrate that hydrophobic interactions can be switched on and off by choosing different spatial arrangements of proximal ions on a nanorod. For globally amphiphilic nanorods, we find that the magnitude of the interaction can be further tuned using proximal ions with varying ionic sizes. In general, univalent proximal anions are found to weaken hydrophobic interactions. This is in contrast to the effect of free ions, which according to our simulations strengthen hydrophobic interactions. In addition, immobilized anions of increasing ionic size do not follow the same ordering (Hofmeister-like ranking) as free ions when it comes to their impact on hydrophobic interactions. The immobilized ion effect is not simply correlated with the water density fluctuation near the nonpolar side of the amphiphilic nanorod. We propose a molecular picture that explains the contrasting effects of immobilized versus free ions.

Hadron rapidity spectra within a hybrid model

NASA Astrophysics Data System (ADS)

Khvorostukhin, A. S.; Toneev, V. D.

2017-03-01

A multistage hybrid model is constructed what joins the initial non-equilibrium stage of interaction, described by the hadron string dynamics (HSD) model, to subsequent evolution of the expanding system treated within ideal hydrodynamics (the second stage). Particles can still rescatter after hydrodynamical expansion that is the third interaction stage. The developed hybrid model is assigned to describe heavy-ion collisions in the energy range of the NICA collider. Generally, the model is in reasonable agreement with the available data on proton rapidity spectra.

Reply to "Comment on 'A Self-Consistent Model of the Interacting Ring Current Ions and Electromagnetic Ion Cyclotron Waves, Initial Results: Waves and Precipitation Fluxes' and 'Self-Consistent Model of the Magnetospheric Ring Current and Propagating Electromagnetic Ion Cyclotron Waves: Waves in Multi-Ion Magnetosphere' by Khazanov et al. et al."

NASA Technical Reports Server (NTRS)

Khazanov, G. V.; Gamayunov, K. V.; Gallagher, D. L.; Kozyra, J. W.

2007-01-01

It is well-known that the effects of electromagnetic ion cyclotron (EMIC) waves on ring current (RC) ion and radiation belt (RB) electron dynamics strongly depend on such particle/wave characteristics as the phase-space distribution function, frequency, wavenormal angle, wave energy, and the form of wave spectral energy density. The consequence is that accurate modeling of EMIC waves and RC particles requires robust inclusion of the interdependent dynamics of wave growth/damping, wave propagation, and[ particles. Such a self-consistent model is being progressively developed by Khazanov et al. [2002, 2006, 2007]. This model is based on a system of coupled kinetic equations for the RC and EMIC wave power spectral density along with the ray tracing equations. Thome and Home [2007] (hereafter referred to as TH2007) call the Khazanov et al. [2002, 2006] results into question in their Comment. The points in contention can be summarized as follows. TH2007 claim that: (1) "the important damping of waves by thermal heavy ions is completely ignored", and Landau damping during resonant interaction with thermal electrons is not included in our model; (2) EMIC wave damping due to RC O + is not included in our simulation; (3) non-linear processes limiting EMIC wave amplitude are not included in our model; (4) growth of the background fluctuations to a physically significantamplitude"must occur during a single transit of the unstable region" with subsequent damping below bi-ion latitudes,and consequently"the bounce averaged wave kinetic equation employed in the code contains a physically erroneous 'assumption". Our reply will address each of these points as well as other criticisms mentioned in the Comment. TH2007 are focused on two of our papers that are separated by four years. Significant progress in the self-consistent treatment of the RC-EMIC wave system has been achieved during those years. The paper by Khazanov et al. [2006] presents the latest version of our model, and in this Reply we refer mostly to this paper.

Modeling the human Nav1.5 sodium channel: structural and mechanistic insights of ion permeation and drug blockade

PubMed Central

Ahmed, Marawan; Jalily Hasani, Horia; Ganesan, Aravindhan; Houghton, Michael; Barakat, Khaled

2017-01-01

Abnormalities in the human Nav1.5 (hNav1.5) voltage-gated sodium ion channel (VGSC) are associated with a wide range of cardiac problems and diseases in humans. Current structural models of hNav1.5 are still far from complete and, consequently, their ability to study atomistic interactions of this channel is very limited. Here, we report a comprehensive atomistic model of the hNav1.5 ion channel, constructed using homology modeling technique and refined through long molecular dynamics simulations (680 ns) in the lipid membrane bilayer. Our model was comprehensively validated by using reported mutagenesis data, comparisons with previous models, and binding to a panel of known hNav1.5 blockers. The relatively long classical MD simulation was sufficient to observe a natural sodium permeation event across the channel’s selectivity filters to reach the channel’s central cavity, together with the identification of a unique role of the lysine residue. Electrostatic potential calculations revealed the existence of two potential binding sites for the sodium ion at the outer selectivity filters. To obtain further mechanistic insight into the permeation event from the central cavity to the intracellular region of the channel, we further employed “state-of-the-art” steered molecular dynamics (SMD) simulations. Our SMD simulations revealed two different pathways through which a sodium ion can be expelled from the channel. Further, the SMD simulations identified the key residues that are likely to control these processes. Finally, we discuss the potential binding modes of a panel of known hNav1.5 blockers to our structural model of hNav1.5. We believe that the data presented here will enhance our understanding of the structure–property relationships of the hNav1.5 ion channel and the underlying molecular mechanisms in sodium ion permeation and drug interactions. The results presented here could be useful for designing safer drugs that do not block the hNav1.5 channel. PMID:28831242

Saturn's Magnetosphere and Properties of Upstream Flow at Titan: Preliminary Results

NASA Technical Reports Server (NTRS)

Sittler, E. C., Jr.; Hartle, R. E.; Cooper, J. F.; Lipatov, A.; Bertucci, C.; Coates, A. J.; Arridge, C.; Szego, K.; Shappirio, M.; Simipson, D. G.;

Simulation of diatomic gas-wall interaction and accommodation coefficients for negative ion sources and accelerators.

PubMed

Sartori, E; Brescaccin, L; Serianni, G

2016-02-01

Particle-wall interactions determine in different ways the operating conditions of plasma sources, ion accelerators, and beams operating in vacuum. For instance, a contribution to gas heating is given by ion neutralization at walls; beam losses and stray particle production-detrimental for high current negative ion systems such as beam sources for fusion-are caused by collisional processes with residual gas, with the gas density profile that is determined by the scattering of neutral particles at the walls. This paper shows that Molecular Dynamics (MD) studies at the nano-scale can provide accommodation parameters for gas-wall interactions, such as the momentum accommodation coefficient and energy accommodation coefficient: in non-isothermal flows (such as the neutral gas in the accelerator, coming from the plasma source), these affect the gas density gradients and influence efficiency and losses in particular of negative ion accelerators. For ideal surfaces, the computation also provides the angular distribution of scattered particles. Classical MD method has been applied to the case of diatomic hydrogen molecules. Single collision events, against a frozen wall or a fully thermal lattice, have been simulated by using probe molecules. Different modelling approximations are compared.

Simulation of diatomic gas-wall interaction and accommodation coefficients for negative ion sources and accelerators

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

Sartori, E., E-mail: emanuele.sartori@igi.cnr.it; Serianni, G.; Brescaccin, L.

2016-02-15

Particle-wall interactions determine in different ways the operating conditions of plasma sources, ion accelerators, and beams operating in vacuum. For instance, a contribution to gas heating is given by ion neutralization at walls; beam losses and stray particle production—detrimental for high current negative ion systems such as beam sources for fusion—are caused by collisional processes with residual gas, with the gas density profile that is determined by the scattering of neutral particles at the walls. This paper shows that Molecular Dynamics (MD) studies at the nano-scale can provide accommodation parameters for gas-wall interactions, such as the momentum accommodation coefficient andmore » energy accommodation coefficient: in non-isothermal flows (such as the neutral gas in the accelerator, coming from the plasma source), these affect the gas density gradients and influence efficiency and losses in particular of negative ion accelerators. For ideal surfaces, the computation also provides the angular distribution of scattered particles. Classical MD method has been applied to the case of diatomic hydrogen molecules. Single collision events, against a frozen wall or a fully thermal lattice, have been simulated by using probe molecules. Different modelling approximations are compared.« less

Ionic strength independence of charge distributions in solvation of biomolecules

NASA Astrophysics Data System (ADS)

Virtanen, J. J.; Sosnick, T. R.; Freed, K. F.

2014-12-01

Electrostatic forces enormously impact the structure, interactions, and function of biomolecules. We perform all-atom molecular dynamics simulations for 5 proteins and 5 RNAs to determine the dependence on ionic strength of the ion and water charge distributions surrounding the biomolecules, as well as the contributions of ions to the electrostatic free energy of interaction between the biomolecule and the surrounding salt solution (for a total of 40 different biomolecule/solvent combinations). Although water provides the dominant contribution to the charge density distribution and to the electrostatic potential even in 1M NaCl solutions, the contributions of water molecules and of ions to the total electrostatic interaction free energy with the solvated biomolecule are comparable. The electrostatic biomolecule/solvent interaction energies and the total charge distribution exhibit a remarkable insensitivity to salt concentrations over a huge range of salt concentrations (20 mM to 1M NaCl). The electrostatic potentials near the biomolecule's surface obtained from the MD simulations differ markedly, as expected, from the potentials predicted by continuum dielectric models, even though the total electrostatic interaction free energies are within 11% of each other.

Quantum Otto engine using a single ion and a single thermal bath

NASA Astrophysics Data System (ADS)

Biswas, Asoka; Chand, Suman

2016-05-01

Quantum heat engines employ a quantum system as the working fluid, that gives rise to large work efficiency, beyond the limit for classical heat engines. Existing proposals for implementing quantum heat engines require that the system interacts with the hot bath and the cold bath (both modelled as a classical system) in an alternative fashion and therefore assumes ability to switch off the interaction with the bath during a certain stage of the heat-cycle. However, it is not possible to decouple a quantum system from its always-on interaction with the bath without use of complex pulse sequences. It is also hard to identify two different baths at two different temperatures in quantum domain, that sequentially interact with the system. Here, we show how to implement a quantum Otto engine without requiring to decouple the bath in a sequential manner. This is done by considering a single thermal bath, coupled to a single trapped ion. The electronic degree of freedom of the ion is chosen as a two-level working fluid while the vibrational degree of freedom plays the role of the cold bath. Measuring the electronic state mimics the release of heat into the cold bath. Thus, our model is fully quantum and exhibits very large work efficiency, asymptotically close to unity.

Importance of the ion-pair interactions in the OPEP coarse-grained force field: parametrization and validation.

PubMed

Sterpone, Fabio; Nguyen, Phuong H; Kalimeri, Maria; Derreumaux, Philippe

2013-10-08

We have derived new effective interactions that improve the description of ion-pairs in the OPEP coarse-grained force field without introducing explicit electrostatic terms. The iterative Boltzmann inversion method was used to extract these potentials from all atom simulations by targeting the radial distribution function of the distance between the center of mass of the side-chains. The new potentials have been tested on several systems that differ in structural properties, thermodynamic stabilities and number of ion-pairs. Our modeling, by refining the packing of the charged amino-acids, impacts the stability of secondary structure motifs and the population of intermediate states during temperature folding/unfolding; it also improves the aggregation propensity of peptides. The new version of the OPEP force field has the potentiality to describe more realistically a large spectrum of situations where salt-bridges are key interactions.

A fast plasma analyser for the study of the solar wind interaction with Mars

NASA Astrophysics Data System (ADS)

James, Adrian Martin

This thesis describes the design and development of the FONEMA instrument to be flown aboard the Russian mission to Mars in 1996. Many probes have flown to Mars yet despite this many mysteries still remain, among them the nature of the interaction of the solar wind with the planetary obstacle. In this thesis I will present some of the results from earlier spacecraft and the models of the interaction that they suggest paying particular attention to the contribution of ion analysers. From these results it will become clear that a fast ion sensor is needed to resolve many of the questions about the magnetosphere of Mars. The FONEMA instrument was designed for this job making use of a novel electrostatic mirror and particle collimator combined with parallel magnetic and electrostatic fields to resolve the ions into mass and energy bins. Development and production of the individual elements is discussed in detail.

Toward the description of electrostatic interactions between globular proteins: potential of mean force in the primitive model.

PubMed

Dahirel, Vincent; Jardat, Marie; Dufrêche, Jean-François; Turq, Pierre

2007-09-07

Monte Carlo simulations are used to calculate the exact potential of mean force between charged globular proteins in aqueous solution. The aim of the present paper is to study the influence of the ions of the added salt on the effective interaction between these nanoparticles. The charges of the model proteins, either identical or opposite, are either central or distributed on a discrete pattern. Contrarily to Poisson-Boltzmann predictions, attractive, and repulsive direct forces between proteins are not screened similarly. Moreover, it has been shown that the relative orientations of the charge patterns strongly influence salt-mediated interactions. More precisely, for short distances between the proteins, ions enhance the difference of the effective forces between (i) like-charged and oppositely charged proteins, (ii) attractive and repulsive relative orientations of the proteins, which may affect the selectivity of protein/protein recognition. Finally, such results observed with the simplest models are applied to a more elaborate one to demonstrate their generality.

Double Photoionization Near Threshold

NASA Technical Reports Server (NTRS)

Wehlitz, Ralf

2007-01-01

The threshold region of the double-photoionization cross section is of particular interest because both ejected electrons move slowly in the Coulomb field of the residual ion. Near threshold both electrons have time to interact with each other and with the residual ion. Also, different theoretical models compete to describe the double-photoionization cross section in the threshold region. We have investigated that cross section for lithium and beryllium and have analyzed our data with respect to the latest results in the Coulomb-dipole theory. We find that our data support the idea of a Coulomb-dipole interaction.

Interaction of slow highly charged ions with a metal surface covered with a thin dielectric film. The role of the neutralization energy in the nanostructures formation

NASA Astrophysics Data System (ADS)

Majkić, M. D.; Nedeljković, N. N.; Dojčilović, R. J.

2017-09-01

We consider the slow highly charged ions impinging upon a metal surface covered with a thin dielectric film, and formation of the surface nanostructures (craters) from the standpoint of the required energy. For the moderate ionic velocities, the size of the surface features depends on the deposited kinetic energy of the projectile and the ionic neutralization energy. The neutralization energy is calculated by employing the recently developed quasi-resonant two-state vector model for the intermediate Rydberg state population and the micro-staircase model for the cascade neutralization. The electron interactions with the ionic core, polarized dielectric and charge induced on the metal surface are modelled by the appropriate asymptotic expressions and the method for calculation of the effective ionic charges in the dielectric is proposed. The results are presented for the interaction of \\text{X}{{\\text{e}}Z+} ions (velocity v=0.25 a.u.; 25) with the metal surface (Co) covered with a thin dielectric film, for model values of dielectric constant inside the interaction region. In the absence of dielectric film, the neutralization energy is lower than the potential (ionization) energy due to the incomplete neutralization. The presence of dielectric film additionally decreases the neutralization energy. We calculate the projectile neutralization energy in the perturbed dielectric (perturbation is caused by the ionic motion and the surface structure formation). We correlate the neutralization energy added to the deposited kinetic energy with the experimentally obtained energy necessary for the formation of the nano-crater of a given depth.

Ion-neutral potential models in atmospheric pressure ion mobility time-of-flight mass spectrometry IM(tof)MS.

PubMed

Steiner, Wes E; English, William A; Hill, Herbert H

2006-02-09

The ion mobilities and their respective masses of several classes of amines (primary, secondary, and tertiary) were measured by electrospray ionization atmospheric pressure ion mobility time-of-flight mass spectrometry IM(tof)MS. The experimental data obtained were comparatively analyzed by the one-temperature kinetic theory of Chapman-Enskog. Several theoretical models were used to estimate the collision cross-sections; they include the rigid-sphere, polarization-limit, 12-6-4, and 12-4 potential models. These models were investigated to represent the interaction potentials contained within the collision integral that occurs between the polyatomic ions and the neutral drift gas molecules. The effectiveness of these collision cross-section models on predicting the mobility of these amine ions was explored. Moreover, the effects of drift gas selectivity on the reduced-mass term and in the collision cross-section term was examined. Use of a series of drift gases, namely, helium, neon, argon, nitrogen, and carbon dioxide, made it possible to distinguish between mass effects and polarizability effects. It was found that the modified 12-4 potential that compensates for the center of charge not being at the same location as the centers of mass showed improved agreement over the other collision cross-section models with respect to experimental data.

Interaction between calcium and phosphate adsorption on goethite.

PubMed

Rietra, R P; Hiemstra, T; van Riemsdijk, W H

2001-08-15

Quantitatively, little is known about the ion interaction processes that are responsible for the binding of phosphate in soil, water, and sediment, which determine the bioavailability and mobility of phosphate. Studies have shown that metal hydroxides are often responsible for the binding of PO4 in soils and sediments, but the binding behavior of PO4 in these systems often differs significantly from adsorption studies on metal hydroxides in laboratory. The interaction between PO4 and Ca adsorption was studied on goethite because Ca can influence the PO4 adsorption equilibria. Since adsorption interactions are very difficult to discriminate from precipitation reactions, conditions were chosen to prevent precipitation of Ca-PO4 solids. Adsorption experiments of PO4 and Ca, individually and in combination, show a strong interaction between adsorbed Ca and PO4 on goethite for conditions below the saturation index of apatite. It is shown that it is possible to predict the adsorption and interaction of PO4 and Ca on electrostatic arguments using the model parameter values derived from the single-ion systems and without invoking ternary complex formation or precipitation. The model enables the prediction of the Ca-PO4 interaction for environmentally relevant calcium and phosphate concentrations.

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.

A Nuclear Interaction Model for Understanding Results of Single Event Testing with High Energy Protons

NASA Technical Reports Server (NTRS)

Culpepper, William X.; ONeill, Pat; Nicholson, Leonard L.

2000-01-01

An internuclear cascade and evaporation model has been adapted to estimate the LET spectrum generated during testing with 200 MeV protons. The model-generated heavy ion LET spectrum is compared to the heavy ion LET spectrum seen on orbit. This comparison is the basis for predicting single event failure rates from heavy ions using results from a single proton test. Of equal importance, this spectra comparison also establishes an estimate of the risk of encountering a failure mode on orbit that was not detected during proton testing. Verification of the general results of the model is presented based on experiments, individual part test results, and flight data. Acceptance of this model and its estimate of remaining risk opens the hardware verification philosophy to the consideration of radiation testing with high energy protons at the board and box level instead of the more standard method of individual part testing with low energy heavy ions.

Photonuclear absorption cross sections

NASA Technical Reports Server (NTRS)

Norbury, John W.

1989-01-01

Neutron multiplicity in photonuclear reactions; invariance of classical electromagnetism; momentum transfer models in ion collisions; cosmic ray electromagnetic interactions; quadrupole excitations in nucleus-nucleus collisons and Y-89 interactions with relativistic nuclei; and the Weizsacker-Williams theory for nucleon emission via electromagnetic excitations in nucleus-nucleus collisions are discussed.

Magnetic field effect corroborated with docking study to explore photoinduced electron transfer in drug-protein interaction.

PubMed

Chakraborty, Brotati; Roy, Atanu Singha; Dasgupta, Swagata; Basu, Samita

2010-12-30

Conventional spectroscopic tools such as absorption, fluorescence, and circular dichroism spectroscopy used in the study of photoinduced drug-protein interactions can yield useful information about ground-state and excited-state phenomena. However, photoinduced electron transfer (PET) may be a possible phenomenon in the drug-protein interaction, which may go unnoticed if only conventional spectroscopic observations are taken into account. Laser flash photolysis coupled with an external magnetic field can be utilized to confirm the occurrence of PET and authenticate the spin states of the radicals/radical ions formed. In the study of interaction of the model protein human serum albumin (HSA) with acridine derivatives, acridine yellow (AY) and proflavin (PF(+)), conventional spectroscopic tools along with docking study have been used to decipher the binding mechanism, and laser flash photolysis technique with an associated magnetic field (MF) has been used to explore PET. The results of fluorescence study indicate that fluorescence resonance energy transfer takes place from the protein to the acridine-based drugs. Docking study unveils the crucial role of Ser 232 residue of HSA in explaining the differential behavior of the two drugs towards the model protein. Laser flash photolysis experiments help to identify the radicals/radical ions formed in the due course of PET (PF(•), AY(•-), TrpH(•+), Trp(•)), and the application of an external MF has been used to characterize their initial spin-state. Owing to its distance dependence, MF effect gives an idea about the proximity of the radicals/radical ions during interaction in the system and also helps to elucidate the reaction mechanisms. A prominent MF effect is observed in homogeneous buffer medium owing to the pseudoconfinement of the radicals/radical ions provided by the complex structure of the protein.

Counter ion induced irreversible denaturation of hen egg white lysozyme upon electrostatic interaction with iron oxide nanoparticles: a predicted model.

PubMed

Ghosh, Goutam; Panicker, Lata; Ningthoujam, R S; Barick, K C; Tewari, R

2013-03-01

The effects of electrostatic interaction between the hen egg white lysozyme (HEWL) and the functionalized iron oxide nanoparticles (IONPs) have been investigated using several techniques, e.g., CD, DSC, ζ-potential, UV-visible spectroscopy, DLS, TEM. Nanoparticles (IONPs) were functionalized with three hydrophilic ligands, viz., poly(ethylene glycol) (PEG), trisodium citrate (TSC) and sodium triphosphate (STP); where both TSC and STP contain Na(+) counter ions. It has been observed that the secondary structure of HEWL was not affected by PEG functionalized IONPs, but was partially and almost completely perturbed by TSC and STP functionalized IONPs, respectively. The perturbation of the secondary structure was irreversible. We have predicted an interaction model to explain the origin of perturbation of HEWL structure. We have also investigated the stability of nanoparticles dispersions after interaction with HEWL and used the DLVO theory to explain results. Copyright © 2012 Elsevier B.V. All rights reserved.

Volumetric, rheological, and optical properties of hydroxylamine hydrochloride aqueous solutions containing NaCl, KCl, and NH4Cl at 30°C

NASA Astrophysics Data System (ADS)

Deosarkar, S. D.; Puyad, A. L.; Shaikh, U. B.; Solanke, S. S.

2014-04-01

Densities, viscosities, and refractive indices of aqueous solutions of hydroxylamine hydrochloride containing 0.05, 0.10, and 0.15 mol/dm3 NaCl, KCl, and NH4Cl were measured at different concentrations of hydroxylamine hydrochloride at 30°C. Viscosity coefficients A and B representing ion-ion and ion-solvent interactions were determined from Jones-Dole equation. Experimental properties and viscosity coefficients have been interpreted in terms of ion-ion and ion-solvent interactions. Ion-solvent interactions were found to be dominating over the ion-ion interactions in studied systems.

Solar Wind Interaction with the Martian Upper Atmosphere at Early Mars/Extreme Solar Conditions

NASA Astrophysics Data System (ADS)

Dong, C.; Bougher, S. W.; Ma, Y.; Toth, G.; Lee, Y.; Nagy, A. F.; Tenishev, V.; Pawlowski, D. J.; Combi, M. R.

2014-12-01

The investigation of ion escape fluxes from Mars, resulting from the solar wind interaction with its upper atmosphere/ionosphere, is important due to its potential impact on the long-term evolution of Mars atmosphere (e.g., loss of water) over its history. In the present work, we adopt the 3-D Mars cold neutral atmosphere profiles (0 ~ 300 km) from the newly developed and validated Mars Global Ionosphere Thermosphere Model (M-GITM) and the 3-D hot oxygen profiles (100 km ~ 5 RM) from the exosphere Monte Carlo model Adaptive Mesh Particle Simulator (AMPS). We apply these 3-D model output fields into the 3-D BATS-R-US Mars multi-fluid MHD (MF-MHD) model (100 km ~ 20 RM) that can simulate the interplay between Mars upper atmosphere and solar wind by considering the dynamics of individual ion species. The multi-fluid MHD model solves separate continuity, momentum and energy equations for each ion species (H+, O+, O2+, CO2+). The M-GITM model together with the AMPS exosphere model take into account the effects of solar cycle and seasonal variations on both cold and hot neutral atmospheres. This feature allows us to investigate the corresponding effects on the Mars upper atmosphere ion escape by using a one-way coupling approach, i.e., both the M-GITM and AMPS model output fields are used as the input for the multi-fluid MHD model and the M-GITM is used as input into the AMPS exosphere model. In this study, we present M-GITM, AMPS, and MF-MHD calculations (1-way coupled) for 2.5 GYA conditions and/or extreme solar conditions for present day Mars (high solar wind velocities, high solar wind dynamic pressure, and high solar irradiance conditions, etc.). Present day extreme conditions may result in MF-MHD outputs that are similar to 2.5 GYA cases. The crustal field orientations are also considered in this study. By comparing estimates of past ion escape rates with the current ion loss rates to be returned by the MAVEN spacecraft (2013-2016), we can better constrain the total ion loss to space over Mars history, and thus enhance the science returned from the MAVEN mission.

Spectroscopic properties of the molecular ions BeX+ (X=Na, K, Rb): forming cold molecular ions from an ion-atom mixture by stimulated Raman adiabatic process

NASA Astrophysics Data System (ADS)

Ladjimi, Hela; Sardar, Dibyendu; Farjallah, Mohamed; Alharzali, Nisrin; Naskar, Somnath; Mlika, Rym; Berriche, Hamid; Deb, Bimalendu

2018-07-01

In this theoretical work, we calculate potential energy curves, spectroscopic parameters and transition dipole moments of molecular ions BeX+ (X=Na, K, Rb) composed of alkaline ion Be and alkali atom X with a quantum chemistry approach based on the pseudopotential model, Gaussian basis sets, effective core polarisation potentials and full configuration interaction. We study in detail collisions of the alkaline ion and alkali atom in quantum regime. Besides, we study the possibility of the formation of molecular ions from the ion-atom colliding systems by stimulated Raman adiabatic process and discuss the parameters regime under which the population transfer is feasible. Our results are important for ion-atom cold collisions and experimental realisation of cold molecular ion formation.

Computational membrane biophysics: From ion channel interactions with drugs to cellular function.

PubMed

Miranda, Williams E; Ngo, Van A; Perissinotti, Laura L; Noskov, Sergei Yu

2017-11-01

The rapid development of experimental and computational techniques has changed fundamentally our understanding of cellular-membrane transport. The advent of powerful computers and refined force-fields for proteins, ions, and lipids has expanded the applicability of Molecular Dynamics (MD) simulations. A myriad of cellular responses is modulated through the binding of endogenous and exogenous ligands (e.g. neurotransmitters and drugs, respectively) to ion channels. Deciphering the thermodynamics and kinetics of the ligand binding processes to these membrane proteins is at the heart of modern drug development. The ever-increasing computational power has already provided insightful data on the thermodynamics and kinetics of drug-target interactions, free energies of solvation, and partitioning into lipid bilayers for drugs. This review aims to provide a brief summary about modeling approaches to map out crucial binding pathways with intermediate conformations and free-energy surfaces for drug-ion channel binding mechanisms that are responsible for multiple effects on cellular functions. We will discuss post-processing analysis of simulation-generated data, which are then transformed to kinetic models to better understand the molecular underpinning of the experimental observables under the influence of drugs or mutations in ion channels. This review highlights crucial mathematical frameworks and perspectives on bridging different well-established computational techniques to connect the dynamics and timescales from all-atom MD and free energy simulations of ion channels to the physiology of action potentials in cellular models. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

Enhanced ion acceleration in transition from opaque to transparent plasmas

NASA Astrophysics Data System (ADS)

Mishra, R.; Fiuza, F.; Glenzer, S.

2018-04-01

Using particle-in-cell simulations, we investigate ion acceleration in the interaction of high intensity lasers with plasmas which transition from opaque to transparent during the interaction process. We show that the highest ion energies are achieved when the laser traverses the target around the peak intensity and re-heats the electron population responsible for the plasma expansion, enhancing the corresponding sheath electric field. This process can lead to an increase of up to 2x in ion energy when compared with the standard Target Normal Sheath Acceleration in opaque targets under the same laser conditions. A theoretical model is developed to predict the optimal target areal density as a function of laser intensity and pulse duration. A systematic parametric scan for a wide range of target densities and thicknesses is performed in 1D, 2D and 3D and shown consistent with the theory and with recent experimental results. These results open the way for a better optimization of the ion energy in future laser–solid experiments.

A New Global Multi-fluid MHD Model of the Solar Corona

NASA Astrophysics Data System (ADS)

van der Holst, B.; Chandran, B. D. G.; Alterman, B. L.; Kasper, J. C.; Toth, G.

2017-12-01

We present a multi-fluid generalization of the AWSoM model, a global magnetohydrodynamic (MHD) solar corona model with low-frequency Alfven wave turbulence (van der Holst et al., 2014). This new extended model includes electron and multi-ion temperatures and velocities (protons and alpha particles). The coronal heating and acceleration is addressed via outward propagating low-frequency Alfven waves that are partially reflected by Alfven speed gradients. The nonlinear interaction of these counter-propagating waves results in turbulent energy cascade. To apportion the wave dissipation to the electron and ion temperatures, we employ the results of the theories of linear wave damping and nonlinear stochastic heating as described by Chandran et al. (2011, 2013). This heat partitioning results in a more than mass proportional heating among ions.

Ion Association versus Ion Interaction Models in Examining Electrolyte Solutions: Application to Calcium Hydroxide Solubility Equilibrium

ERIC Educational Resources Information Center

Menéndez, M. Isabel; Borge, Javier

2014-01-01

The heterogeneous equilibrium of the solubility of calcium hydroxide in water is used to predict both its solubility product from solubility and solubility values from solubility product when inert salts, in any concentration, are present. Accepting the necessity of including activity coefficients to treat the saturated solution of calcium…

Structure and dynamics of microbe-exuded polymers and their interactions with calcite surfaces.

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

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

2005-12-01

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 organo-cation interactions are well suited to predictive molecular modeling studies for investigating the roles of conformation and configuration of polysaccharides on cation binding. In this study, alginic acid was chosen as a model polymer and representative disaccharide and polysaccharide subunits were modeled. The ability of disaccharide subunits to bind calcium and to associate with the surface of calcite was investigated. The findings were extended to modeling polymer interactions with calcium ions.

Four faces of the interaction between ions and aromatic rings.

PubMed

Papp, Dóra; Rovó, Petra; Jákli, Imre; Császár, Attila G; Perczel, András

2017-07-15

Non-covalent interactions between ions and aromatic rings play an important role in the stabilization of macromolecular complexes; of particular interest are peptides and proteins containing aromatic side chains (Phe, Trp, and Tyr) interacting with negatively (Asp and Glu) and positively (Arg and Lys) charged amino acid residues. The structures of the ion-aromatic-ring complexes are the result of an interaction between the large quadrupole moment of the ring and the charge of the ion. Four attractive interaction types are proposed to be distinguished based on the position of the ion with respect to the plane of the ring: perpendicular cation-π (CP ⊥ ), co-planar cation-π (CP ∥ ), perpendicular anion-π (AP ⊥ ), and co-planar anion-π (AP ∥ ). To understand more than the basic features of these four interaction types, a systematic, high-level quantum chemical study is performed, using the X -  + C 6 H 6 , M +  + C 6 H 6 , X -  + C 6 F 6 , and M +  + C 6 F 6 model systems with X -  = H - , F - , Cl - , HCOO - , CH 3 COO - and M +  = H + , Li + , Na + , NH4+, CH 3 NH3+, whereby C 6 H 6 and C 6 F 6 represent an electron-rich and an electron-deficient π system, respectively. Benchmark-quality interaction energies with small uncertainties, obtained via the so-called focal-point analysis (FPA) technique, are reported for the four interaction types. The computations reveal that the interactions lead to significant stabilization, and that the interaction energy order, given in kcal mol -1 in parentheses, is CP ⊥ (23-37) > AP ⊥ (14-21) > CP ∥ (9-22) > AP ∥ (6-16). A natural bond orbital analysis performed leads to a deeper qualitative understanding of the four interaction types. To facilitate the future quantum chemical characterization of ion-aromatic-ring interactions in large biomolecules, the performance of three density functional theory methods, B3LYP, BHandHLYP, and M06-2X, is tested against the FPA benchmarks, with the result that the M06-2X functional performs best. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

How to Connect Cardiac Excitation to the Atomic Interactions of Ion Channels.

PubMed

Silva, Jonathan R

2018-01-23

Many have worked to create cardiac action potential models that explicitly represent atomic-level details of ion channel structure. Such models have the potential to define new therapeutic directions and to show how nanoscale perturbations to channel function predispose patients to deadly cardiac arrhythmia. However, there have been significant experimental and theoretical barriers that have limited model usefulness. Recently, many of these barriers have come down, suggesting that considerable progress toward creating these long-sought models may be possible in the near term. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Solar Wind Interaction and Crustal Field Influences on Mars' Upper Ionosphere: MAVEN Observations Compared to Model Results

NASA Astrophysics Data System (ADS)

Luhmann, J. G.; Alvarez, K.; Curry, S.; Dong, C.; Ma, Y.; Bougher, S. W.; Benna, M.; Elrod, M. K.; Mahaffy, P. R.; Withers, P.; Girazian, Z.; Connerney, J. E. P.; Brain, D.; Jakosky, B. M.

2016-12-01

Since the two Viking Landers, progress on improving our global knowledge of the Martian ionosphere's characteristics has been limited by the available instrumentation and sampling geometries. In particular, while remote sensing and the lower energy plasma spectrometer observations on missions including MGS and MEX provided insights on the effects of the crustal magnetic fields of Mars and the solar wind interaction, these measurements did not allow the broader thermal ion surveys necessary to test our current understanding of the region between the exobase at 200 km altitude and the solar wind interaction boundary. In this study we use the MAVEN NGIMS thermal ion mass spectrometer observations from the prime mission year 2015 to construct some statistical pictures of the increasingly collisionless region of the ionosphere between 200 and 500 km where crustal field and solar wind interaction effects should begin to dominate its behavior. Comparisons with models of the solar wind interaction with Mars provide important global context for these observations, including the roles of system diversity associated with changing crustal field and interplanetary field orientations.

Kinetic Monte Carlo simulations of ion-induced ripple formation: Dependence on flux, temperature, and defect concentration in the linear regime

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

Chason, E.; Chan, W. L.; Bharathi, M. S.

Low-energy ion bombardment produces spontaneous periodic structures (sputter ripples) on many surfaces. Continuum theories describe the pattern formation in terms of ion-surface interactions and surface relaxation kinetics, but many features of these models (such as defect concentration) are unknown or difficult to determine. In this work, we present results of kinetic Monte Carlo simulations that model surface evolution using discrete atomistic versions of the physical processes included in the continuum theories. From simulations over a range of parameters, we obtain the dependence of the ripple growth rate, wavelength, and velocity on the ion flux and temperature. The results are discussedmore » in terms of the thermally dependent concentration and diffusivity of ion-induced surface defects. We find that in the early stages of ripple formation the simulation results are surprisingly well described by the predictions of the continuum theory, in spite of simplifying approximations used in the continuum model.« less

Cascade of Magnetic Field Induced Spin Transitions in LaCoO3

NASA Astrophysics Data System (ADS)

Altarawneh, M. M.; Chern, G.-W.; Harrison, N.; Batista, C. D.; Uchida, A.; Jaime, M.; Rickel, D. G.; Crooker, S. A.; Mielke, C. H.; Betts, J. B.; Mitchell, J. F.; Hoch, M. J. R.

2012-07-01

We present magnetization and magnetostriction studies of LaCoO3 in magnetic fields approaching 100 T. In contrast with expectations from single-ion models, the data reveal two distinct first-order transitions and well-defined magnetization plateaus. The magnetization at the higher plateau is only about half the saturation value expected for spin-1 Co3+ ions. These findings strongly suggest collective behavior induced by interactions between different electronic configurations of Co3+ ions. We propose a model that predicts crystalline spin textures and a cascade of four magnetic phase transitions at high fields, of which the first two account for the experimental data.

Correlation, Breit and Quantum Electrodynamics effects on energy level and transition properties of W54+ ion

NASA Astrophysics Data System (ADS)

Ding, Xiaobin; Sun, Rui; Koike, Fumihiro; Kato, Daiji; Murakami, Izumi; Sakaue, Hiroyuki A.; Dong, Chenzhong

2017-03-01

The electron correlation effects and Breit interaction as well as Quantum Electro-Dynamics (QED) effects were expected to have important contribution to the energy level and transition properties of heavy highly charged ions. The ground states [Ne]3s23p63d2 and first excited states [Ne]3s23p53d3 of W54+ ion have been studied by using Multi-Configuration Dirac-Fock method with the implementation of Grasp2K package. A restricted active space method was employed to investigate the correlation contribution from different models. The Breit interaction and QED effects were taken into account in the relativistic configuration interaction calculation with the converged wavefunction. It is found that the correlation contribution from 3s and 3p orbital have important contribution to the energy level, transition wavelength and probability of the ground and the first excited state of W54+ ion. Contribution to the Topical Issue "Atomic and Molecular Data and their Applications", edited by Gordon W.F. Drake, Jung-Sik Yoon, Daiji Kato, Grzegorz Karwasz.

Groundwater and solute transport modeling at Hyporheic zone of upper part Citarum River

NASA Astrophysics Data System (ADS)

Iskandar, Irwan; Farazi, Hendy; Fadhilah, Rahmat; Purnandi, Cipto; Notosiswoyo, Sudarto

2017-06-01

Groundwater and surface water interaction is an interesting topic to be studied related to the water resources and environmental studies. The study of interaction between groundwater and river water at the Upper Part Citarum River aims to know the contribution of groundwater to the river or reversely and also solute transport of dissolved ions between them. Analysis of drill logs, vertical electrical sounding at the selected sections, measurement of dissolved ions, and groundwater modeling were applied to determine the flow and solute transport phenomena at the hyporheic zone. It showed the hyporheic zone dominated by silt and clay with hydraulic conductivity range from 10-4∼10-8 m/s. The groundwater flowing into the river with very low gradient and it shows that the Citarum River is a gaining stream. The groundwater modeling shows direct seepage of groundwater into the Citarum River is only 186 l/s, very small compared to the total discharge of the river. Total dissolved ions of the groundwater ranged from 200 to 480 ppm while the river water range from 200 to 2,000 ppm. Based on solute transport modeling it indicates dissolved ions dispersion of the Citarum River into groundwater may occur in some areas such as Bojongsoang-Dayeuh Kolot and Nanjung. This situation would increase the dissolved ions in groundwater in the region due to the contribution of the Citarum River. The results of the research can be a reference for further studies related to the mechanism of transport of the pollutants in the groundwater around the Citarum River.

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

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

Vlcek, Lukas; Uhlik, Filip; Moucka, Filip

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

Comparison of 3D ion velocity distribution measurements and models in the vicinity of an absorbing boundary oriented obliquely to a magnetic field

NASA Astrophysics Data System (ADS)

Henriquez, Miguel F.; Thompson, Derek S.; Kenily, Shane; Khaziev, Rinat; Good, Timothy N.; McIlvain, Julianne; Siddiqui, M. Umair; Curreli, Davide; Scime, Earl E.

2016-10-01

Understanding particle distributions in plasma boundary regions is critical to predicting plasma-surface interactions. Ions in the presheath exhibit complex behavior because of collisions and due to the presence of boundary-localized electric fields. Complete understanding of particle dynamics is necessary for understanding the critical problems of tokamak wall loading and Hall thruster channel wall erosion. We report measurements of 3D argon ion velocity distribution functions (IVDFs) in the vicinity of an absorbing boundary oriented obliquely to a background magnetic field. Measurements were obtained via argon ion laser induced fluorescence throughout a spatial volume upstream of the boundary. These distribution functions reveal kinetic details that provide a point-to-point check on particle-in-cell and 1D3V Boltzmann simulations. We present the results of this comparison and discuss some implications for plasma boundary interaction physics.

Renormalization of spin excitations in hexagonal HoMnO3 by magnon-phonon coupling

NASA Astrophysics Data System (ADS)

Kim, Taehun; Leiner, Jonathan C.; Park, Kisoo; Oh, Joosung; Sim, Hasung; Iida, Kazuki; Kamazawa, Kazuya; Park, Je-Geun

2018-05-01

Hexagonal HoMnO3, a two-dimensional Heisenberg antiferromagnet, has been studied via inelastic neutron scattering. A simple Heisenberg model with a single-ion anisotropy describes most features of the spin-wave dispersion curves. However, there is shown to be a renormalization of the magnon energies located at around 11 meV. Since both the magnon-magnon interaction and magnon-phonon coupling can affect the renormalization in a noncollinear magnet, we have accounted for both of these couplings by using a Heisenberg XXZ model with 1 /S expansions [1] and the Einstein site phonon model [13], respectively. This quantitative analysis leads to the conclusion that the renormalization effect primarily originates from the magnon-phonon coupling, while the spontaneous magnon decay due to the magnon-magnon interaction is suppressed by strong two-ion anisotropy.

A model of spin crossover in manganese(III) compounds: effects of intra- and intercenter interactions.

PubMed

Klokishner, Sophia I; Roman, Marianna A; Reu, Oleg S

2011-11-21

A microscopic approach to the problem of cooperative spin crossover in the [MnL2]NO3 crystal, which contains Mn(III) ions as structural units, is elaborated on, and the main mechanisms governing this effect are revealed. The proposed model also takes into account the splitting of the low-spin 3T1 (t(2)(4)) and high-spin 5E (t(2)(3)e) terms by the low-symmetry crystal field. The low-spin → high-spin transition has been considered as a cooperative phenomenon driven by interaction of the electronic shells of the Mn(III) ions with the all-around full-symmetric deformation that is extended over the crystal lattice via the acoustic phonon field. The model well explains the observed thermal dependencies of the magnetic susceptibility and the effective magnetic moment.

Optical model calculations of heavy-ion target fragmentation

NASA Technical Reports Server (NTRS)

Townsend, L. W.; Wilson, J. W.; Cucinotta, F. A.; Norbury, J. W.

1986-01-01

The fragmentation of target nuclei by relativistic protons and heavy ions is described within the context of a simple abrasion-ablation-final-state interaction model. Abrasion is described by a quantum mechanical formalism utilizing an optical model potential approximation. Nuclear charge distributions of the excited prefragments are calculated by both a hypergeometric distribution and a method based upon the zero-point oscillations of the giant dipole resonance. Excitation energies are estimated from the excess surface energy resulting from the abrasion process and the additional energy deposited by frictional spectator interactions of the abraded nucleons. The ablation probabilities are obtained from the EVA-3 computer program. Isotope production cross sections for the spallation of copper targets by relativistic protons and for the fragmenting of carbon targets by relativistic carbon, neon, and iron projectiles are calculated and compared with available experimental data.

Using X-ray spectroscopy of relativistic laser plasma interaction to reveal parametric decay instabilities: a modeling tool for astrophysics.

PubMed

Oks, E; Dalimier, E; Faenov, A Ya; Angelo, P; Pikuz, S A; Tubman, E; Butler, N M H; Dance, R J; Pikuz, T A; Skobelev, I Yu; Alkhimova, M A; Booth, N; Green, J; Gregory, C; Andreev, A; Zhidkov, A; Kodama, R; McKenna, P; Woolsey, N

2017-02-06

By analyzing profiles of experimental x-ray spectral lines of Si XIV and Al XIII, we found that both Langmuir and ion acoustic waves developed in plasmas produced via irradiation of thin Si foils by relativistic laser pulses (intensities ~10²¹ W/cm²). We prove that these waves are due to the parametric decay instability (PDI). This is the first time that the PDI-induced ion acoustic turbulence was discovered by the x-ray spectroscopy in laser-produced plasmas. These conclusions are also supported by PIC simulations. Our results can be used for laboratory modeling of physical processes in astrophysical objects and a better understanding of intense laser-plasma interactions.

Effects of Kinetic Processes in Shaping Io's Global Plasma Environment: A 3D Hybrid Model

NASA Technical Reports Server (NTRS)

Lipatov, Alexander S.; Combi, Michael R.

2004-01-01

The global dynamics of the ionized and neutral components in the environment of Io plays an important role in the interaction of Jupiter's corotating magnetospheric plasma with Io. The stationary simulation of this problem was done in the MHD and the electrodynamics approaches. One of the main significant results from the simplified two-fluid model simulations was a production of the structure of the double-peak in the magnetic field signature of the I0 flyby that could not be explained by standard MHD models. In this paper, we develop a method of kinetic ion simulation. This method employs the fluid description for electrons and neutrals whereas for ions multilevel, drift-kinetic and particle, approaches are used. We also take into account charge-exchange and photoionization processes. Our model provides much more accurate description for ion dynamics and allows us to take into account the realistic anisotropic ion distribution that cannot be done in fluid simulations. The first results of such simulation of the dynamics of ions in the Io's environment are discussed in this paper.

The impact of auxins used in assisted phytoextraction of metals from the contaminated environment on the alterations caused by lead(II) ions in the organization of model lipid membranes.

PubMed

Hąc-Wydro, Katarzyna; Sroka, Aleksandra; Jabłońska, Klaudia

2016-07-01

Auxins are successfully used to improve phytoextraction efficiency of metal ions from the contaminated environment, however, the mechanism of their activity in this field is not explained. Auxins are known to exert various biochemical alterations in the plant membranes and cells, but their activity involves also direct interactions with lipids leading to changes in membrane organization. Following the suggestion that the auxins-induced modifications in membrane properties alleviate toxic effect of metal ions in this paper we have undertaken the comparative studies on the effect of metal ions and metal ions/auxins mixtures on model membrane systems. The experiments were done on lipid monolayers differing in their composition spread on water subphase and on Pb(2+), Indole-3-acetic acid (IAA), 1-Naphthaleneacetic acid (NAA) and Pb(2+)/IAA and Pb(2+)/NAA water solutions. The analysis of the collected data suggests that metal ions and auxins can change fluidity of the lipid systems and weaken the interactions between monolayer components. This manifested in the increase of the mean area per molecule and the excess area per molecule values for the films on Pb(2+), auxins as well as Pb(2+)/auxin solutions as compared to the values on pure water subphase. However, the presence of auxin in the mixture with lead(II) ions makes the alterations induced by sole metal ions weaker. This effect was more pronounced for the membranes of a higher packing. Thus it was proposed that auxins may enhance phytoextraction of metal ions by weakening their destabilizing effect on membrane. Copyright © 2016 Elsevier B.V. All rights reserved.

Polarization and charge transfer in the hydration of chloride ions

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

Zhao Zhen; Rogers, David M.; Beck, Thomas L.

2010-01-07

A theoretical study of the structural and electronic properties of the chloride ion and water molecules in the first hydration shell is presented. The calculations are performed on an ensemble of configurations obtained from molecular dynamics simulations of a single chloride ion in bulk water. The simulations utilize the polarizable AMOEBA force field for trajectory generation and MP2-level calculations are performed to examine the electronic structure properties of the ions and surrounding waters in the external field of more distant waters. The ChelpG method is employed to explore the effective charges and dipoles on the chloride ions and first-shell waters.more » The quantum theory of atoms in molecules (QTAIM) is further utilized to examine charge transfer from the anion to surrounding water molecules. The clusters extracted from the AMOEBA simulations exhibit high probabilities of anisotropic solvation for chloride ions in bulk water. From the QTAIM analysis, 0.2 elementary charges are transferred from the ion to the first-shell water molecules. The default AMOEBA model overestimates the average dipole moment magnitude of the ion compared to the quantum mechanical value. The average magnitude of the dipole moment of the water molecules in the first shell treated at the MP2-level, with the more distant waters handled with an AMOEBA effective charge model, is 2.67 D. This value is close to the AMOEBA result for first-shell waters (2.72 D) and is slightly reduced from the bulk AMOEBA value (2.78 D). The magnitude of the dipole moment of the water molecules in the first solvation shell is most strongly affected by the local water-water interactions and hydrogen bonds with the second solvation shell, rather than by interactions with the ion.« less

Modeling of the energetic ion observations in the vicinity of Rhea and Dione

NASA Astrophysics Data System (ADS)

Kotova, Anna; Roussos, Elias; Krupp, Norbert; Dandouras, Iannis

2015-09-01

During several flybys of the Cassini spacecraft by the saturnian moons Rhea and Dione the energetic particle detector MIMI/LEMMS measured a significant reduction of energetic ion fluxes (20-300 keV) in their vicinity, which is caused by the absorption of those ions at the moon surfaces. In order to simulate the observed depletion profiles we developed an energetic particle tracer, which can be used to simulate the charged particle trajectories considering different models of the saturnian magnetosphere. This particle tracer is using an adaptive fourth order Gauss Runge-Kutta calculation method and its background magnetospheric model can be varied from that of a simple dipole, to a more complex one that includes also non-dipolar perturbations. The electromagnetic environment of each local, moon-magnetosphere interaction region is modeled through a hybrid plasma simulation code. Using this energetic particle tracer we explore which of these magnetospheric characteristics are more important in shaping the MIMI/LEMMS ion profiles. We also examine if MIMI/LEMMS responds primarily to protons (as typically assumed in many studies) or also to heavier ions, using calibration information, observations of the energy flux spectrum by the MIMI/CHEMS instrument (on board of Cassini as well) and different simulation results. Our results show that MIMI/LEMMS indeed measures heavier ions as well. Also we discovered that wrapping of magnetic field lines, even if it caused local perturbations only about few percent of the background magnetic field, can cause measurable changes in the spatial and energy distribution of fluxes measured by MIMI/LEMMS. These results are important for correct interpretation of MIMI/LEMMS data, and offer capabilities for a precise in-flight instruments' cross-calibration. Besides that, our simulation approach can be employed in similar environments (Titan, Enceladus, jovian moons, etc.) for constraining the magnetic topology of their interaction region and for identifying the composition and charge-states of ions at high energies, where capabilities of the available or future instruments can be limited.

Effect and interactions of commercial additives and chloride ion in copper electrowinning

NASA Astrophysics Data System (ADS)

Cui, Wenyuan

This thesis is to understand and compare the effects and interactions of modified polysaccharide (HydroStar), polyacrylamide (Cyquest N-900) and chloride ion on copper electrowinning. A study of the nucleation and growth was conducted in a synthetic electrolyte (40 g/L Cu, 160 g/L H2SO 4, 20 mg/L Cl-) with the addition of HydroStar or Cyquest N-900 using potential step measurements. The current responses generated were compared to theoretical models of nucleation and growth mechanisms. The nucleation and growth mechanism changed as function of potential and the presence of organic additives. The nucleation and growth mechanisms were confirmed using scanning electron microscopy (SEM). At low overpotentials, electrodeposition from the electrolyte without additives proceeded by progressive nucleation with three-dimensional (3-D) growth. The addition of HydroStar produced smaller nuclei and changed the mechanism to progressive nucleation and 2-D growth. Cyquest N-900 used there appeared to be progressive nucleation with 2-D growth and polarize the cathodes. In addition, instantaneous nucleation under diffusion control occurred at high overpotentials. Chloride ion and its interaction with HydroStar and Cyquest N-900 were further characterized by cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). The trends observed from Nyquist plots and equivalent circuit models were consistent with the CV results. Chloride, on its own, depolarized copper electrodeposition, while chloride ion associated with Cyquest N-900 inhibited the reaction. It is proposed that Cl- acted as a bridging ligand between copper and Cyquest N-900. The addition of HydroStar depolarized copper deposition, but it did not interact with.

Free-energy relationships in ion channels activated by voltage and ligand

PubMed Central

Chowdhury, Sandipan

2013-01-01

Many ion channels are modulated by multiple stimuli, which allow them to integrate a variety of cellular signals and precisely respond to physiological needs. Understanding how these different signaling pathways interact has been a challenge in part because of the complexity of underlying models. In this study, we analyzed the energetic relationships in polymodal ion channels using linkage principles. We first show that in proteins dually modulated by voltage and ligand, the net free-energy change can be obtained by measuring the charge-voltage (Q-V) relationship in zero ligand condition and the ligand binding curve at highly depolarizing membrane voltages. Next, we show that the voltage-dependent changes in ligand occupancy of the protein can be directly obtained by measuring the Q-V curves at multiple ligand concentrations. When a single reference ligand binding curve is available, this relationship allows us to reconstruct ligand binding curves at different voltages. More significantly, we establish that the shift of the Q-V curve between zero and saturating ligand concentration is a direct estimate of the interaction energy between the ligand- and voltage-dependent pathway. These free-energy relationships were tested by numerical simulations of a detailed gating model of the BK channel. Furthermore, as a proof of principle, we estimate the interaction energy between the ligand binding and voltage-dependent pathways for HCN2 channels whose ligand binding curves at various voltages are available. These emerging principles will be useful for high-throughput mutagenesis studies aimed at identifying interaction pathways between various regulatory domains in a polymodal ion channel. PMID:23250866

Modeling Electric Field Influences on Plasmaspheric Refilling

NASA Technical Reports Server (NTRS)

Liemohn, M. W.; Kozyra, J. U.; Khazanov, G. V.; Craven, Paul D.

1998-01-01

We have a new model of ion transport that we have applied to the problem of plasmaspheric flux tube refilling after a geomagnetic disturbance. This model solves the Fokker-Planck kinetic equation by applying discrete difference numerical schemes to the various operators. Features of the model include a time-varying ionospheric source, self-consistent Coulomb collisions, field-aligned electric field, hot plasma interactions, and ion cyclotron wave heating. We see refilling rates similar to those of earlier observations and models, except when the electric field is included. In this case, the refilling rates can be quite different that previously predicted. Depending on the populations included and the values of relevant parameters, trap zone densities can increase or decrease. In particular, the inclusion of hot populations near the equatorial region (specifically warm pancake distributions and ring current ions) can dramatically alter the refilling rate. Results are compared with observations as well as previous hydrodynamic and kinetic particle model simulations.

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).

L-H transitions driven by ion heating in scrape-off layer turbulence (SOLT) model simulations

NASA Astrophysics Data System (ADS)

Russell, D. A.; D'Ippolito, D. A.; Myra, J. R.

2015-11-01

The original SOLT model now includes the evolution of ion pressure consistent with drift-ordering. It is a two-dimensional, electrostatic reduced model wherein closure relations, obtained by integrating the equations along the B-field, model parallel physics that includes sheath-mediated current and heat flux in the scrape-off-layer and electron drift waves inside the separatrix. Low (L) and high (H) confinement regimes are observed in SOLT simulations, depending on the strength of an ion pressure (i.e., ion heating) source localized inside the separatrix: With increasing heating, particle and energy confinement times at first decrease in the L-mode then rise in the H-mode. The L-H transition is marked by distinct changes in sheared-flow profiles. The addition of ion pressure dynamics enables modeling the self-consistent interaction between the ion diamagnetic drift and the radial electric field (mean and zonal flows). The roles of these sheared flows in mediating the L-H transition are explored. A new diagnostic, based on the density correlation function, is applied to study blob velocities in different regimes. Work supported by the U.S. Department of Energy Office of Science, Office of Fusion Energy Sciences, under Award Number DE-FG02-97ER54392.

NH2- in a cold ion trap with He buffer gas: Ab initio quantum modeling of the interaction potential and of state-changing multichannel dynamics

NASA Astrophysics Data System (ADS)

Hernández Vera, Mario; Yurtsever, Ersin; Wester, Roland; Gianturco, Franco A.

2018-05-01

We present an extensive range of accurate ab initio calculations, which map in detail the spatial electronic potential energy surface that describes the interaction between the molecular anion NH2 - (1A1) in its ground electronic state and the He atom. The time-independent close-coupling method is employed to generate the corresponding rotationally inelastic cross sections, and then the state-changing rates over a range of temperatures from 10 to 30 K, which is expected to realistically represent the experimental trapping conditions for this ion in a radio frequency ion trap filled with helium buffer gas. The overall evolutionary kinetics of the rotational level population involving the molecular anion in the cold trap is also modelled during a photodetachment experiment and analyzed using the computed rates. The present results clearly indicate the possibility of selectively detecting differences in behavior between the ortho- and para-anions undergoing photodetachment in the trap.

Origin of poor doping efficiency in solution processed organic semiconductors.

PubMed

Jha, Ajay; Duan, Hong-Guang; Tiwari, Vandana; Thorwart, Michael; Miller, R J Dwayne

2018-05-21

Doping is an extremely important process where intentional insertion of impurities in semiconductors controls their electronic properties. In organic semiconductors, one of the convenient, but inefficient, ways of doping is the spin casting of a precursor mixture of components in solution, followed by solvent evaporation. Active control over this process holds the key to significant improvements over current poor doping efficiencies. Yet, an optimized control can only come from a detailed understanding of electronic interactions responsible for the low doping efficiencies. Here, we use two-dimensional nonlinear optical spectroscopy to examine these interactions in the course of the doping process by probing the solution mixture of doped organic semiconductors. A dopant accepts an electron from the semiconductor and the two ions form a duplex of interacting charges known as ion-pair complexes. Well-resolved off-diagonal peaks in the two-dimensional spectra clearly demonstrate the electronic connectivity among the ions in solution. This electronic interaction represents a well resolved electrostatically bound state, as opposed to a random distribution of ions. We developed a theoretical model to recover the experimental data, which reveals an unexpectedly strong electronic coupling of ∼250 cm -1 with an intermolecular distance of ∼4.5 Å between ions in solution, which is approximately the expected distance in processed films. The fact that this relationship persists from solution to the processed film gives direct evidence that Coulomb interactions are retained from the precursor solution to the processed films. This memory effect renders the charge carriers equally bound also in the film and, hence, results in poor doping efficiencies. This new insight will help pave the way towards rational tailoring of the electronic interactions to improve doping efficiencies in processed organic semiconductor thin films.

Fragile X mental retardation protein controls ion channel expression and activity.

PubMed

Ferron, Laurent

2016-10-15

Fragile X-associated disorders are a family of genetic conditions resulting from the partial or complete loss of fragile X mental retardation protein (FMRP). Among these disorders is fragile X syndrome, the most common cause of inherited intellectual disability and autism. FMRP is an RNA-binding protein involved in the control of local translation, which has pleiotropic effects, in particular on synaptic function. Analysis of the brain FMRP transcriptome has revealed hundreds of potential mRNA targets encoding postsynaptic and presynaptic proteins, including a number of ion channels. FMRP has been confirmed to bind voltage-gated potassium channels (K v 3.1 and K v 4.2) mRNAs and regulates their expression in somatodendritic compartments of neurons. Recent studies have uncovered a number of additional roles for FMRP besides RNA regulation. FMRP was shown to directly interact with, and modulate, a number of ion channel complexes. The sodium-activated potassium (Slack) channel was the first ion channel shown to directly interact with FMRP; this interaction alters the single-channel properties of the Slack channel. FMRP was also shown to interact with the auxiliary β4 subunit of the calcium-activated potassium (BK) channel; this interaction increases calcium-dependent activation of the BK channel. More recently, FMRP was shown to directly interact with the voltage-gated calcium channel, Ca v 2.2, and reduce its trafficking to the plasma membrane. Studies performed on animal models of fragile X syndrome have revealed links between modifications of ion channel activity and changes in neuronal excitability, suggesting that these modifications could contribute to the phenotypes observed in patients with fragile X-associated disorders. © 2016 The Authors. The Journal of Physiology © 2016 The Physiological Society.

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.

Molecular simulation study on Hofmeister cations and the aqueous solubility of benzene.

PubMed

Ganguly, Pritam; Hajari, Timir; van der Vegt, Nico F A

2014-05-22

We study the ion-specific salting-out process of benzene in aqueous alkali chloride solutions using Kirkwood-Buff (KB) theory of solutions and molecular dynamics simulations with different empirical force field models for the ions and benzene. Despite inaccuracies in the force fields, the simulations indicate that the decrease of the Setchenow salting-out coefficient for the series NaCl > KCl > RbCl > CsCl is determined by direct benzene-cation correlations, with the larger cations showing weak interactions with benzene. Although ion-specific aqueous solubilities of benzene may be affected by indirect ion-ion, ion-water, and water-water correlations, too, these correlations are found to be unimportant, with little to no effect on the Setchenow salting-out coefficients of the various salts. We further considered LiCl, which is experimentally known to be a weaker salting-out agent than NaCl and KCl and, therefore, ranks at an unusual position within the Hofmeister cation series. The simulations indicate that hydrated Li(+) ions can take part of the benzene hydration shell while the other cations are repelled by it. This causes weaker Li(+) exclusion around the solute and a resulting, weaker salting-out propensity of LiCl compared to that of the other salts. Removing benzene-water and benzene-salt electrostatic interactions in the simulations does not affect this mechanism, which may therefore also explain the smaller effect of LiCl, as compared to that of NaCl or KCl, on aqueous solvation and hydrophobic interaction of nonpolar molecules.

Characterization and relevance of physicochemical interactions among components of a novel multiparticulate formulation for colonic delivery.

PubMed

Singh, Brahma N; Kim, Kwon H

2007-08-16

The primary objective of this study was to investigate potential interactions among a model drug (azathioprine; AZA), polymers and a divalent metal ion, which were utilized in the development of a novel multiparticulate formulation for colonic delivery. The approach involved preparation of beads by ionotropic gelation of deacylated gellan gum (DGG) in the presence of Ca(2+) ions, followed by coating with Eudragit S-100. Various possible physicochemical interactions among formulation components were characterized by DSC, FT-IR, XRPD, (1)H-NMR, and an isothermal stress test. Results of isothermal stress testing indicated that there was no significant interaction of AZA with DGG and Eudragit S-100. However, results of DSC and XRPD studies suggested that there could be interactions between AZA and DGG, and ionotropic gelation can affect the physical state of AZA, which may have implications for drug release characteristics and, physical and chemical stability. The results of FT-IR studies were suggestive of interactions of DGG with AZA and Eudragit S-100, and provided evidence for interactions of AZA and DGG with Ca(2+) ions. The electrostatic interaction of DGG with Ca(2+) was also supported by results of DSC studies while that between AZA and Ca(2+) was confirmed by (1)H-NMR studies. This study, to our knowledge, is first reported investigation in which the unique thermal property of gellan gum gels, and possible interactions between a drug and counter ions of an ionotropic agent have been demonstrated through bead characterization studies. The formation of AZA-Ca(2+) complex could have an impact on drug release kinetics, product stability and clinical efficacy for treatment of inflammatory bowel diseases or other diseases, which merit further investigation.

Cometary pick-up ions observed near Giacobini-Zinner

NASA Technical Reports Server (NTRS)

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

1986-01-01

The number and energy density of cometary water-group ions observed near Comet Giacobini-Zinner are derived using the rest-frame distribution functions. The data reveal that density profiles of inbound and outbound passes and their shape correlate with pick-up ion production model predictions. The lose rate and production rate of water-group cometary molecules calculated from predicted and measured density profiles are 2 x 10 to the -6th/sec and 2.6 x 10 to the 28th/sec respectively. The shapes of the distribution functions are examined to study the solar wind/cometary ions interaction process.

Cometary pick-up ions observed near Giacobini-Zinner

NASA Astrophysics Data System (ADS)

Gloeckler, G.; Hovestadt, D.; Ipavich, F. M.; Scholer, M.; Klecker, B.; Galvin, A. B.

1986-03-01

The number and energy density of cometary water-group ions observed near Comet Giacobini-Zinner are derived using the rest-frame distribution functions. The data reveal that density profiles of inbound and outbound passes and their shape correlate with pick-up ion production model predictions. The lose rate and production rate of water-group cometary molecules calculated from predicted and measured density profiles are 2 x 10 to the -6th/sec and 2.6 x 10 to the 28th/sec respectively. The shapes of the distribution functions are examined to study the solar wind/cometary ions interaction process.

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

Kim, G.-H.; Pesaran, A.; Smith, K.

The objectives of this paper are: (1) continue to explore thermal abuse behaviors of Li-ion cells and modules that are affected by local conditions of heat and materials; (2) use the 3D Li-ion battery thermal abuse 'reaction' model developed for cells to explore the impact of the location of internal short, its heating rate, and thermal properties of the cell; (3) continue to understand the mechanisms and interactions between heat transfer and chemical reactions during thermal runaway for Li-ion cells and modules; and (4) explore the use of the developed methodology to support the design of abuse-tolerant Li-ion battery systems.

X-ray scattering measurements of strong ion-ion correlations in shock-compressed aluminum.

PubMed

Ma, T; Döppner, T; Falcone, R W; Fletcher, L; Fortmann, C; Gericke, D O; Landen, O L; Lee, H J; Pak, A; Vorberger, J; Wünsch, K; Glenzer, S H

2013-02-08

The strong ion-ion correlation peak characteristic of warm dense matter (WDM) is observed for the first time using simultaneous angularly, temporally, and spectrally resolved x-ray scattering measurements in laser-driven shock-compressed aluminum. Laser-produced molybdenum x-ray line emission at an energy of 17.9 keV is employed to probe aluminum compressed to a density of ρ>8 g/cm(3). We observe a well pronounced peak in the static structure factor at a wave number of k=4.0 Å(-1). The measurements of the magnitude and position of this correlation peak are precise enough to test different theoretical models for the ion structure and show that only models taking the complex interaction in WDM into account agree with the data. This also demonstrates a new highly accurate diagnostic to directly measure the state of compression of warm dense matter.

Far-field analysis of coupled bulk and boundary layer diffusion toward an ion channel entrance.

PubMed Central

Schumaker, M F; Kentler, C J

1998-01-01

We present a far-field analysis of ion diffusion toward a channel embedded in a membrane with a fixed charge density. The Smoluchowski equation, which represents the 3D problem, is approximated by a system of coupled three- and two-dimensional diffusions. The 2D diffusion models the quasi-two-dimensional diffusion of ions in a boundary layer in which the electrical potential interaction with the membrane surface charge is important. The 3D diffusion models ion transport in the bulk region outside the boundary layer. Analytical expressions for concentration and flux are developed that are accurate far from the channel entrance. These provide boundary conditions for a numerical solution of the problem. Our results are used to calculate far-field ion flows corresponding to experiments of Bell and Miller (Biophys. J. 45:279, 1984). PMID:9591651

Brownian Dynamics Simulations of Ion Transport through the VDAC

PubMed Central

Lee, Kyu Il; Rui, Huan; Pastor, Richard W.; Im, Wonpil

2011-01-01

It is important to gain a physical understanding of ion transport through the voltage-dependent anion channel (VDAC) because this channel provides primary permeation pathways for metabolites and electrolytes between the cytosol and mitochondria. We performed grand canonical Monte Carlo/Brownian dynamics (GCMC/BD) simulations to explore the ion transport properties of human VDAC isoform 1 (hVDAC1; PDB:2K4T) embedded in an implicit membrane. When the MD-derived, space-dependent diffusion constant was used in the GCMC/BD simulations, the current-voltage characteristics and ion number profiles inside the pore showed excellent agreement with those calculated from all-atom molecular-dynamics (MD) simulations, thereby validating the GCMC/BD approach. Of the 20 NMR models of hVDAC1 currently available, the third one (NMR03) best reproduces both experimental single-channel conductance and ion selectivity (i.e., the reversal potential). In addition, detailed analyses of the ion trajectories, one-dimensional multi-ion potential of mean force, and protein charge distribution reveal that electrostatic interactions play an important role in the channel structure and ion transport relationship. Finally, the GCMC/BD simulations of various mutants based on NMR03 show good agreement with experimental ion selectivity. The difference in ion selectivity between the wild-type and the mutants is the result of altered potential of mean force profiles that are dominated by the electrostatic interactions. PMID:21281575

Soil-modified carbon paste electrode: a useful tool in environmental assessment of heavy metal ion binding interactions.

PubMed

Svegl, I G; Ogorevc, B

2000-08-01

Carbon paste electrodes (CPEs) modified with different soils in their native form were prepared to create a soil-like solid phase suitable for application in studies of heavy metal ion uptake and binding interactions. The preparation of CPEs modified with five different soils was examined and their heavy metal ion uptake behavior investigated using a model Cu(II) aqueous solution. Metal ions were accumulated under open circuit conditions and were determined after a medium exchange using differential pulse anodic stripping voltammetry, applying preelectrolysis at -0.7 V. The soil-modified CPE accumulation behavior, including the linearity of the current response versus Cu(II) concentration, the influence of the pH on the solution, and the uptake kinetics, was thoroughly investigated. The correlation between the soil-modified CPE uptake capability and the standard soil parameters, such as ion exchange capacity, soil pH, organic matter and clay content, were evaluated for all five examined soils. The influence of selected endogenous cations (K(I), Ca(II), Fe(III)) on the transfer of Cu(II) ions from a solution to the simulated soil solid phase was examined and is discussed. Preliminary examinations of the soil-modified CPE uptake behavior with some exogenous heavy metal ions of strong environmental interest (Pb(II), Hg(II), Cd(II) and Ag(I)) are also presented. This work demonstrates some attractive possibilities for the application of a soil-modified CPE in studying soil-heavy metal ion binding interactions, with a further potential use as a new environmental sensor appropriate for fist on-site testing of polluted soils.

Spectroscopy and excitation dynamics of the trivalent lanthanides Tm(3+) and Ho(3+) in LiYF4

NASA Technical Reports Server (NTRS)

Walsh, Brian M.

1995-01-01

A detailed study of the spectroscopy and excitation dynamics Tm3+ and Ho3+ in yttrium lithium fluoride, LiYF4 (YLF), has been done. Absorption spectroscopy is utilized in the Judd-Ofelt theory to determine radiative transition rates of spontaneous emission. Luminescence spectroscopy is studied under cw diode laser excitation at 785nm. The effect of dopant ion concentration and excitation power on the observed luminescence are considered in these measurements. An analysis of these measurements have been used to determine channels of energy transfer between Tm3+ and Ho3+ ions. The temporal response of Tm and Ho in singly and co-doped YLF to pulsed laser excitation with a Ti:Al2O3 laser and a CoMgF2 laser turned to various wavelengths have also been studied. The energy transfer mechanisms of cross relaxation, upconversion, and resonant energy transfer between Tm3+ and Ho3+ ions have been modeled, and the model parameters extracted by a fitting procedure to the measured temporal response curves. Rate equation approaches to modeling are presented that result in predictions of rate constants for energy transfer processes, as well as more conventional approaches to modeling such as the Forster-Dexter models, which give the interaction strengths in terms of microscopic interaction parameters.

Self-Consistent Model of Magnetospheric Electric Field, Ring Current, Plasmasphere, and Electromagnetic Ion Cyclotron Waves: Initial Results

NASA Technical Reports Server (NTRS)

Gamayunov, K. V.; Khazanov, G. V.; Liemohn, M. W.; Fok, M.-C.; Ridley, A. J.

2009-01-01

Further development of our self-consistent model of interacting ring current (RC) ions and electromagnetic ion cyclotron (EMIC) waves is presented. This model incorporates large scale magnetosphere-ionosphere coupling and treats self-consistently not only EMIC waves and RC ions, but also the magnetospheric electric field, RC, and plasmasphere. Initial simulations indicate that the region beyond geostationary orbit should be included in the simulation of the magnetosphere-ionosphere coupling. Additionally, a self-consistent description, based on first principles, of the ionospheric conductance is required. These initial simulations further show that in order to model the EMIC wave distribution and wave spectral properties accurately, the plasmasphere should also be simulated self-consistently, since its fine structure requires as much care as that of the RC. Finally, an effect of the finite time needed to reestablish a new potential pattern throughout the ionosphere and to communicate between the ionosphere and the equatorial magnetosphere cannot be ignored.

One-dimension modeling on the parallel-plate ion extraction process based on a non-electron-equilibrium fluid model

NASA Astrophysics Data System (ADS)

Li, He-Ping; Chen, Jian; Guo, Heng; Jiang, Dong-Jun; Zhou, Ming-Sheng; Department of Engineering Physics Team

2017-10-01

Ion extraction from a plasma under an externally applied electric field involve multi-particle and multi-field interactions, and has wide applications in the fields of materials processing, etching, chemical analysis, etc. In order to develop the high-efficiency ion extraction methods, it is indispensable to establish a feasible model to understand the non-equilibrium transportation processes of the charged particles and the evolutions of the space charge sheath during the extraction process. Most of the previous studies on the ion extraction process are mainly based on the electron-equilibrium fluid model, which assumed that the electrons are in the thermodynamic equilibrium state. However, it may lead to some confusions with neglecting the electron movement during the sheath formation process. In this study, a non-electron-equilibrium model is established to describe the transportation of the charged particles in a parallel-plate ion extraction process. The numerical results show that the formation of the Child-Langmuir sheath is mainly caused by the charge separation. And thus, the sheath shielding effect will be significantly weakened if the charge separation is suppressed during the extraction process of the charged particles.

Investigation of magnetic properties in the case of three families of 1-dimensional magnets: M(II)A(4,4'-bipyridine); M = iron, cobalt, nickel, copper; A = chloride, nitrogen, (ox)

NASA Astrophysics Data System (ADS)

Danilovic, Dusan S.

Magnetic properties of three families of metal-organic coordinated networks which have the general form of M(II)A(4,4'-bipyridine), where M=Fe, Ni, Co, and Cu and A=Cl2, (ox) and (N3)2, are studied in this dissertation. Novel Ni(N3)2(4,4'-bipyridine), Co(N3)2(4,4'-bipyridine) and Cu(N 3)2(4,4'-bipyridine) have been synthesized. We applied different synthesis procedures and produced Ni, Co, and Cu azide compounds for the first time, thus leaving the hydrothermal route procedure. Powder x-ray diffraction at room temperature was done in order to establish the crystal structure of the members of these three families. It was found that all of them crystallize in orthorhombic structure, where transitional metals have an octahedral coordination. Since all three families have identical crystal structure we got opportunity to examine how ligands facilitate magnetic interaction between metallic centers and also to test existing magnetic theoretical models. Since 4,4'-bipyridine is much longer than other ligands, our systems can be considered as 1-D magnetic systems. Their interchain magnetic interactions are very weak, and they order magnetically at very low temperatures of the order of few K. Measurements of M(H) at temperatures T=1.9K and T=2K and chi(T) in different external magnetic fields in zero field and field cooled modes have been made. In the case of MCl2(4,4'-bipyridine) family of compounds, we observed ferromagnetic interactions between metal ions within the chains and antiferromagnetic interactions between adjacent chains. M(ox)(4,4'-bipyridine) family of metal-organic compounds has antiferromagnetic interactions between the transitional metal ions within the chain, while weak ferromagnetic interaction exists between the chains. All members in the M(N3)2(4,4'-bipyridine) family except in the case of the copper compound were found to have ferromagnetic interactions between metal ions within the chains and then antiferromagnetic interactions between adjacent chains. The copper compound does not show magnetic ordering in the temperature range we considered. All the metal ions in these compounds were detected in high spin states. The magnetic susceptibility data was fit to appropriate 1-D models, which in the case of MCl2(4,4'-bipyridine) and M(N3)2(4,4'-bipyridine) were the Classical Spin Fisher model, and the Bonner Fisher model in the case M(ox)(4,4'-bipyridine). The experimental results and fitting to the appropriate model with the accuracy of 0.995 suggests that shorter Cl-M-Cl distances facilitate ferromagnetic interactions, which are more sensitive to the total spin value then to the sole distance between metal ions. The magnetic behavior of M(N3) 2(4,4'-bipyridine) family of coordinated metal-organic compounds is very interesting because family members exhibit both ferromagnetic and antiferromagnetic behavior. The ferromagnetic characteristics decrease with decreasing spin. Fitting the results for all compounds of the M(ox)(4,4'-bipyridine) family have shown that strong anisotropy exists in all of them, being highest in Ni(ox)(4,'4-bipyridine) and lowest in Co(ox)(4,4'-bipyridine). Specific heat measurements were performed in the case of cobalt and copper azide compounds and then compared with previously obtained results for the iron coordinated network of the same family. Although none of these compounds show the characteristic lambda shaped transition indicating magnetic ordering, all of them have unusually large values of the constant gamma, which indicates significant magnetic contribution to the observed specific heat, since the free electron contribution in these observed families is negligible. We have concluded that total spin of the transitional metal plays a more important role than the distance between ions within the chain in determining magnitude of interaction, and that (N3)2 is a better facilitator of ferromagnetic interaction between ions than Cl2.

Angular distributions and mechanisms of fragmentation by relativistic heavy ions

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

Stoenner, R.W.; Haustein, P.E.; Cumming, J.B.

1984-07-23

Angular distributions of massive fragments from relativistic heavy-ion interactions are reported. Sideward peaking is observed for the light fragment /sup 37/Ar, from 25-GeV /sup 12/C+Au, while the distribution for /sup 127/Xe is strongly forward peaked. Conflicts of these observations and other existing data with predictions of models for the fragmentation process are discussed.

Theory and simulation of ion noise in microwave tubes

NASA Astrophysics Data System (ADS)

Manheimer, W. M.; Freund, H. P.; Levush, B.; Antonsen, T. M.

2001-01-01

Since there is always some ambient gas in electron beam devices, background ionization is ubiquitous. For long pulse times, the electrostatic potentials associated with this ionization can reach significant levels and give rise to such observed phenomena as phase noise in microwave tubes. This noise is usually associated with the motion of ions in the device; therefore, it is called ion noise. It often manifests itself as a slow phase fluctuation on the output signal. Observations of noise in microwave tubes such as coupled-cavity traveling wave tubes (CC-TWTs) and klystrons have been discussed in the literature. In this paper, a hybrid model is discussed in which the electron beam is described by the beam envelope equation, and the ions generated by beam ionization are treated as discrete particles using the one-dimensional equations of motion. The theoretical model provides good qualitative as well as reasonable quantitative insight into the origin of ion noise phenomena. The numerical results indicate that the model reproduces the salient features of the phase oscillations observed experimentally. That is, the scaling of the frequency of the phase oscillations with gas pressure in the device and the sensitive dependence of the phase oscillations on the focusing magnetic field. Two distinct time scales are observed in simulation. The fastest time scale oscillation is related to the bounce motion of ions in the axial potential wells formed by the scalloping of the electron beam. Slower sawtooth oscillations are observed to correlate with the well-to-well interactions induced by the ion coupling to the electron equilibrium. These oscillations are also correlated with ion dumping to the cathode or collector. As a practical matter, simulations indicate that the low frequency oscillations can be reduced significantly by using a well-matched electron beam propagating from the electron gun into the interaction circuit.

The Receptacle Model of Salting-In by Tetramethylammonium Ions

PubMed Central

Hribar–Lee, Barbara; Dill, Ken A.; Vlachy, Vojko

2010-01-01

Water is a poor solvent for nonpolar solutes. Water containing ions is an even poorer solvent. According to standard terminology, the tendency of salts to precipitate oils from water is called salting-out. However, interestingly, some salt ions, such as tetramethylammonium (TMA), cause instead the salting-in of hydrophobic solutes. Even more puzzling, there is a systematic dependence on solute size. TMA causes the salting-out of small hydrophobes and the salting-in of larger nonpolar solutes. We study these effects using NPT Monte Carlo simulations of the MB + dipole model of water, which was previously shown to account for hydrophobic effects and ion solubilities in water. The present model gives a structural interpretation for the thermodynamics of salting-in. The TMA structure allows deep penetration by a first shell of waters, the dipoles of which interact electrostatically with the ion. This first water shell sets up a second water shell that is shaped to act as a receptacle that binds the nonpolar solute. In this way, a nonpolar solute can actually bind more tightly to the TMA ion than to another hydrophobe, leading to the increased solubility and salting-in. Such structuring may also explain why molecular ions do not follow the same charge density series’ as atomic ions do. PMID:21028768

Receptacle model of salting-in by tetramethylammonium ions.

PubMed

Hribar-Lee, Barbara; Dill, Ken A; Vlachy, Vojko

2010-11-25

Water is a poor solvent for nonpolar solutes. Water containing ions is an even poorer solvent. According to standard terminology, the tendency of salts to precipitate oils from water is called salting-out. However, interestingly, some salt ions, such as tetramethylammonium (TMA), cause instead the salting-in of hydrophobic solutes. Even more puzzling, there is a systematic dependence on solute size. TMA causes the salting-out of small hydrophobes and the salting-in of larger nonpolar solutes. We study these effects using NPT Monte Carlo simulations of the Mercedes-Benz (MB) + dipole model of water, which was previously shown to account for hydrophobic effects and ion solubilities in water. The present model gives a structural interpretation for the thermodynamics of salting-in. The TMA structure allows deep penetration by a first shell of waters, the dipoles of which interact electrostatically with the ion. This first water shell sets up a second water shell that is shaped to act as a receptacle that binds the nonpolar solute. In this way, a nonpolar solute can actually bind more tightly to the TMA ion than to another hydrophobe, leading to the increased solubility and salting-in. Such structuring may also explain why molecular ions do not follow the same charge density series as atomic ions do.

Modeling and design of a beam emission spectroscopy diagnostic for the negative ion source NIO1

NASA Astrophysics Data System (ADS)

Barbisan, M.; Zaniol, B.; Cavenago, M.; Pasqualotto, R.

2014-02-01

Consorzio RFX and INFN-LNL are building a flexible small ion source (Negative Ion Optimization 1, NIO1) capable of producing about 130 mA of H- ions accelerated at 60 KeV. Aim of the experiment is to test and develop the instrumentation for SPIDER and MITICA, the prototypes, respectively, of the negative ion sources and of the whole neutral beam injectors which will operate in the ITER experiment. As SPIDER and MITICA, NIO1 will be monitored with beam emission spectroscopy (BES), a non-invasive diagnostic based on the analysis of the spectrum of the Hα emission produced by the interaction of the energetic ions with the background gas. Aim of BES is to monitor direction, divergence, and uniformity of the ion beam. The precision of these measurements depends on a number of factors related to the physics of production and acceleration of the negative ions, to the geometry of the beam, and to the collection optics. These elements were considered in a set of codes developed to identify the configuration of the diagnostic which minimizes the measurement errors. The model was already used to design the BES diagnostic for SPIDER and MITICA. The paper presents the model and describes its application to design the BES diagnostic in NIO1.

Pitch Angle Dependence of Drift Resonant Ions Observed by the Van Allen Probes

NASA Astrophysics Data System (ADS)

Rankin, R.; Wang, C.; Wang, Y.; Zong, Q. G.; Zhou, X.

2017-12-01

Acceleration and modulation of ring current ions by poloidal mode ULF waves is investigated. A simplified MHD model of ULF waves in a dipole magnetic field is presented that includes phase mixing to perpendicular scales determined by the ionospheric Pedersen conductivity. The wave model is combined with a full Lorentz force test particle code to study drift and drift bounce resonance wave-particle interactions. Ion trajectories are traced backward-in-time to an assumed form of the distribution function, and Liouville's method is used to reconstruct the phase space density response (PSD) poloidal mode waves observed by the Van Allen Probes. In spite of its apparent simplicity, simulations using the wave and test particle models are able to explain the acceleration of ions and energy dispersion observed by the Van Allen Probes. The paper focuses on the pitch angle evolution of the initial PSD as it responds to the action of ULF waves. An interesting aspect of the study is the formation of butterfly ion distributions as ions make periodic radial oscillations across L. Ions become trapped in an effective potential well across a limited range of L and follow trajectories that cause them to surf along constant phase fronts. The impications of this new trapping mechanism for both ions and electrons is discussed.

Gas-Phase Interaction of Anions with Polyisobutylenes: Collision-Induced Dissociation Study and Quantum Chemical Modeling.

PubMed

Nagy, Lajos; Kuki, Ákos; Deák, György; Purgel, Mihály; Vékony, Ádám; Zsuga, Miklós; Kéki, Sándor

2016-09-01

The gas-phase interaction of anions including fluoride, chloride, bromide, iodide, ethyl sulfate, chlorate, and nitrate with polyisobutylene (PIB) derivatives was studied using collision-induced dissociation (CID). The gas-phase adducts of anions with PIBs ([PIB + anion](-)) were generated from the electrosprayed solution of PIBs in the presence of the corresponding anions. The so-formed adducts subjected to CID showed a loss of anion at different characteristic collision energies, thus allowing the study of the strength of interaction between the anions and nonpolar PIBs having different end-groups. The values of characteristic collision energies (the energy needed to obtain 50% fragmentation) obtained by CID experiments correlated linearly with the binding enthalpies between the anion and PIB, as determined by density functional theory calculations. In the case of halide ions, the critical energies for dissociation, that is, the binding enthalpies for [PIB + anion](-) adducts, increased in the order of I(-) < Br(-) < Cl(-) < F(-). Furthermore, it was found that the binding enthalpies for the adducts formed with halide ions decreased approximately with the square radius of the halide ion, suggesting that the strength of interaction is mainly determined by the "surface" charge density of the halide ion. In addition, the characteristic collision energy versus the number of isobutylene units revealed a linear dependence.

A Physical Model of the Proton Radiation Belts of Jupiter inside Europa's Orbit

NASA Astrophysics Data System (ADS)

Nénon, Q.; Sicard, A.; Kollmann, P.; Garrett, H. B.; Sauer, S. P. A.; Paranicas, C.

2018-05-01

A physical model of the Jovian trapped protons with kinetic energies higher than 1 MeV inward of the orbit of the icy moon Europa is presented. The model, named Salammbô, takes into account the radial diffusion process, the absorption effect of the Jovian moons, and the Coulomb collisions and charge exchanges with the cold plasma and neutral populations of the inner Jovian magnetosphere. Preliminary modeling of the wave-particle interaction with electromagnetic ion cyclotron waves near the moon Io is also performed. Salammbô is validated against in situ proton measurements of Pioneer 10, Pioneer 11, Voyager 1, Galileo Probe, and Galileo Orbiter. A prominent feature of the MeV proton intensity distribution in the modeled area is the 2 orders of magnitude flux depletion observed in MeV measurements near the orbit of Io. Our simulations reveal that this is not due to direct interactions with the moon or its neutral environment but results from scattering of the protons by electromagnetic ion cyclotron waves.

Interaction of Solar Wind and Magnetic Anomalies - Modelling from Moon to Mars

NASA Astrophysics Data System (ADS)

Alho, Markku; Kallio, Esa; Wedlund, Cyril Simon; Wurz, Peter

2015-04-01

The crustal magnetic anomalies on both the Moon and Mars strongly affect the local plasma environment. On the Moon, the impinging solar wind is decelerated or deflected when interacting with the magnetic field anomaly, visible in the lunar surface as energetic neutral atom (ENA) emissions or as reflected protons, and may play a part in the space weathering of the lunar soil. At Mars, the crustal magnetic fields have been shown to be associated with, e.g., enhanced electron scale heights and modified convection of ionospheric plasma, resulting in the plasma environment being dominated by crustal magnetic fields up to altitudes of 400km. Our previous modelling work suggested that Hall currents are a dominant feature in a Moon-like magnetic anomaly interaction at scales at or below the proton inertial length. In this work we study the solar wind interaction with magnetic anomalies and compare the plasma environments of a Moon-like anomaly with a Mars-like anomaly by introducing an ionosphere and an exosphere to probe the transition from an atmosphere-less anomaly interaction to an ionospheric one. We utilize a 3D hybrid plasma model, in which ions are modelled as particles while electrons form a charge-neutralizing massless fluid. The hybrid model gives a full description of ion kinetics and associated plasma phenomena at the simulation region ranging from instabilities to possible reconnection. The model can thus be used to interpret both in-situ particle and field observations and remotely-sensed ENA emissions. A self-consistent ionosphere package for the model is additionally in development.

Isoscalar-vector interaction and hybrid quark core in massive neutron stars

NASA Astrophysics Data System (ADS)

Shao, G. Y.; Colonna, M.; Di Toro, M.; Liu, Y. X.; Liu, B.

2013-05-01

The hadron-quark phase transition in the core of massive neutron stars is studied with a newly constructed two-phase model. For nuclear matter, a nonlinear Walecka type model with general nucleon-meson and meson-meson couplings, recently calibrated by Steiner, Hemper and Fischer, is taken. For quark matter, a modified Polyakov-Nambu—Jona-Lasinio model, which gives consistent results with lattice QCD data, is used. Most importantly, we introduce an isoscalar-vector interaction in the description of quark matter, and we study its influence on the hadron-quark phase transition in the interior of massive neutron stars. With the constraints of neutron star observations, our calculation shows that the isoscalar-vector interaction between quarks is indispensable if massive hybrids star exist in the universe, and its strength determines the onset density of quark matter, as well as the mass-radius relations of hybrid stars. Furthermore, as a connection with heavy-ion-collision experiments we give some discussions about the strength of isoscalar-vector interaction and its effect on the signals of hadron-quark phase transition in heavy-ion collisions, in the energy range of the NICA at JINR-Dubna and FAIR at GSI-Darmstadt facilities.

Self-Consistent Ring Current Modeling with Propagating Electromagnetic Ion Cyclotron Waves in the Presence of Heavy Ions

NASA Technical Reports Server (NTRS)

Khazanov, George V.

2006-01-01

The self-consistent treatment of the RC ion dynamics and EMIC waves, which are thought to exert important influences on the ion dynamical evolution, is an important missing element in our understanding of the storm-and recovery-time ring current evolution. Under certain conditions, relativistic electrons, with energies 21 MeV, can be removed from the outer radiation belt by EMIC wave scattering during a magnetic storm. That is why the modeling of EMIC waves is critical and timely issue in magnetospheric physics. To describe the RC evolution itself this study uses the ring current-atmosphere interaction model (RAM). RAM solves the gyration and bounce-averaged Boltzmann-Landau equation inside of geosynchronous orbit. Originally developed at the University of Michigan, there are now several branches of this model currently in use as describe by Liemohn namely those at NASA Goddard Space Flight Center This study will generalize the self-consistent theoretical description of RC ions and EMIC waves that has been developed by Khazanov and include the heavy ions and propagation effects of EMIC waves in the global dynamic of self-consistent RC - EMIC waves coupling. The results of our newly developed model that will be presented at GEM meeting, focusing mainly on the dynamic of EMIC waves and comparison of these results with the previous global RC modeling studies devoted to EMIC waves formation. We also discuss RC ion precipitations and wave induced thermal electron fluxes into the ionosphere.

Plasma Inter-Particle and Particle-Wall Interactions

NASA Astrophysics Data System (ADS)

Patino, Marlene Idy

An improved understanding of plasma inter-particle and particle-wall interactions is critical to the advancement of plasma devices used for space electric propulsion, fusion, high-power communications, and next-generation energy systems. Two interactions of particular importance are (1) ion-atom collisions in the plasma bulk and (2) secondary electron emission from plasma-facing materials. For ion-atom collisions, interactions between fast ions and slow atoms are commonly dominated by charge-exchange and momentum-exchange collisions that are important to understanding the performance and behavior of many plasma devices. To investigate this behavior, this work developed a simple, well-characterized experiment that accurately measures the effects of high energy xenon ions incident on a background of xenon neutral atoms. By comparing these results to both analytical and computational models of ion-atom interactions, we discovered the importance of (1) accurately treating the differential cross-sections for momentum-exchange and charge-exchange collisions over all neutral background pressures, and (2) commonly overlooked interactions, including ion-induced electron emission and neutral-neutral ionization collisions, at high pressures. Data provide vital information on the angular scattering distributions of charge-exchange and momentum-exchange ions at 1.5 keV relevant for ion thrusters, and serve as canonical data for validation of plasma models. This work also investigates electron-induced secondary electron emission behavior relevant to materials commonly considered for plasma thrusters, fusion systems, and many other plasma devices. For such applications, secondary electron emission can alter the sheath potential, which can significantly affect device performance and life. Secondary electron emission properties were measured for materials that are critical to the efficient operation of many plasma devices, including: graphite (for tokamaks, ion thrusters, and traveling wave tubes), lithium (for tokamak walls), tungsten (the most promising material for future tokamaks such as ITER), and nickel (for plasma-enhanced chemistry). Measurements were made for incident electron energies up to 1.5 keV and angles between 0 and 78°. The most significant results from these measurements are as follows: (1) first-ever measurements of naturally-forming tungsten fuzz show a more than 40% reduction in secondary electron emission and an independence on incidence angle; (2) original measurements of lithium oxide show a 2x and 6x increase in secondary electron emission for 17% and 100% oxidation; and (3) unique measurements of Ni(110) single crystal show extrema in secondary electron emission when incidence angle is varied and an up to 36% increase at 0° over polycrystalline nickel. Each of these results are important discoveries for improving plasma devices. For example, from (1), the growth of tungsten fuzz in tokamaks is desirable for minimizing adverse secondary electron emission effects. From (2), the opposite is true for tokamaks with lithium coatings which are oxidized by typical residual gases. From (3), secondary electron emission from Ni(110) catalysts in plasma-enhanced chemistry may facilitate further reactions.

Ion pickup, scattering, and stochastic acceleration in the cometary environment of P/Giacobini-Zinner

NASA Technical Reports Server (NTRS)

Barbosa, D. D.

1991-01-01

Observations and theory related to the scattering and acceleration of cometary pickup ions are reviewed with emphasis on Comet P/Giacobini-Zinner. A comparison of the regions upstream and downstream of the bow shock is made to assess the relative merits of each as a site for stochastic acceleration of ions above the pickup energy through interaction with low-frequency MHD waves. In the far upstream region the data are most consistent with a model where pickup ions generate a low level of MHD waves but remain relatively scatter-free. In the downstream region intense magnetic fluctuations gives rise to rapid isotropization of the ions and a second-order stochastic acceleration. The properties of the MHD power spectrum are related to the energetic ion spectrum in the framework of a leaky box model where the bulk of the acceleration occurs downstream of the shock throughout the cometosheath. Good agreement of the observations with theory is evident for both P/Giacobini-Zinner and P/Halley.

Verification of nonlinear particle simulation of radio frequency waves in fusion plasmas

NASA Astrophysics Data System (ADS)

Kuley, Animesh; Bao, Jian; Lin, Zhihong

2015-11-01

Nonlinear global particle simulation model has been developed in GTC to study the nonlinear interactions of radio frequency (RF) waves with plasmas in tokamak. In this model, ions are considered as fully kinetic particles using the Vlasov equation and electrons are treated as guiding centers using the drift kinetic. Boris push scheme for the ion motion has been implemented in the toroidal geometry using magnetic coordinates and successfully verified for the ion cyclotron, ion Bernstein and lower hybrid waves. The nonlinear GTC simulation of the lower hybrid wave shows that the amplitude of the electrostatic potential is oscillatory due to the trapping of resonant electrons by the electric field of the lower hybrid wave. The nonresonant parametric decay is observed an IBW sideband and an ion cyclotron quasimode (ICQM). The ICQM induces an ion perpendicular heating with a heating rate proportional to the pump wave intensity. This work is supported by PPPL subcontract number S013849-F and US Department of Energy (DOE) SciDAC GSEP Program.

Space Weather at Mars: 3-D studies using one-way coupling between the Multi-fluid MHD, M-GITM and M-AMPS models

NASA Astrophysics Data System (ADS)

Dong, Chuanfei

This dissertation presents numerical simulation results of the solar wind interaction with the Martian upper atmosphere by using three comprehensive 3-D models: the Mars Global Ionosphere Thermosphere Model (M-GITM), the Mars exosphere Monte Carlo model Adaptive Mesh Particle Simulator (M-AMPS), and the BATS-R-US Mars multi-fluid MHD (MF-MHD) model. The coupled framework has the potential to provide improved predictions for ion escape rates for comparison with future data to be returned by the MAVEN mission (2014-2016) and thereby improve our understanding of present day escape processes. Estimates of ion escape rates over Mars history must start from properly validated models that can be extrapolated into the past. This thesis aims to build a model library for the NASA Mars Atmosphere and Volatile EvolutioN (MAVEN) mission, which will thus enhance the science return from the MAVEN mission. In this thesis, we aim to address the following four main scientific questions by adopting the one-way coupled framework developed here: (1) What are the Martian ion escape rates at the current epoch and ancient times? (2) What controls the ion escape processes at the current epoch? How are the ion escape variations connected to the solar cycle, crustal field orientation and seasonal variations? (3) How do the variable 3-D cold neutral thermosphere and hot oxygen corona affect the solar wind-Mars interaction? (4) How does the Martian atmosphere respond to extreme variations (e.g., ICMEs) in the solar wind and its interplanetary environment? These questions are closely related to the primary scientific goals of NASA's MAVEN mission and European Space Agency's Mars Express (MEX) mission. We reasonably answer all these four questions at the end of this thesis by employing the one-way coupled framework and comparing the simulation results with both MEX and MAVEN observational data.

Mean ionic activity coefficients in aqueous NaCl solutions from molecular dynamics simulations

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

Mester, Zoltan; Panagiotopoulos, Athanassios Z., E-mail: azp@princeton.edu

The mean ionic activity coefficients of aqueous NaCl solutions of varying concentrations at 298.15 K and 1 bar have been obtained from molecular dynamics simulations by gradually turning on the interactions of an ion pair inserted into the solution. Several common non-polarizable water and ion models have been used in the simulations. Gibbs-Duhem equation calculations of the thermodynamic activity of water are used to confirm the thermodynamic consistency of the mean ionic activity coefficients. While the majority of model combinations predict the correct trends in mean ionic activity coefficients, they overestimate their values at high salt concentrations. The solubility predictionsmore » also suffer from inaccuracies, with all models underpredicting the experimental values, some by large factors. These results point to the need for further ion and water model development.« less

Measurement of Charged Particle Interactions in Spacecraft and Planetary Habitat Shielding Materials

NASA Technical Reports Server (NTRS)

Zeitlin, Cary J.; Heilbronn, Lawrence H.; Miller, Jack; Wilson, John W.; Singleterry, Robert C., Jr.

2003-01-01

Accurate models of health risks to astronauts on long-duration missions outside the geomagnetosphere will require a full understanding of the radiation environment inside a spacecraft or planetary habitat. This in turn requires detailed knowledge of the flux of incident particles and their propagation through matter, including the nuclear interactions of heavy ions that are a part of the Galactic Cosmic Radiation (GCR). The most important ions are likely to be iron, silicon, oxygen, and carbon. Transport of heavy ions through complex shielding materials including self-shielding of tissue modifies the radiation field at points of interest (e.g., at the blood-forming organs). The incident flux is changed by two types of interactions: (1) ionization energy loss, which results in reduced particle velocity and higher LET (Linear Energy Transfer); and (2) nuclear interactions that fragment the incident nuclei into less massive ions. Ionization energy loss is well understood, nuclear interactions less so. Thus studies of nuclear fragmentation at GCR-like energies are needed to fill the large gaps that currently exist in the database. These can be done at only a few accelerator facilities where appropriate beams are available. Here we report results from experiments performed at the Brookhaven National Laboratory s Alternating Gradient Synchrotron (AGS) and the Heavy Ion Medical Accelerator in Chiba, Japan (HIMAC). Recent efforts have focused on extracting charge-changing and fragment production cross sections from silicon beams at 400, 600, and 1200 MeV/nucleon. Some energy dependence is observed in the fragment production cross sections, and as in other data sets the production of fragments with even charge numbers is enhanced relative to those with odd charge numbers. These data are compared to the NASA-LaRC model NUCFRG2. The charge-changing cross section data are compared to recent calculations using an improved model due to Tripathi, which accurately predicts the observed (slight) energy dependence. An additional set of data will be presented from an analysis of shielding material performance in the 1 GeV/nucleon iron beam at the AGS. A wide variety of candidate materials for spacecraft construction, as well as elemental targets, have been placed in this beam and their effects on transmitted dose and dose equivalent measured. The results support a prediction by J. Wilson et al. that hydrogen-loaded materials give the greatest dose reduction per unit mass.

Interaction of reflected ions with the firehose marginally stable current sheet - Implications for plasma sheet convection

NASA Technical Reports Server (NTRS)

Pritchett, P. L.; Coroniti, F. V.

1992-01-01

The firehose marginally stable current sheet, which may model the flow away from the distant reconnection neutral line, assumes that the accelerated particles escape and never return to re-encounter the current region. This assumption fails on the earthward side where the accelerated ions mirror in the geomagnetic dipole field and return to the current sheet at distances up to about 30 R(E) down the tail. Two-dimensional particle simulations are used to demonstrate that the reflected ions drive a 'shock-like' structure in which the incoming flow is decelerated and the Bz field is highly compressed. These effects are similar to those produced by adiabatic choking of steady convection. Possible implications of this interaction for the dynamics of the tail are considered.

Physical Investigations of Small Particles: (I) Aerosol Particle Charging and Flux Enhancement and (II) Whispering Gallery Mode Sensing

NASA Astrophysics Data System (ADS)

Lopez-Yglesias, Xerxes

Part I: Particles are a key feature of planetary atmospheres. On Earth they represent the greatest source of uncertainty in the global energy budget. This uncertainty can be addressed by making more measurement, by improving the theoretical analysis of measurements, and by better modeling basic particle nucleation and initial particle growth within an atmosphere. This work will focus on the latter two methods of improvement. Uncertainty in measurements is largely due to particle charging. Accurate descriptions of particle charging are challenging because one deals with particles in a gas as opposed to a vacuum, so different length scales come into play. Previous studies have considered the effects of transition between the continuum and kinetic regime and the effects of two and three body interactions within the kinetic regime. These studies, however, use questionable assumptions about the charging process which resulted in skewed observations, and bias in the proposed dynamics of aerosol particles. These assumptions affect both the ions and particles in the system. Ions are assumed to be point monopoles that have a single characteristic speed rather than follow a distribution. Particles are assumed to be perfect conductors that have up to five elementary charges on them. The effects of three body interaction, ion-molecule-particle, are also overestimated. By revising this theory so that the basic physical attributes of both ions and particles and their interactions are better represented, we are able to make more accurate predictions of particle charging in both the kinetic and continuum regimes. The same revised theory that was used above to model ion charging can also be applied to the flux of neutral vapor phase molecules to a particle or initial cluster. Using these results we can model the vapor flux to a neutral or charged particle due to diffusion and electromagnetic interactions. In many classical theories currently applied to these models, the finite size of the molecule and the electromagnetic interaction between the molecule and particle, especially for the neutral particle case, are completely ignored, or, as is often the case for a permanent dipole vapor species, strongly underestimated. Comparing our model to these classical models we determine an "enhancement factor" to characterize how important the addition of these physical parameters and processes is to the understanding of particle nucleation and growth. Part II: Whispering gallery mode (WGM) optical biosensors are capable of extraordinarily sensitive specific and non-specific detection of species suspended in a gas or fluid. Recent experimental results suggest that these devices may attain single-molecule sensitivity to protein solutions in the form of stepwise shifts in their resonance wavelength, lambdaR, but present sensor models predict much smaller steps than were reported. This study examines the physical interaction between a WGM sensor and a molecule adsorbed to its surface, exploring assumptions made in previous efforts to model WGM sensor behavior, and describing computational schemes that model the experiments for which single protein sensitivity was reported. The resulting model is used to simulate sensor performance, within constraints imposed by the limited material property data. On this basis, we conclude that nonlinear optical effects would be needed to attain the reported sensitivity, and that, in the experiments for which extreme sensitivity was reported, a bound protein experiences optical energy fluxes too high for such effects to be ignored.

Energetic ion leakage from foreshock transient cores

NASA Astrophysics Data System (ADS)

Liu, Terry Z.; Angelopoulos, Vassilis; Hietala, Heli

2017-07-01

Earth's foreshock is filled with backstreaming particles that can interact with the ambient solar wind and its discontinuities to form foreshock transients. Many foreshock transients have a core with low dynamic pressure that can significantly perturb the bow shock and the magnetosphere-ionosphere system. Foreshock transients have also been recently recognized as sites of particle acceleration, which may be important for seeding the parent shock with energetic particles. A relevant step of this seeding would be energetic ion leakage into the surrounding foreshock environment. On the other hand, such leakage would also suppress the energetic particle flux contrast across foreshock transients' boundaries masking their perceived contribution to ion energization. To further examine this hypothesis of ion leakage, we report on multipoint case studies of three foreshock transient events selected from a large database. The cases were selected to exemplify, in increasing complexity, the nature and consequences of energetic ion leakage. Ion energy dispersion, observed upstream and/or downstream of the foreshock transients, is explained with a simple, ballistic model of ions leaking from the foreshock transients. Larger energies are required for leaked ions to reach the spacecraft as the distance between the transient and spacecraft increases. Our model, which explains well the observed ion energy dispersion and velocity distributions, can also be used to reveal the shape of the foreshock transients in three dimensions. Our results suggest that ion leakage from foreshock transient cores needs to be accounted for both in statistical studies and in global models of ion acceleration under quasi-parallel foreshock conditions.

Ion-ion dynamic structure factor of warm dense mixtures

DOE PAGES

Gill, N. M.; Heinonen, R. A.; Starrett, C. E.; ...

2015-06-25

In this study, the ion-ion dynamic structure factor of warm dense matter is determined using the recently developed pseudoatom molecular dynamics method [Starrett et al., Phys. Rev. E 91, 013104 (2015)]. The method uses density functional theory to determine ion-ion pair interaction potentials that have no free parameters. These potentials are used in classical molecular dynamics simulations. This constitutes a computationally efficient and realistic model of dense plasmas. Comparison with recently published simulations of the ion-ion dynamic structure factor and sound speed of warm dense aluminum finds good to reasonable agreement. Using this method, we make predictions of the ion-ionmore » dynamical structure factor and sound speed of a warm dense mixture—equimolar carbon-hydrogen. This material is commonly used as an ablator in inertial confinement fusion capsules, and our results are amenable to direct experimental measurement.« less

Interactions of atrazine with transition metal ions in aqueous media: experimental and computational approach.

PubMed

Kumar, Vijay; Kumar, Virender; Upadhyay, Niraj; Sharma, Sitansh

2015-10-01

Transition metal ions have their own significances and utility. Externally applied pesticides may alter the bioavailability of these metal ions to plants through the coordinating ability of these pesticides with metal ions. In current study a series of metal complexes containing atrazine (Atr) group(s) attached to metal(II) (M) frame, with the formula; [M(Atr) n .xH 2 O.yCl] (where M = Mn, Fe, Co, Ni, Cu or Zn; n = 1 or 2; x = 1-4; y = 1-2), have been synthesized for the first time to check the interactions of atrazine with transition metal ions. More importantly, all the complexes were synthesized at neutral pH in aqueous medium. The major differences among the FTIR spectra were observed between 3,700-2,800 and 1,800-1,350 cm -1 . On the basis of FTIR, CHN and computational study, it was observed that Mn, Ni and Cu formed complexes in 1:2 and Fe, Co and Zn in 1:1. The obtained results were supported by 3D molecular modeling using GAMESS computations as a package of ChemBio3D Ultra14 program. The FTIR spectral analysis and 3D molecular modeling suggests that the Atr can show coordination through the nitrogen (in between two side chains) of ring as well as nitrogen (non steric amine) of side chain with different metal ions.

Exact mapping of the 2+1 Dirac oscillator onto the Jaynes-Cummings model: Ion-trap experimental proposal

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

Bermudez, A.; Martin-Delgado, M. A.; Solano, E.

2007-10-15

We study the dynamics of the 2+1 Dirac oscillator exactly and find spin oscillations due to a Zitterbewegung of purely relativistic origin. We find an exact mapping of this quantum-relativistic system onto a Jaynes-Cummings model, describing the interaction of a two-level atom with a quantized single-mode field. This equivalence allows us to map a series of quantum optical phenomena onto the relativistic oscillator and vice versa. We make a realistic experimental proposal, in reach with current technology, for studying the equivalence of both models using a single trapped ion.

Applications of the trilinear Hamiltonian with three trapped ions

NASA Astrophysics Data System (ADS)

Hablutzel Marrero, Roland Esteban; Ding, Shiqian; Maslennikov, Gleb; Gan, Jaren; Nimmrichter, Stefan; Roulet, Alexandre; Dai, Jibo; Scarani, Valerio; Matsukevich, Dzmitry

2017-04-01

The trilinear Hamiltonian a† bc + ab†c† , which describes a nonlinear interaction between harmonic oscillators, can be implemented to study different phenomena ranging from simple quantum models to quantum thermodynamics. We engineer this coupling between three modes of motion of three trapped 171Yb+ ions, where the interaction arises naturally from their mutual (anharmonic) Coulomb repulsion. By tuning our trapping parameters we are able to turn on / off resonant exchange of energy between the modes on demand. We present applications of this Hamiltonian for simulations of the parametric down conversion process in the regime of depleted pump, a simple model of Hawking radiation, and the Tavis-Cummings model. We also discuss the implementation of the quantum absorption refrigerator in such system and experimentally study effects of quantum coherence on its performance. This research is supported by the National Research Foundation, Prime Minister's Office, Singapore and the Ministry of Education, Singapore under the Research Centres of Excellence programme.

Modeling viscosity and diffusion of plasma mixtures across coupling regimes

NASA Astrophysics Data System (ADS)

Arnault, Philippe

2014-10-01

Viscosity and diffusion of plasma for pure elements and multicomponent mixtures are modeled from the high-temperature low-density weakly coupled regime to the low-temperature high-density strongly coupled regime. Thanks to an atom in jellium modeling, the effect of electron screening on the ion-ion interaction is incorporated through a self-consistent definition of the ionization. This defines an effective One Component Plasma, or an effective Binary Ionic Mixture, that is representative of the strength of the interaction. For the viscosity and the interdiffusion of mixtures, approximate kinetic expressions are supplemented by mixing laws applied to the excess viscosity and self-diffusion of pure elements. The comparisons with classical and quantum molecular dynamics results reveal deviations in the range 20--40% on average with almost no predictions further than a factor of 2 over many decades of variation. Applications in the inertial confinement fusion context could help in predicting the growth of hydrodynamic instabilities.

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.

The formation of magnetic silicide Fe3Si clusters during ion implantation

NASA Astrophysics Data System (ADS)

Balakirev, N.; Zhikharev, V.; Gumarov, G.

2014-05-01

A simple two-dimensional model of the formation of magnetic silicide Fe3Si clusters during high-dose Fe ion implantation into silicon has been proposed and the cluster growth process has been computer simulated. The model takes into account the interaction between the cluster magnetization and magnetic moments of Fe atoms random walking in the implanted layer. If the clusters are formed in the presence of the external magnetic field parallel to the implanted layer, the model predicts the elongation of the growing cluster in the field direction. It has been proposed that the cluster elongation results in the uniaxial magnetic anisotropy in the plane of the implanted layer, which is observed in iron silicide films ion-beam synthesized in the external magnetic field.

Low-Energy Collisions of Protonated Enantiopure Amino Acids with Chiral Target Gases

NASA Astrophysics Data System (ADS)

Kulyk, K.; Rebrov, O.; Ryding, M.; Thomas, R. D.; Uggerud, E.; Larsson, M.

2017-12-01

Here we report on the gas-phase interactions between protonated enantiopure amino acids ( l- and d-enantiomers of Met, Phe, and Trp) and chiral target gases [( R)- and ( S)-2-butanol, and ( S)-1-phenylethanol] in 0.1-10.0 eV low-energy collisions. Two major processes are seen to occur over this collision energy regime, collision-induced dissociation and ion-molecule complex formation. Both processes were found to be independent of the stereo-chemical composition of the interacting ions and targets. These data shed light on the currently debated mechanisms of gas-phase chiral selectivity by demonstrating the inapplicability of the three-point model to these interactions, at least under single collision conditions. [Figure not available: see fulltext.

Superionic state in double-layer capacitors with nanoporous electrodes.

PubMed

Kondrat, S; Kornyshev, A

2011-01-19

In recent experiments (Chmiola et al 2006 Science 313 1760; Largeot et al 2008 J. Am. Chem. Soc. 130 2730) an anomalous increase of the capacitance with a decrease of the pore size of a carbon-based porous electric double-layer capacitor has been observed. We explain this effect by image forces which exponentially screen out the electrostatic interactions of ions in the interior of a pore. Packing of ions of the same sign becomes easier and is mainly limited by steric interactions. We call this state 'superionic' and suggest a simple model to describe it. The model reveals the possibility of a voltage-induced first order transition between a cation(anion)-deficient phase and a cation(anion)-rich phase which manifests itself in a jump of capacitance as a function of voltage.

Single ICMEs and Complex Transient Structures in the Solar Wind in 2010 - 2011

NASA Astrophysics Data System (ADS)

Rodkin, D.; Slemzin, V.; Zhukov, A. N.; Goryaev, F.; Shugay, Y.; Veselovsky, I.

2018-05-01

We analyze the statistics, solar sources, and properties of interplanetary coronal mass ejections (ICMEs) in the solar wind. The total number of coronal mass ejections (CMEs) registered in the Coordinated Data Analysis Workshops catalog (CDAW) during the first eight years of Cycle 24 was 61% larger than in the same period of Cycle 23, but the number of X-ray flares registered by the Geostationary Operational Environmental Satellite (GOES) was 20 % smaller because the solar activity was lower. The total number of ICMEs in the given period of Cycle 24 in the Richardson and Cane list was 29% smaller than in Cycle 23, which may be explained by a noticeable number of non-classified ICME-like events in the beginning of Cycle 24. For the period January 2010 - August 2011, we identify solar sources of the ICMEs that are included in the Richardson and Cane list. The solar sources of ICME were determined from coronagraph observations of the Earth-directed CMEs, supplemented by modeling of their propagation in the heliosphere using kinematic models (a ballistic and drag-based model). A detailed analysis of the ICME solar sources in the period under study showed that in 11 cases out of 23 (48%), the observed ICME could be associated with two or more sources. For multiple-source events, the resulting solar wind disturbances can be described as complex (merged) structures that are caused by stream interactions, with properties depending on the type of the participating streams. As a reliable marker to identify interacting streams and their sources, we used the plasma ion composition because it freezes in the low corona and remains unchanged in the heliosphere. According to the ion composition signatures, we classify these cases into three types: complex ejecta originating from weak and strong CME-CME interactions, as well as merged interaction regions (MIRs) originating from the CME high-speed stream (HSS) interactions. We describe temporal profiles of the ion composition for the single-source and multi-source solar wind structures and compared them with the ICME signatures determined from the kinematic and magnetic field parameters of the solar wind. In single-source events, the ion charge state, as a rule, has a one-peak enhancement with an average duration of about one day, which is similar to the mean ICME duration of 1.12 days derived from the Richardson and Cane list. In the multi-source events, the total profile of the ion charge state consists of a sequence of enhancements that is associated with the interaction between the participating streams. On average, the total duration of the complex structures that appear as a result of the CME-CME and CME-HSS interactions as determined from their ion composition is 2.4 days, which is more than twice longer than that of the single-source events.

Dielectric Self-Energy in Poisson-Boltzmann and Poisson-Nernst-Planck Models of Ion Channels

PubMed Central

Corry, Ben; Kuyucak, Serdar; Chung, Shin-Ho

2003-01-01

We demonstrated previously that the two continuum theories widely used in modeling biological ion channels give unreliable results when the radius of the conduit is less than two Debye lengths. The reason for this failure is the neglect of surface charges on the protein wall induced by permeating ions. Here we attempt to improve the accuracy of the Poisson-Boltzmann and Poisson-Nernst-Planck theories, when applied to channel-like environments, by including a specific dielectric self-energy term to overcome spurious shielding effects inherent in these theories. By comparing results with Brownian dynamics simulations, we show that the inclusion of an additional term in the equations yields significant qualitative improvements. The modified theories perform well in very wide and very narrow channels, but are less successful at intermediate sizes. The situation is worse in multi-ion channels because of the inability of the continuum theories to handle the ion-to-ion interactions correctly. Thus, further work is required if these continuum theories are to be reliably salvaged for quantitative studies of biological ion channels in all situations. PMID:12770869

Electrostatic model for protein adsorption in ion-exchange chromatography and application to monoclonal antibodies, lysozyme and chymotrypsinogen A.

PubMed

Guélat, Bertrand; Ströhlein, Guido; Lattuada, Marco; Morbidelli, Massimo

2010-08-27

A model for the adsorption equilibrium of proteins in ion-exchange chromatography explicitly accounting for the effect of pH and salt concentration in the limit of highly diluted systems was developed. It is based on the use of DLVO theory to estimate the electrostatic interactions between the charged surface of the ion-exchanger and the proteins. The corresponding charge distributions were evaluated as a function of pH and salt concentration using a molecular approach. The model was verified for the adsorption equilibrium of lysozyme, chymotrypsinogen A and four industrial monoclonal antibodies on two strong cation-exchangers. The adsorption equilibrium constants of these proteins were determined experimentally at various pH values and salt concentrations and the model was fitted with a good agreement using three adjustable parameters for each protein in the whole range of experimental conditions. Despite the simplifications of the model regarding the geometry of the protein-ion-exchanger system, the physical meaning of the parameters was retained. 2010 Elsevier B.V. All rights reserved.

An ion quencher operated lamp for multiplexed fluorescent bioassays.

PubMed

Qing, Taiping; Sun, Huanhuan; He, Xiaoxiao; Huang, Xiaoqin; He, Dinggeng; Bu, Hongchang; Qiao, Zhenzhen; Wang, Kemin

2018-02-01

A novel and adjustable lamp based on competitive interaction among dsDNA-SYBR Green I (SGI), ion quencher, and analyte was designed for bioanalysis. The "filament" and switch of the lamp could be customized by employing different dsDNA and ion quencher. The poly(AT/TA) dsDNA was successfully screened as the most effective filament of the lamp. Two common ions, Hg 2+ and Fe 3+ , were selected as the model switch, and the corresponding ligand molecules cysteine (Cys) and pyrophosphate ions (PPi) were selected as the targets. When the fluorescence-quenched dsDNA/SGI-ion complex was introduced into a target-containing system, ions could be bound by competitive molecules and separate from the complex, thereby lighting the lamp. However, no light was observed if the biomolecule could not snatch the metal ions from the complex. Under the optimal conditions, sensitive and selective detection of Cys and PPi was achieved by the lamp, with practical applications in fetal bovine serum and human urine. This ion quencher regulated lamp for fluorescent bioassays is simple in design, fast in operation, and is more convenient than other methods. Significantly, as many molecules could form stable complexes with metal ions selectively, this ion quencher operated lamp has potential for the detection of a wide spectrum of analytes. Graphical abstract A novel and adjustable lamp on the basis of competitive interaction among dsDNA-SYBR Green I, ions quencher and analyte was designed for bioanalysis. The filament and switch of lamp could be customized by employing different dsDNA and ions quencher.

Mechanism of amido-thiourea catalyzed enantioselective imine hydrocyanation: transition state stabilization via multiple non-covalent interactions.

PubMed

Zuend, Stephan J; Jacobsen, Eric N

2009-10-28

An experimental and computational investigation of amido-thiourea promoted imine hydrocyanation has revealed a new and unexpected mechanism of catalysis. Rather than direct activation of the imine by the thiourea, as had been proposed previously in related systems, the data are consistent with a mechanism involving catalyst-promoted proton transfer from hydrogen isocyanide to imine to generate diastereomeric iminium/cyanide ion pairs that are bound to catalyst through multiple noncovalent interactions; these ion pairs collapse to form the enantiomeric alpha-aminonitrile products. This mechanistic proposal is supported by the observation of a statistically significant correlation between experimental and calculated enantioselectivities induced by eight different catalysts (P < 0.01). The computed models reveal a basis for enantioselectivity that involves multiple stabilizing and destabilizing interactions between substrate and catalyst, including thiourea-cyanide and amide-iminium interactions.

Phase diagram of the quantum Ising model with long-range interactions on an infinite-cylinder triangular lattice

NASA Astrophysics Data System (ADS)

Saadatmand, S. N.; Bartlett, S. D.; McCulloch, I. P.

2018-04-01

Obtaining quantitative ground-state behavior for geometrically-frustrated quantum magnets with long-range interactions is challenging for numerical methods. Here, we demonstrate that the ground states of these systems on two-dimensional lattices can be efficiently obtained using state-of-the-art translation-invariant variants of matrix product states and density-matrix renormalization-group algorithms. We use these methods to calculate the fully-quantitative ground-state phase diagram of the long-range interacting triangular Ising model with a transverse field on six-leg infinite-length cylinders and scrutinize the properties of the detected phases. We compare these results with those of the corresponding nearest neighbor model. Our results suggest that, for such long-range Hamiltonians, the long-range quantum fluctuations always lead to long-range correlations, where correlators exhibit power-law decays instead of the conventional exponential drops observed for short-range correlated gapped phases. Our results are relevant for comparisons with recent ion-trap quantum simulator experiments that demonstrate highly-controllable long-range spin couplings for several hundred ions.

Magnetic and magnetocaloric properties in Gd1-yPryNi2 compounds

NASA Astrophysics Data System (ADS)

Alho, B. P.; Lopes, P. H. O.; Ribeiro, P. O.; Alvarenga, T. S. T.; Nóbrega, E. P.; de Sousa, V. S. R.; Carvalho, A. M. G.; Caldas, A.; Tedesco, J. C. G.; Coelho, A. A.; de Oliveira, N. A.; von Ranke, P. J.

2018-03-01

In this work, we report the magnetic and magnetocaloric properties of the Gd1-yPryNi2 compounds from both experimental and theoretical points of view. It is worth noting that this series shows a variety of magnetic arrangements depending on the Pr concentration, including paramagnetism, ferrimagnetism and ferromagnetism. Our experimental work consists of the systematic analysis of the magnetic properties of the compounds with y = 0.0, 0.25, 0.5, 0.75 and 1.0, which includes temperature and magnetic field dependence of the magnetization, heat capacity and isothermal entropy change obtained by isothermal magnetization curves. Also, we developed a model Hamiltonian, which takes into account the exchange interactions among Gd-Gd, Gd-Pr and Pr-Pr ions, the Zeeman interaction for both ions and the crystalline electrical field interaction for the Pr ions. We systematically investigated the magnetic properties of the series and obtained a good agreement when compared with our experimental data.

Baryons and baryon resonances in nuclear matter

NASA Astrophysics Data System (ADS)

Lenske, Horst; Dhar, Madhumita; Gaitanos, Theodoros; Cao, Xu

2018-01-01

Theoretical approaches to the production of hyperons and baryon resonances in elementary hadronic reactions and heavy ion collisions are reviewed. The focus is on the production and interactions of baryons in the lowest SU(3) flavor octet and states from the next higher SU(3) flavor decuplet. Approaches using the SU(3) formalism for interactions of mesons and baryons and effective field theory for hyperons are discussed. An overview of application to free space and in-medium baryon-baryon interactions is given and the relation to a density functional theory is indicated. The intimate connection between baryon resonances and strangeness production is shown first for reactions on the nucleon. Pion-induced hypernuclear reactions are shown to proceed essentially through the excitation of intermediate nucleon resonances. Transport theory in conjunction with a statistical fragmentation model is an appropriate description of hypernuclear production in antiproton and heavy ion induced fragmentation reactions. The excitation of subnuclear degrees of freedom in peripheral heavy ion collisions at relativistic energies is reviewed. The status of in-medium resonance physics is discussed.

An orientation sensitive approach in biomolecule interaction quantitative structure-activity relationship modeling and its application in ion-exchange chromatography.

PubMed

Kittelmann, Jörg; Lang, Katharina M H; Ottens, Marcel; Hubbuch, Jürgen

2017-01-27

Quantitative structure-activity relationship (QSAR) modeling for prediction of biomolecule parameters has become an established technique in chromatographic purification process design. Unfortunately available descriptor sets fail to describe the orientation of biomolecules and the effects of ionic strength in the mobile phase on the interaction with the stationary phase. The literature describes several special descriptors used for chromatographic retention modeling, all of these do not describe the screening of electrostatic potential by the mobile phase in use. In this work we introduce two new approaches of descriptor calculations, namely surface patches and plane projection, which capture an oriented binding to charged surfaces and steric hindrance of the interaction with chromatographic ligands with regard to electrostatic potential screening by mobile phase ions. We present the use of the developed descriptor sets for predictive modeling of Langmuir isotherms for proteins at different pH values between pH 5 and 10 and varying ionic strength in the range of 10-100mM. The resulting model has a high correlation of calculated descriptors and experimental results, with a coefficient of determination of 0.82 and a predictive coefficient of determination of 0.92 for unknown molecular structures and conditions. The agreement of calculated molecular interaction orientations with both, experimental results as well as molecular dynamic simulations from literature is shown. The developed descriptors provide the means for improved QSAR models of chromatographic processes, as they reflect the complex interactions of biomolecules with chromatographic phases. Copyright © 2016 Elsevier B.V. All rights reserved.

Diamond formation due to a pH drop during fluid–rock interactions

DOE PAGES

Sverjensky, Dimitri A.; Huang, Fang

2015-11-03

Diamond formation has typically been attributed to redox reactions during precipitation from fluids or magmas. Either the oxidation of methane or the reduction of carbon dioxide has been suggested, based on simplistic models of deep fluids consisting of mixtures of dissolved neutral gas molecules without consideration of aqueous ions. The role of pH changes associated with water–silicate rock interactions during diamond formation is unknown. Here we show that diamonds could form due to a drop in pH during water–rock interactions. We use a recent theoretical model of deep fluids that includes ions, to show that fluid can react irreversibly withmore » eclogite at 900 °C and 5.0 GPa, generating diamond and secondary minerals due to a decrease in pH at almost constant oxygen fugacity. Overall, our results constitute a new quantitative theory of diamond formation as a consequence of the reaction of deep fluids with the rock types that they encounter during migration. Diamond can form in the deep Earth during water–rock interactions without changes in oxidation state.« less

Diamond formation due to a pH drop during fluid–rock interactions

PubMed Central

Sverjensky, Dimitri A.; Huang, Fang

2015-01-01

Diamond formation has typically been attributed to redox reactions during precipitation from fluids or magmas. Either the oxidation of methane or the reduction of carbon dioxide has been suggested, based on simplistic models of deep fluids consisting of mixtures of dissolved neutral gas molecules without consideration of aqueous ions. The role of pH changes associated with water–silicate rock interactions during diamond formation is unknown. Here we show that diamonds could form due to a drop in pH during water–rock interactions. We use a recent theoretical model of deep fluids that includes ions, to show that fluid can react irreversibly with eclogite at 900 °C and 5.0 GPa, generating diamond and secondary minerals due to a decrease in pH at almost constant oxygen fugacity. Overall, our results constitute a new quantitative theory of diamond formation as a consequence of the reaction of deep fluids with the rock types that they encounter during migration. Diamond can form in the deep Earth during water–rock interactions without changes in oxidation state. PMID:26529259

Electric Double-Layer Structure in Primitive Model Electrolytes. Comparing Molecular Dynamics with Local-Density Approximations

DOE PAGES

Giera, Brian; Lawrence Livermore National Lab.; Henson, Neil; ...

2015-02-27

We evaluate the accuracy of local-density approximations (LDAs) using explicit molecular dynamics simulations of binary electrolytes comprised of equisized ions in an implicit solvent. The Bikerman LDA, which considers ions to occupy a lattice, poorly captures excluded volume interactions between primitive model ions. Instead, LDAs based on the Carnahan–Starling (CS) hard-sphere equation of state capture simulated values of ideal and excess chemical potential profiles extremely well, as is the relationship between surface charge density and electrostatic potential. Excellent agreement between the EDL capacitances predicted by CS-LDAs and computed in molecular simulations is found even in systems where ion correlations drivemore » strong density and free charge oscillations within the EDL, despite the inability of LDAs to capture the oscillations in the detailed EDL profiles.« less

Enhanced ion acceleration in transition from opaque to transparent plasmas

DOE PAGES

Mishra, R.; Fiuza, F.; Glenzer, S.

2018-04-20

Using particle-in-cell simulations, we investigate ion acceleration in the interaction of high intensity lasers with plasmas which transition from opaque to transparent during the interaction process. We show that the highest ion energies are achieved when the laser traverses the target around the peak intensity and re-heats the electron population responsible for the plasma expansion, enhancing the corresponding sheath electric field. This process can lead to an increase of up to 2x in ion energy when compared with the standard Target Normal Sheath Acceleration in opaque targets under the same laser conditions. A theoretical model is developed to predict themore » optimal target areal density as a function of laser intensity and pulse duration. A systematic parametric scan for a wide range of target densities and thicknesses is performed in 1D, 2D and 3D and shown consistent with the theory and with recent experimental results. Thus, these results open the way for a better optimization of the ion energy in future laser–solid experiments.« less

Enhanced ion acceleration in transition from opaque to transparent plasmas

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

Mishra, R.; Fiuza, F.; Glenzer, S.

Using particle-in-cell simulations, we investigate ion acceleration in the interaction of high intensity lasers with plasmas which transition from opaque to transparent during the interaction process. We show that the highest ion energies are achieved when the laser traverses the target around the peak intensity and re-heats the electron population responsible for the plasma expansion, enhancing the corresponding sheath electric field. This process can lead to an increase of up to 2x in ion energy when compared with the standard Target Normal Sheath Acceleration in opaque targets under the same laser conditions. A theoretical model is developed to predict themore » optimal target areal density as a function of laser intensity and pulse duration. A systematic parametric scan for a wide range of target densities and thicknesses is performed in 1D, 2D and 3D and shown consistent with the theory and with recent experimental results. Thus, these results open the way for a better optimization of the ion energy in future laser–solid experiments.« less

Magnetic properties of manganites doped with gallium, iron, and chromium ions

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

Troyanchuk, I. O., E-mail: troyan@physics.by; Bushinsky, M. V.; Tereshko, N. V.

The magnetization and the crystal structure of the La{sub 0.7}Sr{sub 0.3}Mn{sub 1−x}M{sub x}O{sub 3} (M = Ga, Fe, Cr; x ≤ 0.3) systems are studied. The substitution of gallium and chromium is shown to cause phase separation into antiferromagnetic and ferromagnetic phases, whereas the substitution of iron for manganese stabilizes a spinglass state. The ferromagnetic phase in the chromium-substituted compositions is much more stable than that in the case of substitution by iron ions or diamagnetic gallium ions. The magnetic properties are explained in terms of the model of superexchange interactions and the localization of most e{sub g} electrons ofmore » manganese. The stabilization of ferromagnetism in the chromium-substituted compositions can be caused by the fact that the positive and negative contributions to the superexchange interaction between Mn{sup 3+} and Cr{sup 3+} ions are close to each other but the antiferromagnetic part of the exchange is predominant. Moreover, some chromium ions are in the tetravalent state, which maintains the optimum doping conditions.« less

Dependence of the rate of LiF ion pairing on the description of molecular interaction

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

Pluharova, Eva; Baer, Marcel D.; Schenter, Gregory K.

2016-03-03

We present an analysis of the dynamics of ion-pairing of Lithium Fluoride (LiF) in aqueous solvent using both detailed molecular simulation as well as reduced models within a Gener- alized Langevin Equation (GLE) framework. We explored the sensitivity of the ion-pairing phenomena to the details of descriptions of molecular interaction, comparing two empirical potentials to explicit quantum based density functional theory. We find quantitative differences in the potentials of mean force for ion-pairing as well as time dependent frictions that lead to variations in the rate constant and reactive flux correlation functions. These details reflect differences in solvent response tomore » ion-pairing between different representations of molecular interaction and influence anharmonicity of the dynamic response. We find that the short time anharmonic response is recovered with a GLE parameterization. Recovery of the details of long time response may require extensions to the reduced model. We show that the utility of using a reduced model leads to a straight forward application of variational transition state the- ory concepts to the condensed phase system. The significance of this is reflected in the analysis of committor distributions and the variation of planar hypersurfaces, leading to an improved understanding of factors that determine the rate of LiF ion-pairing. CJM and GKS are supported by the U.S. Department of Energy‘s (DOE) Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest Na- tional Laboratory (PNNL) is operated for the Department of Energy by Battelle. MDB is grateful for the support of Laboratory Directed Research and Development funding under the auspices of PNNL’s Laboratory Initiative Materials Synthesis and Simulation across Scales (MS3). Additional computing resources were generously allocated by PNNL’s Institutional Computing program. EP acknowledges support from PNNL’s Alternate Sponsored Fellowship program and IMPRS Dres- den.Support to P.J. from the Czech Science Foundation (grant P208/12/G016) and the Academy of Sciences (Praemium Academie award) is gratefully acknowledged.« less

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.

Trivalent Ions under Charged Langmuir Monolayers: Nanoscale Mechanisms for Charge Inversion and Liquid-Liquid Extraction

NASA Astrophysics Data System (ADS)

Miller, Mitchell

Ions dissolved in solution are known to interact in remarkable ways with charged Langmuir monolayers. The organic monolayer can be used as a molecular template for ordered nucleation of inorganic crystals (biomineralization) and functional nanoparticles. However, the clear majority of experiments demonstrating these behaviors have been performed with divalent ions. Trivalent ions are present in several important processes that are unique from previously studied divalent systems. We will demonstrate that trivalent ions under floating monolayers can model two important systems: charge inversion and liquid-liquid solvent extraction. Using in situ synchrotron x-ray scattering and emission methods, we can make direct, nanoscale observations of the interactions between ion and monolayer. Charge inversion is a fascinating phenomenon in which small ions of an opposite charge to some large object (colloidal particle, DNA molecule, etc.) will attach to and reverse the object's charge, rather than simply neutralizing it. There are many experimental systems demonstrating this behavior and an enormous body of theoretical work to explain it. Two classes of explanation exist for how charge inversion may occur, "chemical" and "physical" mechanism. Using grazing incidence diffraction (GID), we have found that ions can form an ordered lattice which is incommensurate to a floating, charged monolayer. Because the ions are incommensurate, they cannot be specifically attached to molecules in the monolayer and must be, therefore, held in place by "physical" means. Solvent extraction can be an extremely complex procedure, so our approach to studying it is to simplify the system into a basic model. Ordinarily, two immiscible liquids--an aqueous phase containing some desired species and other impurities and an organic phase, which sometimes contains extractant molecules that improve efficiency--are mixed together and allowed to separate again. While the liquids are being mixed together, the target species from the aqueous phase is pulled across the interface into the organic phase. The mechanism by which the transfer occurs is very poorly understood and very difficult to study directly since it is a very dynamic process and obscured by the bulk of the liquids. Here we propose that the air-water interface is a model of the liquid-liquid interface; in our model, the hydrophobic "organic" phase is the air above the water. This lets us make direct observations of the interactions between ions dissolved in the aqueous phase and the extractant molecules in the organic phase with x-rays, something which would be impossible in an ordinary solvent extraction experiment. We observed a sharp transition in ordering as the atomic weight of the ion dissolved in solution is increased. One would expect a continuous variation, since the size of the ions varies continuously. Second, using x-ray fluorescence, we find that heavier lanthanides are much more strongly attracted to the monolayer than light ones. The unexpected nature of our results emphasizes the need for bottom-up approaches to understanding these systems rather than the top-down method used for the last century. In addition, our results demonstrate that it is, indeed, possible to overcome the experimental difficulties and make the types of measurements necessary for this approach.

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

Haskey, S. R.; Grierson, B. A.; Stagner, L.

Recent completion of the thirty two channel main-ion (deuterium) charge exchange recombination spectroscopy (CER) diagnostic on DIII-D enables detailed comparisons between impurity and main-ion temperature, density, and toroidal rotation. Sixteen sightlines cover the core of the plasma and another sixteen are densely packed towards the edge, providing high resolution measurements of the pedestal and steep gradient edge region of H-mode plasmas. The complexities of the D α spectrum require fitting with a comprehensive model, as well as using iterative collisional radiative modeling to determine the underlying thermal deuterium ion properties. Large differences in the structure and magnitude of impurity (Cmore » 6+) and main-ion (D +) toroidal rotation profiles are seen in the H-mode pedestal. Additionally the D + temperature can be half the value of the C 6+ temperature at the separatrix and shows more of a pedestal structure. Typically only the impurity properties are measured and the main-ion properties are either assumed to be the same, or inferred using neoclassical models, which require validation in the steep gradient region. Furthermore, these measured differences have implications for transport model validation, intrinsic rotation studies, pedestal stability, and the boundary conditions for scrape off layer and plasma material interactions studies.« less

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.

Proton and metal ion binding to natural organic polyelectrolytes-II. Preliminary investigation with a peat and a humic acid

USGS Publications Warehouse

Marinsky, J.A.; Reddy, M.M.

1984-01-01

We summarize here experimental studies of proton and metal ion binding to a peat and a humic acid. Data analysis is based on a unified physico-chemical model for reaction of simple ions with polyelectrolytes employing a modified Henderson-Hasselbalch equation. Peat exhibited an apparent intrinsic acid dissociation constant of 10-4.05, and an apparent intrinsic metal ion binding constant of: 400 for cadmium ion; 600 for zinc ion; 4000 for copper ion; 20000 for lead ion. A humic acid was found to have an apparent intrinsic proton binding constant of 10-2.6. Copper ion binding to this humic acid sample occurred at two types of sites. The first site exhibited reaction characteristics which were independent of solution pH and required the interaction of two ligands on the humic acid matrix to simultaneously complex with each copper ion. The second complex species is assumed to be a simple monodentate copper ion-carboxylate species with a stability constant of 18. ?? 1984.

Re-examining the tetraphenyl-arsonium/tetraphenyl-borate (TATB) hypothesis for single-ion solvation free energies

NASA Astrophysics Data System (ADS)

Pollard, Travis P.; Beck, Thomas L.

2018-06-01

Attempts to establish an absolute single-ion hydration free energy scale have followed multiple strategies. Two central themes consist of (1) employing bulk pair thermodynamic data and an underlying interfacial-potential-free model to partition the hydration free energy into individual contributions [Marcus, Latimer, and tetraphenyl-arsonium/tetraphenyl-borate (TATB) methods] or (2) utilizing bulk thermodynamic and cluster data to estimate the free energy to insert a proton into water, including in principle an interfacial potential contribution [the cluster pair approximation (CPA)]. While the results for the hydration free energy of the proton agree remarkably well between the three approaches in the first category, the value differs from the CPA result by roughly +10 kcal/mol, implying a value for the effective electrochemical surface potential of water of -0.4 V. This paper provides a computational re-analysis of the TATB method for single-ion free energies using quasichemical theory. A previous study indicated a significant discrepancy between the free energies of hydration for the TA cation and the TB anion. We show that the main contribution to this large computed difference is an electrostatic artifact arising from modeling interactions in periodic boundaries. No attempt is made here to develop more accurate models for the local ion/solvent interactions that may lead to further small free energy differences between the TA and TB ions, but the results clarify the primary importance of interfacial potential effects for analysis of the various free energy scales. Results are also presented, related to the TATB assumption in the organic solvents dimethyl sulfoxide and 1,2-dichloroethane.

Ion-exchange selectivity of diclofenac, ibuprofen, ketoprofen, and naproxen in ureolyzed human urine.

PubMed

Landry, Kelly A; Sun, Peizhe; Huang, Ching-Hua; Boyer, Treavor H

2015-01-01

This research advances the knowledge of ion-exchange of four non-steroidal anti-inflammatory drugs (NSAIDs) - diclofenac (DCF), ibuprofen (IBP), ketoprofen (KTP), and naproxen (NPX) - and one analgesic drug-paracetamol (PCM) - by strong-base anion exchange resin (AER) in synthetic ureolyzed urine. Freundlich, Langmuir, Dubinin-Astakhov, and Dubinin-Radushkevich isotherm models were fit to experimental equilibrium data using nonlinear least squares method. Favorable ion-exchange was observed for DCF, KTP, and NPX, whereas unfavorable ion-exchange was observed for IBP and PCM. The ion-exchange selectivity of the AER was enhanced by van der Waals interactions between the pharmaceutical and AER as well as the hydrophobicity of the pharmaceutical. For instance, the high selectivity of the AER for DCF was due to the combination of Coulombic interactions between quaternary ammonium functional group of resin and carboxylate functional group of DCF, van der Waals interactions between polystyrene resin matrix and benzene rings of DCF, and possibly hydrogen bonding between dimethylethanol amine functional group side chain and carboxylate and amine functional groups of DCF. Based on analysis of covariance, the presence of multiple pharmaceuticals did not have a significant effect on ion-exchange removal when the NSAIDs were combined in solution. The AER reached saturation of the pharmaceuticals in a continuous-flow column at varying bed volumes following a decreasing order of DCF > NPX ≈ KTP > IBP. Complete regeneration of the column was achieved using a 5% (m/m) NaCl, equal-volume water-methanol solution. Results from multiple treatment and regeneration cycles provide insight into the practical application of pharmaceutical ion-exchange in ureolyzed urine using AER.

Simulation of linear and nonlinear Landau damping of lower hybrid waves

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

Qi, Lei; Wang, X. Y.; Lin, Y.

2013-06-15

The linear physics of lower hybrid waves (LHWs) and their nonlinear interaction with particles through Landau damping are studied with the gyrokinetic electron and fully kinetic ion (GeFi) particle simulation model in the electrostatic limit. Unlike most other wave modes, the LHWs can resonantly interact with both electrons and ions, with the former being highly magnetized and latter nearly unmagnetized around the lower hybrid frequency. Direct interactions of LHWs with electrons and/or ions are investigated for cases with various k{sub ∥}/k,T{sub i}/T{sub e}, and wave amplitudes. In the linear electron Landau damping (ELD), the dispersion relation and the linear dampingmore » rate obtained from our simulation agree well with the analytical linear theory. As the wave amplitude increases, the nonlinear Landau effects are present, and a transition from strong decay at smaller amplitudes to weak decay at larger amplitudes is observed. In the nonlinear stage, the LHWs in the long time evolution finally exhibit a steady Bernstein-Greene-Kruskal mode, in which the wave amplitude is saturated above the noise level. While the resonant electrons are trapped in the wave field in the nonlinear ELD, the resonant ions are untrapped in the LHW time scales. The ion Landau damping is thus predominantly in a linear fashion, leading to a wave saturation level significantly lower than that in the ELD. On the long time scales, however, the ions are still weakly trapped. The results show a coupling between the LHW frequency and the ion cyclotron frequency during the long-time LHW evolution.« less

Error analysis and prevention of cosmic ion-induced soft errors in static CMOS RAMs

NASA Astrophysics Data System (ADS)

Diehl, S. E.; Ochoa, A., Jr.; Dressendorfer, P. V.; Koga, P.; Kolasinski, W. A.

1982-12-01

Cosmic ray interactions with memory cells are known to cause temporary, random, bit errors in some designs. The sensitivity of polysilicon gate CMOS static RAM designs to logic upset by impinging ions has been studied using computer simulations and experimental heavy ion bombardment. Results of the simulations are confirmed by experimental upset cross-section data. Analytical models have been extended to determine and evaluate design modifications which reduce memory cell sensitivity to cosmic ions. A simple design modification, the addition of decoupling resistance in the feedback path, is shown to produce static RAMs immune to cosmic ray-induced bit errors.

Investigating the role of ion-pair strategy in regulating nicotine release from patch: Mechanistic insights based on intermolecular interaction and mobility of pressure sensitive adhesive.

PubMed

Li, Qiaoyun; Wan, Xiaocao; Liu, Chao; Fang, Liang

2018-07-01

The aim of this study was to prepare a drug-in-adhesive patch of nicotine (NIC) and use ion-pair strategy to regulate drug delivery rate. Moreover, the mechanism of how ion-pair strategy regulated drug release was elucidated at molecular level. Formulation factors including pressure sensitive adhesives (PSAs), drug loading and counter ions (C 4 , C 6 , C 8 , C 10 , and C 12 ) were screened. In vitro release experiment and in vitro transdermal experiment were conducted to determine the rate-limiting step in drug delivery process. FT-IR and molecular modeling were used to characterize the interaction between drug and PSA. Thermal analysis and rheology study were conducted to investigate the mobility variation of PSA. The optimized patch prepared with NIC-C 8 had the transdermal profile fairly close to that of the commercial product (p > 0.05). The release rate constants (k) of NIC, NIC-C 4 and NIC-C 10 were 21.1, 14.4 and 32.4, respectively. Different release rates of NIC ion-pair complexes were attributed to the dual effect of ion-pair strategy on drug release. On one hand, ion-pair strategy enhanced the interaction between drug and PSA, which inhibited drug release. On the other hand, using ion-pair strategy improved the mobility of PSA, which facilitated drug release. Drug release behavior was determined by combined effect of two aspects above. These conclusions provided a new idea for us to regulate drug release behavior from patch. Copyright © 2018 Elsevier B.V. All rights reserved.

A novel method for assessment of fragmentation and beam-material interactions in helium ion radiotherapy with a miniaturized setup.

PubMed

Gallas, Raya R; Arico, Giulia; Burigo, Lucas N; Gehrke, Tim; Jakůbek, Jan; Granja, Carlos; Tureček, Daniel; Martišíková, Maria

2017-10-01

Radiotherapy with protons and carbon ions enables to deliver dose distributions of high conformation to the target. Treatment with helium ions has been suggested due to their physical and biological advantages. A reliable benchmarking of the employed physics models with experimental data is required for treatment planning. However, experimental data for helium interactions is limited, in part due to the complexity and large size of conventional experimental setups. We present a novel method for the investigation of helium interactions with matter using miniaturized instrumentation based on highly integrated pixel detectors. The versatile setup consisted of a monitoring detector in front of the PMMA phantom of varying thickness and a detector stack for investigation of outgoing particles. The ion type downstream from the phantom was determined by high-resolution pattern recognition analysis of the single particle signals in the pixelated detectors. The fractions of helium and hydrogen ions behind the used targets were determined. As expected for the stable helium nucleus, only a minor decrease of the primary ion fluence along the target depth was found. E.g. the detected fraction of hydrogen ions on axis of a 220MeV/u 4 He beam was below 6% behind 24.5cm of PMMA. Monte-Carlo simulations using Geant4 reproduce the experimental data on helium attenuation and yield of helium fragments qualitatively, but significant deviations were found for some combinations of target thickness and beam energy. The presented method is promising to contribute to the reduction of the uncertainty of treatment planning for helium ion radiotherapy. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Promoting the Adsorption of Metal Ions on Kaolinite by Defect Sites: A Molecular Dynamics Study

PubMed Central

Li, Xiong; Li, Hang; Yang, Gang

2015-01-01

Defect sites exist abundantly in minerals and play a crucial role for a variety of important processes. Here molecular dynamics simulations are used to comprehensively investigate the adsorption behaviors, stabilities and mechanisms of metal ions on defective minerals, considering different ionic concentrations, defect sizes and contents. Outer-sphere adsorbed Pb2+ ions predominate for all models (regular and defective), while inner-sphere Na+ ions, which exist sporadically only at concentrated solutions for regular models, govern the adsorption for all defective models. Adsorption quantities and stabilities of metal ions on kaolinite are fundamentally promoted by defect sites, thus explaining the experimental observations. Defect sites improve the stabilities of both inner- and outer-sphere adsorption, and (quasi) inner-sphere Pb2+ ions emerge only at defect sites that reinforce the interactions. Adsorption configurations are greatly altered by defect sites but respond weakly by changing defect sizes or contents. Both adsorption quantities and stabilities are enhanced by increasing defect sizes or contents, while ionic concentrations mainly affect adsorption quantities. We also find that adsorption of metal ions and anions can be promoted by each other and proceeds in a collaborative mechanism. Results thus obtained are beneficial to comprehend related processes for all types of minerals. PMID:26403873

H+ diffusion and electrochemical stability of Li1+x+yAlxTi2-xSiyP3-yO12 glass in aqueous Li/air battery electrolytes

NASA Astrophysics Data System (ADS)

Ding, Fei; Xu, Wu; Shao, Yuyan; Chen, Xilin; Wang, Zhiguo; Gao, Fei; Liu, Xingjiang; Zhang, Ji-Guang

2012-09-01

It is well known that LATP (Li1+x+yAlxTi2-xSiyP3-yO12) glass is a good lithium (Li)-ion conductor. However, the interaction between LATP glass and H+ ions in aqueous electrolytes (including the diffusion and surface adsorption of H+ ions) needs to be well understood before the long-term application of LATP glass in an aqueous electrolyte can be realized. In this work, we investigate H+-ion diffusion in LATP glass and their interactions with the glass surface using both experimental and modeling approaches. Our results indicate that the apparent H+-related current observed in the initial cyclic voltammetry scan should be attributed to the adsorption of H+ ions on the LATP glass rather than the bulk diffusion of H+ ions. Furthermore, density functional theory calculations indicate that the H+-ion diffusion energy barrier (3.21 eV) is much higher than that for Li+ ions (0.79 eV) and Na+ ions (0.79 eV) in a NASICON-type LiTi2(PO4)3 material. As a result, H+-ion conductivity in LATP glass is negligible at room temperature. However, significant surface corrosion was found after the LATP glass in a strong alkaline electrolyte. Therefore, to prevent LATP glass from corrosion, appropriate electrolytes must be developed for long-term operation of LATP in aqueous Li-air batteries.

Radial evolution of ion distribution functions

NASA Technical Reports Server (NTRS)

Marsch, E.

1983-01-01

A survey of solar wind ion velocity distributions and derived parameters (temperature, ion differential speed, heat flux, adiabatic invariants) is presented with emphasis on the heliocentric distance range between 0.3 and 1 AU traversed by the Helios solar probe. The radial evolution of nonthermal features are discussed which are observed to be most pronounced at perihelion. Within the framework of quasilinear plasma theory, wave particle interactions that may shape the ion distributions are considered. Some results of a self consistent model calculation are presented accounting for ion acceleration and heating by resonant momentum and energy exchange with ion cyclotron and magnetosonic waves propagating away from the Sun along the interplanetary magnetic field. Another tentative explanation for the occurrence of large perpendicular proton temperatures is offered in terms of heating by Landau damping of lower hybrid waves.

Heliosheath Space Environment Interactions with Icy Bodies in the Outermost Solar System

NASA Technical Reports Server (NTRS)

Cooper, John F.; Hill, Matthew E.; Richardson, John D.; Sturner, Steven J.

2006-01-01

The Voyager 1 and 2 spacecraft are exploring the space environment of the outermost solar system at the same time that earth-based astronomy continues to discover new icy bodies, one larger than Pluto, in the transitional region outward from the Classical Kuiper Belt to the Inner Oort Cloud. Some of the Scattered Disk Objects in this region periodically pass through the heliosheath, entered by Voyager 1 in Dec. 2004 and later expected to be reached by Voyager 2, and out even beyond the heliopause into the Very Local Interstellar Medium. The less energetic heliosheath ions, important for implantation and sputtering processes, are abundant near and beyond the termination shock inner boundary, but the source region of the more penetrating anomalous cosmic ray component has not yet been found. Advantageous for modeling of icy body interactions, the measured heliosheath flux spectra are relatively more stable within this new regime of isotropic compressional magnetic turbulence than in the upstream heliospheric environment. The deepest interactions and resultant radiation-induced chemistry arise from the inwardly diffusing component of the galactic cosmic ray ions with significant intensity modulation also arising in the heliosheath beyond Voyager 1. Surface gardening by high-velocity impacts of smaller bodies (e.g., fragments of previous KBO collisions) and dust is a further space weathering process setting the time scales for long term exposure of different regolith layers to the ion irradiation. Sputtering and ionization of impact ejecta grains may provide a substantial feedback of pickup ions for multiple cycles of heliosheath acceleration and icy body interaction. Thus the space weathering interactions are potentially of interest not only for effects on sensible surface composition of the icy bodies but also for evolution of the heliosheath plasma energetic ion, and neutral emission environment.

Electrokinetic mechanism of wettability alternation at oil-water-rock interface

NASA Astrophysics Data System (ADS)

Tian, Huanhuan; Wang, Moran

2017-12-01

Design of ions for injection water may change the wettability of oil-brine-rock (OBR) system, which has very important applications in enhanced oil recovery. Though ion-tuned wettability has been verified by various experiments, the mechanism is still not clear. In this review paper, we first present a comprehensive summarization of possible wettability alteration mechanisms, including fines migration or dissolution, multicomponent ion-exchange (MIE), electrical double layer (EDL) interaction between rock and oil, and repulsive hydration force. To clarify the key mechanism, we introduce a complete frame of theories to calculate attribution of EDL repulsion to wettability alteration by assuming constant binding forces (no MIE) and rigid smooth surface (no fines migration or dissolution). The frame consists of three parts: the classical Gouy-Chapman model coupled with interface charging mechanisms to describe EDL in oil-brine-rock systems, three methods with different boundary assumptions to evaluate EDL interaction energy, and the modified Young-Dupré equation to link EDL interaction energy with contact angle. The quantitative analysis for two typical oil-brine-rock systems provides two physical maps that show how the EDL interaction influences contact angle at different ionic composition. The result indicates that the contribution of EDL interaction to ion-tuned wettability for the studied system is not quite significant. The classical and advanced experimental work using microfabrication is reviewed briefly on the contribution of EDL repulsion to wettability alteration and compared with the theoretical results. It is indicated that the roughness of real rock surface may enhance EDL interaction. Finally we discuss some pending questions, perspectives and promising applications based on the mechanism.

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.

Two-stage DNA compaction induced by silver ions suggests a cooperative binding mechanism

NASA Astrophysics Data System (ADS)

Jiang, Wen-Yan; Ran, Shi-Yong

2018-05-01

The interaction between silver ions and DNA plays an important role in the therapeutic use of silver ions and in related technologies such as DNA sensors. However, the underlying mechanism has not been fully understood. In this study, the dynamics of Ag+-DNA interaction at a single-molecule level was studied using magnetic tweezers. AgNO3 solutions with concentrations ranging from 1 μM to 20 μM led to a 1.4-1.8 μm decrease in length of a single λ-DNA molecule, indicating that Ag+ has a strong binding with DNA, causing the DNA conformational change. The compaction process comprises one linear declining stage and another sigmoid-shaped stage, which can be attributed to the interaction mechanism. Considering the cooperative effect, the sigmoid trend was well explained using a phenomenological model. By contrast, addition of silver nanoparticle solution induced no detectable transition of DNA. The dependence of the interaction on ionic strength and DNA concentration was examined via morphology characterization and particle size distribution measurement. The size of the Ag+-DNA complex decreased with an increase in Ag+ ionic strength ranging from 1 μM to 1 mM. Morphology characterization confirmed that silver ions induced DNA to adopt a compacted globular conformation. At a fixed [AgNO3]:[DNA base pairs] ratio, increasing DNA concentration led to increased sizes of the complexes. Intermolecular interaction is believed to affect the Ag+-DNA complex formation to a large extent.

Chemically synthesized glycosides of hydroxylated flavylium ions as suitable models of anthocyanins: binding to iron ions and human serum albumin, antioxidant activity in model gastric conditions.

PubMed

Al Bittar, Sheiraz; Mora, Nathalie; Loonis, Michèle; Dangles, Olivier

2014-12-11

Polyhydroxylated flavylium ions, such as 3',4',7-trihydroxyflavylium chloride (P1) and its more water-soluble 7-O-β-d-glucopyranoside (P2), are readily accessible by chemical synthesis and suitable models of natural anthocyanins in terms of color and species distribution in aqueous solution. Owing to their catechol B-ring, they rapidly bind FeIII, weakly interact with FeII and promote its autoxidation to FeIII. Both pigments inhibit heme-induced lipid peroxidation in mildly acidic conditions (a model of postprandial oxidative stress in the stomach), the colorless (chalcone) forms being more potent than the colored forms. Finally, P1 and P2 are moderate ligands of human serum albumin (HSA), their likely carrier in the blood circulation, with chalcones having a higher affinity for HSA than the corresponding colored forms.

Predicting electromagnetic ion cyclotron wave amplitude from unstable ring current plasma conditions

DOE PAGES

Fu, Xiangrong; Cowee, Misa M.; Jordanova, Vania K.; ...

2016-11-01

Electromagnetic ion cyclotron (EMIC) waves in the Earth's inner magnetosphere are enhanced fluctuations driven unstable by ring current ion temperature anisotropy. EMIC waves can resonate with relativistic electrons and play an important role in precipitation of MeV radiation belt electrons. In this study, we investigate the excitation and saturation of EMIC instability in a homogeneous plasma using both linear theory and nonlinear hybrid simulations. We have explored a four-dimensional parameter space, carried out a large number of simulations, and derived a scaling formula that relates the saturation EMIC wave amplitude to initial plasma conditions. Finally, such scaling can be usedmore » in conjunction with ring current models like ring current-atmosphere interactions model with self-consistent magnetic field to provide global dynamic EMIC wave maps that will be more accurate inputs for radiation belt modeling than statistical models.« less

Nuclear fragmentation energy and momentum transfer distributions in relativistic heavy-ion collisions

NASA Technical Reports Server (NTRS)

Khandelwal, Govind S.; Khan, Ferdous

1989-01-01

An optical model description of energy and momentum transfer in relativistic heavy-ion collisions, based upon composite particle multiple scattering theory, is presented. Transverse and longitudinal momentum transfers to the projectile are shown to arise from the real and absorptive part of the optical potential, respectively. Comparisons of fragment momentum distribution observables with experiments are made and trends outlined based on our knowledge of the underlying nucleon-nucleon interaction. Corrections to the above calculations are discussed. Finally, use of the model as a tool for estimating collision impact parameters is indicated.

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)

Transport properties in the atmosphere of Jupiter

NASA Technical Reports Server (NTRS)

Biolsi, L., Jr.

1979-01-01

Activities reported include: (1) testing of the computer program used to obtain transport properties for the Hulburt-Hirschfelder potential; (2) calculation of transport properties for the C2-C interaction; (3) preliminary calculations for the C2-C2 interaction; (4) calculation of transport properties for the C2H-He interaction; (5) consideration of the effect of inelastic collisions on the transport properties; and (6) the use of the Hulburt-Hirschfelder potential to model ion-atom interactions.

Ion-dipole interactions and their functions in proteins.

PubMed

Sippel, Katherine H; Quiocho, Florante A

2015-07-01

Ion-dipole interactions in biological macromolecules are formed between atomic or molecular ions and neutral protein dipolar groups through either hydrogen bond or coordination. Since their discovery 30 years ago, these interactions have proven to be a frequent occurrence in protein structures, appearing in everything from transporters and ion channels to enzyme active sites to protein-protein interfaces. However, their significance and roles in protein functions are largely underappreciated. We performed PDB data mining to identify a sampling of proteins that possess these interactions. In this review, we will define the ion-dipole interaction and discuss several prominent examples of their functional roles in nature. © 2015 The Protein Society.

Poisson-Boltzmann-Nernst-Planck model

NASA Astrophysics Data System (ADS)

Zheng, Qiong; Wei, Guo-Wei

2011-05-01

The Poisson-Nernst-Planck (PNP) model is based on a mean-field approximation of ion interactions and continuum descriptions of concentration and electrostatic potential. It provides qualitative explanation and increasingly quantitative predictions of experimental measurements for the ion transport problems in many areas such as semiconductor devices, nanofluidic systems, and biological systems, despite many limitations. While the PNP model gives a good prediction of the ion transport phenomenon for chemical, physical, and biological systems, the number of equations to be solved and the number of diffusion coefficient profiles to be determined for the calculation directly depend on the number of ion species in the system, since each ion species corresponds to one Nernst-Planck equation and one position-dependent diffusion coefficient profile. In a complex system with multiple ion species, the PNP can be computationally expensive and parameter demanding, as experimental measurements of diffusion coefficient profiles are generally quite limited for most confined regions such as ion channels, nanostructures and nanopores. We propose an alternative model to reduce number of Nernst-Planck equations to be solved in complex chemical and biological systems with multiple ion species by substituting Nernst-Planck equations with Boltzmann distributions of ion concentrations. As such, we solve the coupled Poisson-Boltzmann and Nernst-Planck (PBNP) equations, instead of the PNP equations. The proposed PBNP equations are derived from a total energy functional by using the variational principle. We design a number of computational techniques, including the Dirichlet to Neumann mapping, the matched interface and boundary, and relaxation based iterative procedure, to ensure efficient solution of the proposed PBNP equations. Two protein molecules, cytochrome c551 and Gramicidin A, are employed to validate the proposed model under a wide range of bulk ion concentrations and external voltages. Extensive numerical experiments show that there is an excellent consistency between the results predicted from the present PBNP model and those obtained from the PNP model in terms of the electrostatic potentials, ion concentration profiles, and current-voltage (I-V) curves. The present PBNP model is further validated by a comparison with experimental measurements of I-V curves under various ion bulk concentrations. Numerical experiments indicate that the proposed PBNP model is more efficient than the original PNP model in terms of simulation time.

Poisson-Boltzmann-Nernst-Planck model

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

Zheng Qiong; Wei Guowei; Department of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824

2011-05-21

The Poisson-Nernst-Planck (PNP) model is based on a mean-field approximation of ion interactions and continuum descriptions of concentration and electrostatic potential. It provides qualitative explanation and increasingly quantitative predictions of experimental measurements for the ion transport problems in many areas such as semiconductor devices, nanofluidic systems, and biological systems, despite many limitations. While the PNP model gives a good prediction of the ion transport phenomenon for chemical, physical, and biological systems, the number of equations to be solved and the number of diffusion coefficient profiles to be determined for the calculation directly depend on the number of ion species inmore » the system, since each ion species corresponds to one Nernst-Planck equation and one position-dependent diffusion coefficient profile. In a complex system with multiple ion species, the PNP can be computationally expensive and parameter demanding, as experimental measurements of diffusion coefficient profiles are generally quite limited for most confined regions such as ion channels, nanostructures and nanopores. We propose an alternative model to reduce number of Nernst-Planck equations to be solved in complex chemical and biological systems with multiple ion species by substituting Nernst-Planck equations with Boltzmann distributions of ion concentrations. As such, we solve the coupled Poisson-Boltzmann and Nernst-Planck (PBNP) equations, instead of the PNP equations. The proposed PBNP equations are derived from a total energy functional by using the variational principle. We design a number of computational techniques, including the Dirichlet to Neumann mapping, the matched interface and boundary, and relaxation based iterative procedure, to ensure efficient solution of the proposed PBNP equations. Two protein molecules, cytochrome c551 and Gramicidin A, are employed to validate the proposed model under a wide range of bulk ion concentrations and external voltages. Extensive numerical experiments show that there is an excellent consistency between the results predicted from the present PBNP model and those obtained from the PNP model in terms of the electrostatic potentials, ion concentration profiles, and current-voltage (I-V) curves. The present PBNP model is further validated by a comparison with experimental measurements of I-V curves under various ion bulk concentrations. Numerical experiments indicate that the proposed PBNP model is more efficient than the original PNP model in terms of simulation time.« less

Poisson–Boltzmann–Nernst–Planck model

PubMed Central

Zheng, Qiong; Wei, Guo-Wei

2011-01-01

The Poisson–Nernst–Planck (PNP) model is based on a mean-field approximation of ion interactions and continuum descriptions of concentration and electrostatic potential. It provides qualitative explanation and increasingly quantitative predictions of experimental measurements for the ion transport problems in many areas such as semiconductor devices, nanofluidic systems, and biological systems, despite many limitations. While the PNP model gives a good prediction of the ion transport phenomenon for chemical, physical, and biological systems, the number of equations to be solved and the number of diffusion coefficient profiles to be determined for the calculation directly depend on the number of ion species in the system, since each ion species corresponds to one Nernst–Planck equation and one position-dependent diffusion coefficient profile. In a complex system with multiple ion species, the PNP can be computationally expensive and parameter demanding, as experimental measurements of diffusion coefficient profiles are generally quite limited for most confined regions such as ion channels, nanostructures and nanopores. We propose an alternative model to reduce number of Nernst–Planck equations to be solved in complex chemical and biological systems with multiple ion species by substituting Nernst–Planck equations with Boltzmann distributions of ion concentrations. As such, we solve the coupled Poisson–Boltzmann and Nernst–Planck (PBNP) equations, instead of the PNP equations. The proposed PBNP equations are derived from a total energy functional by using the variational principle. We design a number of computational techniques, including the Dirichlet to Neumann mapping, the matched interface and boundary, and relaxation based iterative procedure, to ensure efficient solution of the proposed PBNP equations. Two protein molecules, cytochrome c551 and Gramicidin A, are employed to validate the proposed model under a wide range of bulk ion concentrations and external voltages. Extensive numerical experiments show that there is an excellent consistency between the results predicted from the present PBNP model and those obtained from the PNP model in terms of the electrostatic potentials, ion concentration profiles, and current–voltage (I–V) curves. The present PBNP model is further validated by a comparison with experimental measurements of I–V curves under various ion bulk concentrations. Numerical experiments indicate that the proposed PBNP model is more efficient than the original PNP model in terms of simulation time. PMID:21599038

Poisson-Boltzmann-Nernst-Planck model.

PubMed

Zheng, Qiong; Wei, Guo-Wei

2011-05-21

The Poisson-Nernst-Planck (PNP) model is based on a mean-field approximation of ion interactions and continuum descriptions of concentration and electrostatic potential. It provides qualitative explanation and increasingly quantitative predictions of experimental measurements for the ion transport problems in many areas such as semiconductor devices, nanofluidic systems, and biological systems, despite many limitations. While the PNP model gives a good prediction of the ion transport phenomenon for chemical, physical, and biological systems, the number of equations to be solved and the number of diffusion coefficient profiles to be determined for the calculation directly depend on the number of ion species in the system, since each ion species corresponds to one Nernst-Planck equation and one position-dependent diffusion coefficient profile. In a complex system with multiple ion species, the PNP can be computationally expensive and parameter demanding, as experimental measurements of diffusion coefficient profiles are generally quite limited for most confined regions such as ion channels, nanostructures and nanopores. We propose an alternative model to reduce number of Nernst-Planck equations to be solved in complex chemical and biological systems with multiple ion species by substituting Nernst-Planck equations with Boltzmann distributions of ion concentrations. As such, we solve the coupled Poisson-Boltzmann and Nernst-Planck (PBNP) equations, instead of the PNP equations. The proposed PBNP equations are derived from a total energy functional by using the variational principle. We design a number of computational techniques, including the Dirichlet to Neumann mapping, the matched interface and boundary, and relaxation based iterative procedure, to ensure efficient solution of the proposed PBNP equations. Two protein molecules, cytochrome c551 and Gramicidin A, are employed to validate the proposed model under a wide range of bulk ion concentrations and external voltages. Extensive numerical experiments show that there is an excellent consistency between the results predicted from the present PBNP model and those obtained from the PNP model in terms of the electrostatic potentials, ion concentration profiles, and current-voltage (I-V) curves. The present PBNP model is further validated by a comparison with experimental measurements of I-V curves under various ion bulk concentrations. Numerical experiments indicate that the proposed PBNP model is more efficient than the original PNP model in terms of simulation time. © 2011 American Institute of Physics.

Multi-shell model of ion-induced nucleic acid condensation

NASA Astrophysics Data System (ADS)

Tolokh, Igor S.; Drozdetski, Aleksander V.; Pollack, Lois; Baker, Nathan A.; Onufriev, Alexey V.

2016-04-01

We present a semi-quantitative model of condensation of short nucleic acid (NA) duplexes induced by trivalent cobalt(iii) hexammine (CoHex) ions. The model is based on partitioning of bound counterion distribution around single NA duplex into "external" and "internal" ion binding shells distinguished by the proximity to duplex helical axis. In the aggregated phase the shells overlap, which leads to significantly increased attraction of CoHex ions in these overlaps with the neighboring duplexes. The duplex aggregation free energy is decomposed into attractive and repulsive components in such a way that they can be represented by simple analytical expressions with parameters derived from molecular dynamic simulations and numerical solutions of Poisson equation. The attractive term depends on the fractions of bound ions in the overlapping shells and affinity of CoHex to the "external" shell of nearly neutralized duplex. The repulsive components of the free energy are duplex configurational entropy loss upon the aggregation and the electrostatic repulsion of the duplexes that remains after neutralization by bound CoHex ions. The estimates of the aggregation free energy are consistent with the experimental range of NA duplex condensation propensities, including the unusually poor condensation of RNA structures and subtle sequence effects upon DNA condensation. The model predicts that, in contrast to DNA, RNA duplexes may condense into tighter packed aggregates with a higher degree of duplex neutralization. An appreciable CoHex mediated RNA-RNA attraction requires closer inter-duplex separation to engage CoHex ions (bound mostly in the "internal" shell of RNA) into short-range attractive interactions. The model also predicts that longer NA fragments will condense more readily than shorter ones. The ability of this model to explain experimentally observed trends in NA condensation lends support to proposed NA condensation picture based on the multivalent "ion binding shells."

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

Sverjensky, Dimitri A.; Huang, Fang

Diamond formation has typically been attributed to redox reactions during precipitation from fluids or magmas. Either the oxidation of methane or the reduction of carbon dioxide has been suggested, based on simplistic models of deep fluids consisting of mixtures of dissolved neutral gas molecules without consideration of aqueous ions. The role of pH changes associated with water–silicate rock interactions during diamond formation is unknown. Here we show that diamonds could form due to a drop in pH during water–rock interactions. We use a recent theoretical model of deep fluids that includes ions, to show that fluid can react irreversibly withmore » eclogite at 900 °C and 5.0 GPa, generating diamond and secondary minerals due to a decrease in pH at almost constant oxygen fugacity. Overall, our results constitute a new quantitative theory of diamond formation as a consequence of the reaction of deep fluids with the rock types that they encounter during migration. Diamond can form in the deep Earth during water–rock interactions without changes in oxidation state.« less

Glass transition of charged particles in two-dimensional confinement.

PubMed

Yazdi, Anoosheh; Heinen, Marco; Ivlev, Alexei; Löwen, Hartmut; Sperl, Matthias

2015-05-01

The glass transition of mesoscopic charged particles in two-dimensional confinement is studied by mode-coupling theory. We consider two types of effective interactions between the particles, corresponding to two different models for the distribution of surrounding ions that are integrated out in coarse-grained descriptions. In the first model, a planar monolayer of charged particles is immersed in an unbounded isotropic bath of ions, giving rise to an isotropically screened Debye-Hückel (Yukawa)-type effective interaction. The second, experimentally more relevant system is a monolayer of negatively charged particles that levitate atop a flat horizontal electrode, as frequently encountered in laboratory experiments with complex (dusty) plasmas. A steady plasma current toward the electrode gives rise to an anisotropic effective interaction potential between the particles, with an algebraically long-ranged in-plane decay. In a comprehensive parameter scan that covers the typical range of experimentally accessible plasma conditions, we calculate and compare the mode-coupling predictions for the glass transition in both kinds of systems.

Protein-membrane electrostatic interactions: Application of the Lekner summation technique

NASA Astrophysics Data System (ADS)

Juffer, André H.; Shepherd, Craig M.; Vogel, Hans J.

2001-01-01

A model has been developed to calculate the electrostatic interaction between biomolecules and lipid bilayers. The effect of ionic strength is included by means of explicit ions, while water is described as a background continuum. The bilayer is considered at the atomic level. The Lekner summation technique is employed to calculate the long-range electrostatic interactions. The new method is employed to estimate the electrostatic contribution to the free energy of binding of sandostatin, a cyclic eight-residue analogue of the peptide hormone somatostatin, to lipid bilayers with thermodynamic integration. Monte Carlo simulation techniques were employed to determine ion distributions and peptide orientations. Both neutral as well as negatively charged lipid bilayers were used. An error analysis to judge the quality of the computation is also presented. The applicability of the Lekner summation technique to combine it with computer simulation models that simulate the adsorption of peptides (and proteins) into the interfacial region of lipid bilayers is discussed.

Stresses due to Squeeze Flow between Particles Surrounded by an Electrolyte Solution with Application to Lithium-Ion Batteries

NASA Astrophysics Data System (ADS)

Conlisk, A. T.; Zhang, Cong

2013-11-01

Large stresses are induced during lithium-ion battery charging and discharging, termed intercalation and deintercalation stresses. Current models of the stresses in lithium-ion batteries in the literature seldom consider the influence of the interaction between the particles within the electrodes on the stress distribution. The particles within lithium-ion battery electrodes can undergo relative motion with relative velocities of different magnitudes and directions. One important mode of motion manifests itself as two particles approaching each other. The interaction is mediated by the electrolyte between the particles. The relative motion of the particles induces significant pressures and the primary objective of this work is to propose a source of mechanical stresses as a consequence of the dynamic squeezing motion as opposed to a static environment considered in the battery literature. Other applications in the biomedical field are also discussed. Supported by DOE Graduate Automotive Technology Education (GATE), OSU Center for Automotive Research and OSU NSEC Center for the Affordable Nanoengineering of Polymeric Biomedical Devices.

Excited State Atom-Ion Charge-Exchange

NASA Astrophysics Data System (ADS)

Li, Ming; Makrides, Constantinos; Petrov, Alexander; Kotochigova, Svetlana

2017-04-01

We theoretically investigate the exothermic charge-exchange reaction between an excited atom and a ground-state positive ion. In particular, we focus on MOT-excited Ca*(4s4p 1P) atoms colliding with ground-state Yb+ ions, which are under active study by the experimental group of E. Hudson at UCLA. Collisions between an excited atom and an ion are guided by two major contributions to the long-range interaction potentials, the induction C4 /R4 and charge-quadrupole C3 /R3 potentials, and their coupling by the electron-exchange interaction. Our model of these forces leads to close-coupling equations for multiple reaction channels. We find several avoided crossings between the potentials that couple to the nearby asymptotic limits of Yb*+Ca+, some of which can possibly provide large charge exchange rate coefficients above 10-10 cm3 / s. We acknowledge support from the US Army Research Office, MURI Grants W911NF-14-1-0378 and the US National Science Foundation, Grant PHY-1619788.

Molecular modeling study on the relative stabilities of the flotation products for arsenic-containing minerals: dixanthogens and arsenic(III) xanthates.

PubMed

Yekeler, Meftuni; Yekeler, Hülya

2005-04-15

The interactions of As(III) ion with C(2)H(5)OCS(-)(2) and C(2)H(5)SCS(-)(2), known as the most popular collector ions, were studied by density functional theory (DFT) at the B3LYP/6-31G** level in connection with the arsenic-containing minerals realgar, orpiment, and arsenopyrite. The dixanthogen formations of these ions were also investigated at the same level of theory. The central purpose of this paper is to compare the stabilities of the major flotation products, namely As(III) xanthates and dixanthogens. The results show that the magnitudes of the interaction energies for the formations of As(III) xanthates and dixanthogens increase when the oxygen atom is replaced by the sulfur atom in C(2)H(5)OCS(-)(2). Therefore, the C(2)H(5)OCS(-)(2) ion is preferred in these formations. The results obtained are in agreement with the experimental data reported.

Ion-dipole interactions in concentrated organic electrolytes.

PubMed

Chagnes, Alexandre; Nicolis, Stamatios; Carré, Bernard; Willmann, Patrick; Lemordant, Daniel

2003-06-16

An algorithm is proposed for calculating the energy of ion-dipole interactions in concentrated organic electrolytes. The ion-dipole interactions increase with increasing salt concentration and must be taken into account when the activation energy for the conductivity is calculated. In this case, the contribution of ion-dipole interactions to the activation energy for this transport process is of the same order of magnitude as the contribution of ion-ion interactions. The ion-dipole interaction energy was calculated for a cell of eight ions, alternatingly anions and cations, placed on the vertices of an expanded cubic lattice whose parameter is related to the mean interionic distance (pseudolattice theory). The solvent dipoles were introduced randomly into the cell by assuming a randomness compacity of 0.58. The energy of the dipole assembly in the cell was minimized by using a Newton-Raphson numerical method. The dielectric field gradient around ions was taken into account by a distance parameter and a dielectric constant of epsilon = 3 at the surfaces of the ions. A fair agreement between experimental and calculated activation energy has been found for systems composed of gamma-butyrolactone (BL) as solvent and lithium perchlorate (LiClO4), lithium tetrafluoroborate (LiBF4), lithium hexafluorophosphate (LiPF6), lithium hexafluoroarsenate (LiAsF6), and lithium bis(trifluoromethylsulfonyl)imide (LiTFSI) as salts.

Radiation Environment Inside Spacecraft

NASA Technical Reports Server (NTRS)

O'Neill, Patrick

2015-01-01

Dr. Patrick O'Neill, NASA Johnson Space Center, will present a detailed description of the radiation environment inside spacecraft. The free space (outside) solar and galactic cosmic ray and trapped Van Allen belt proton spectra are significantly modified as these ions propagate through various thicknesses of spacecraft structure and shielding material. In addition to energy loss, secondary ions are created as the ions interact with the structure materials. Nuclear interaction codes (FLUKA, GEANT4, HZTRAN, MCNPX, CEM03, and PHITS) transport free space spectra through different thicknesses of various materials. These "inside" energy spectra are then converted to Linear Energy Transfer (LET) spectra and dose rate - that's what's needed by electronics systems designers. Model predictions are compared to radiation measurements made by instruments such as the Intra-Vehicular Charged Particle Directional Spectrometer (IV-CPDS) used inside the Space Station, Orion, and Space Shuttle.

Extracellular Membrane-proximal Domain of HAb18G/CD147 Binds to Metal Ion-dependent Adhesion Site (MIDAS) Motif of Integrin β1 to Modulate Malignant Properties of Hepatoma Cells*

PubMed Central

Li, Yong; Wu, Jiao; Song, Fei; Tang, Juan; Wang, Shi-Jie; Yu, Xiao-Ling; Chen, Zhi-Nan; Jiang, Jian-Li

2012-01-01

Several lines of evidence suggest that HAb18G/CD147 interacts with the integrin variants α3β1 and α6β1. However, the mechanism of the interaction remains largely unknown. In this study, mammalian protein-protein interaction trap (MAPPIT), a mammalian two-hybrid method, was used to study the CD147-integrin β1 subunit interaction. CD147 in human hepatocellular carcinoma (HCC) cells was interfered with by small hairpin RNA. Nude mouse xenograft model and metastatic model of HCC were used to detect the role of CD147 in carcinogenesis and metastasis. We found that the extracellular membrane-proximal domain of HAb18G/CD147 (I-type domain) binds at the metal ion-dependent adhesion site in the βA domain of the integrin β1 subunit, and Asp179 in the I-type domain of HAb18G/CD147 plays an important role in the interaction. The levels of the proteins that act downstream of integrin, including focal adhesion kinase (FAK) and phospho-FAK, were decreased, and the cytoskeletal structures of HCC cells were rearranged bearing the HAb18G/CD147 deletion. Simultaneously, the migration and invasion capacities, secretion of matrix metalloproteinases, colony formation rate in vitro, and tumor growth and metastatic potential in vivo were decreased. These results indicate that the interaction of HAb18G/CD147 extracellular I-type domain with the integrin β1 metal ion-dependent adhesion site motif activates the downstream FAK signaling pathway, subsequently enhancing the malignant properties of HCC cells. PMID:22130661

Ion Transport through Membrane-Spanning Nanopores Studied by Molecular Dynamics Simulations and Continuum Electrostatics Calculations

PubMed Central

Peter, Christine; Hummer, Gerhard

2005-01-01

Narrow hydrophobic regions are a common feature of biological channels, with possible roles in ion-channel gating. We study the principles that govern ion transport through narrow hydrophobic membrane pores by molecular dynamics simulation of model membranes formed of hexagonally packed carbon nanotubes. We focus on the factors that determine the energetics of ion translocation through such nonpolar nanopores and compare the resulting free-energy barriers for pores with different diameters corresponding to the gating regions in closed and open forms of potassium channels. Our model system also allows us to compare the results from molecular dynamics simulations directly to continuum electrostatics calculations. Both simulations and continuum calculations show that subnanometer wide pores pose a huge free-energy barrier for ions, but a small increase in the pore diameter to ∼1 nm nearly eliminates that barrier. We also find that in those wider channels the ion mobility is comparable to that in the bulk phase. By calculating local electrostatic potentials, we show that the long range Coulomb interactions of ions are strongly screened in the wide water-filled channels. Whereas continuum calculations capture the overall energetics reasonably well, the local water structure, which is not accounted for in this model, leads to interesting effects such as the preference of hydrated ions to move along the pore wall rather than through the center of the pore. PMID:16006629

X-ray absorption spectroscopy of LiBF 4 in propylene carbonate. A model lithium ion battery electrolyte

DOE PAGES

Smith, Jacob W.; Lam, Royce K.; Sheardy, Alex T.; ...

2014-08-20

Since their introduction into the commercial marketplace in 1991, lithium ion batteries have become increasingly ubiquitous in portable technology. Nevertheless, improvements to existing battery technology are necessary to expand their utility for larger-scale applications, such as electric vehicles. Advances may be realized from improvements to the liquid electrolyte; however, current understanding of the liquid structure and properties remains incomplete. X-ray absorption spectroscopy of solutions of LiBF 4 in propylene carbonate (PC), interpreted using first-principles electronic structure calculations within the eXcited electron and Core Hole (XCH) approximation, yields new insight into the solvation structure of the Li + ion in thismore » model electrolyte. By generating linear combinations of the computed spectra of Li +-associating and free PC molecules and comparing to the experimental spectrum, we find a Li +–solvent interaction number of 4.5. This result suggests that computational models of lithium ion battery electrolytes should move beyond tetrahedral coordination structures.« less

Modification of porous starch for the adsorption of heavy metal ions from aqueous solution.

PubMed

Ma, Xiaofei; Liu, Xueyuan; Anderson, Debbie P; Chang, Peter R

2015-08-15

Porous starch xanthate (PSX) and porous starch citrate (PSC) were prepared in anticipation of the attached xanthate and carboxylate groups respectively forming chelation and electrostatic interactions with heavy metal ions in the subsequent adsorption process. The lead(II) ion was selected as the model metal and its adsorption by PSX and PSC was characterized. The adsorption capacity was highly dependent on the carbon disulfide/starch and citric acid/starch mole ratios used during preparation. The adsorption behaviors of lead(II) ion on PSXs and PSCs fit both the pseudo-second-order kinetic model and the Langmuir isotherm model. The maximum adsorption capacity from the Langmuir isotherm equation reached 109.1 and 57.6 mg/g for PSX and PSC when preparation conditions were optimized, and the adsorption times were just 20 and 60 min, respectively. PSX and PSC may be used as effective adsorbents for removal of heavy metals from contaminated liquid. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Classical density functional theory and Monte Carlo simulation study of electric double layer in the vicinity of a cylindrical electrode

NASA Astrophysics Data System (ADS)

Zhou, Shiqi; Lamperski, Stanisław; Sokołowska, Marta

2017-07-01

We have performed extensive Monte-Carlo simulations and classical density functional theory (DFT) calculations of the electrical double layer (EDL) near a cylindrical electrode in a primitive model (PM) modified by incorporating interionic dispersion interactions. It is concluded that (i) in general, an unsophisticated use of the mean field (MF) approximation for the interionic dispersion interactions does not distinctly worsen the classical DFT performance, even if the salt ions considered are highly asymmetrical in size (3:1) and charge (5:1), the bulk molar concentration considered is high up to a total bulk ion packing fraction of 0.314, and the surface charge density of up to 0.5 C m-2. (ii) More specifically, considering the possible noises in the simulation, the local volume charge density profiles are the most accurately predicted by the classical DFT in all situations, and the co- and counter-ion singlet distributions are also rather accurately predicted; whereas the mean electrostatic potential profile is relatively less accurately predicted due to an integral amplification of minor inaccuracy of the singlet distributions. (iii) It is found that the layered structure of the co-ion distribution is abnormally possible only if the surface charge density is high enough (for example 0.5 C m-2) moreover, the co-ion valence abnormally influences the peak height of the first counter-ion layer, which decreases with the former. (iv) Even if both the simulation and DFT indicate an insignificant contribution of the interionic dispersion interaction to the above three ‘local’ quantities, it is clearly shown by the classical DFT that the interionic dispersion interaction does significantly influence a ‘global’ quantity like the cylinder surface-aqueous electrolyte interfacial tension, and this may imply the role of the interionic dispersion interaction in explaining the specific Hofmeister effects. We elucidate all of the above observations based on the arguments from the liquid state theory and at the molecular scale.

Effect of Na+ and Ca2+ ions on a lipid Langmuir monolayer: an atomistic description by molecular dynamics simulations.

PubMed

Giner Casares, Juan José; Camacho, Luis; Martín-Romero, Maria Teresa; López Cascales, José Javier

2008-12-01

Studying the effect of alkali and alkaline-earth metal cations on Langmuir monolayers is relevant from biophysical and nanotechnological points of view. In this work, the effect of Na(+) and Ca(2+) on a model of an anionic Langmuir lipid monolayer of dimyristoylphosphatidate (DMPA(-)) is studied by molecular dynamics simulations. The influence of the type of cation on lipid structure, lipid-lipid interactions, and lipid ordering is analyzed in terms of electrostatic interactions. It is found that for a lipid monolayer in its solid phase, the effect of the cations on the properties of the lipid monolayer can be neglected. The influence of the cations is enhanced for the lipid monolayer in its gas phase, where sodium ions show a high degree of dehydration compared with calcium ions. This loss of hydration shell is partly compensated by the formation of lipid-ion-lipid bridges. This difference is ascribed to the higher charge-to-radius ratio q/r for Ca(2+), which makes ion dehydration less favorable compared to Na(+). Owing to the different dehydration behavior of sodium and calcium ions, diminished lipid-lipid coordination, lipid-ion coordination, and lipid ordering are observed for Ca(2+) compared to Na(+). Furthermore, for both gas and solid phases of the lipid Langmuir monolayers, lipid conformation and ion dehydration across the lipid/water interface are studied.

Teaching Ion-Ion, Ion-Dipole, and Dipole-Dipole Interactions

ERIC Educational Resources Information Center

Yoder, Claude H.

1977-01-01

Discusses how electrostatic interactions can be taught quantitatively through Coulomb's Law at a variety of points in a chemistry curriculum. Each type of interaction is shown at both the intramolecular and the inter-"molecular" levels. (MR)

Interactions and Toxicity of Cu-Zn mixtures to Hordeum vulgare in Different Soils Can Be Rationalized with Bioavailability-Based Prediction Models.

PubMed

Qiu, Hao; Versieren, Liske; Rangel, Georgina Guzman; Smolders, Erik

2016-01-19

Soil contamination with copper (Cu) is often associated with zinc (Zn), and the biological response to such mixed contamination is complex. Here, we investigated Cu and Zn mixture toxicity to Hordeum vulgare in three different soils, the premise being that the observed interactions are mainly due to effects on bioavailability. The toxic effect of Cu and Zn mixtures on seedling root elongation was more than additive (i.e., synergism) in soils with high and medium cation-exchange capacity (CEC) but less than additive (antagonism) in a low-CEC soil. This was found when we expressed the dose as the conventional total soil concentration. In contrast, antagonism was found in all soils when we expressed the dose as free-ion activities in soil solution, indicating that there is metal-ion competition for binding to the plant roots. Neither a concentration addition nor an independent action model explained mixture effects, irrespective of the dose expressions. In contrast, a multimetal BLM model and a WHAM-Ftox model successfully explained the mixture effects across all soils and showed that bioavailability factors mainly explain the interactions in soils. The WHAM-Ftox model is a promising tool for the risk assessment of mixed-metal contamination in soils.

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

An investigation of solar wind effects on the evolution of the Martian atmosphere

NASA Technical Reports Server (NTRS)

Luhmann, Janet G.

1994-01-01

This investigation concentrated on the question of how atmosphere escape, related to both photochemistry and the Mars solar wind interaction, may have affected the evolution of Mars' atmosphere over time. The principal investigator and postdoctoral researcher adopted the premise that contemporary escape processes have dominated the losses to space over the past 3.5 billion years, but that the associated loss rates have been modified by solar evolution. A model was constructed for the contemporary escape scenario based on knowledge gained from both Venus in-situ measurements from Pioneer Venus Orbiter and Mars measurements from Phobos-2. Venus provided a valuable second example of a weakly magnetized planet having a similar solar wind interaction where we have more knowledge from observations. The model included photochemical losses from recombining ionospheric molecular ions, scavenging Martian upper atmosphere ('pickup') ions by the solar wind, and sputtering of the atmosphere by reentering pickup ions. The existence of the latter mechanism was realized during the course of the supported investigation, and is now thought by Jakosky and Pepin to explain some of the Martian noble gas isotope ratios.

Effects of electrostatic interactions on ligand dissociation kinetics

NASA Astrophysics Data System (ADS)

Erbaş, Aykut; de la Cruz, Monica Olvera; Marko, John F.

2018-02-01

We study unbinding of multivalent cationic ligands from oppositely charged polymeric binding sites sparsely grafted on a flat neutral substrate. Our molecular dynamics simulations are suggested by single-molecule studies of protein-DNA interactions. We consider univalent salt concentrations spanning roughly a 1000-fold range, together with various concentrations of excess ligands in solution. To reveal the ionic effects on unbinding kinetics of spontaneous and facilitated dissociation mechanisms, we treat electrostatic interactions both at a Debye-Hückel (DH) (or implicit ions, i.e., use of an electrostatic potential with a prescribed decay length) level and by the more precise approach of considering all ionic species explicitly in the simulations. We find that the DH approach systematically overestimates unbinding rates, relative to the calculations where all ion pairs are present explicitly in solution, although many aspects of the two types of calculation are qualitatively similar. For facilitated dissociation (FD) (acceleration of unbinding by free ligands in solution) explicit-ion simulations lead to unbinding at lower free-ligand concentrations. Our simulations predict a variety of FD regimes as a function of free-ligand and ion concentrations; a particularly interesting regime is at intermediate concentrations of ligands where nonelectrostatic binding strength controls FD. We conclude that explicit-ion electrostatic modeling is an essential component to quantitatively tackle problems in molecular ligand dissociation, including nucleic-acid-binding proteins.

Long-range electrostatic screening in ionic liquids

PubMed Central

Gebbie, Matthew A.; Dobbs, Howard A.; Valtiner, Markus; Israelachvili, Jacob N.

2015-01-01

Electrolyte solutions with high concentrations of ions are prevalent in biological systems and energy storage technologies. Nevertheless, the high interaction free energy and long-range nature of electrostatic interactions makes the development of a general conceptual picture of concentrated electrolytes a significant challenge. In this work, we study ionic liquids, single-component liquids composed solely of ions, in an attempt to provide a novel perspective on electrostatic screening in very high concentration (nonideal) electrolytes. We use temperature-dependent surface force measurements to demonstrate that the long-range, exponentially decaying diffuse double-layer forces observed across ionic liquids exhibit a pronounced temperature dependence: Increasing the temperature decreases the measured exponential (Debye) decay length, implying an increase in the thermally driven effective free-ion concentration in the bulk ionic liquids. We use our quantitative results to propose a general model of long-range electrostatic screening in ionic liquids, where thermally activated charge fluctuations, either free ions or correlated domains (quasiparticles), take on the role of ions in traditional dilute electrolyte solutions. This picture represents a crucial step toward resolving several inconsistencies surrounding electrostatic screening and charge transport in ionic liquids that have impeded progress within the interdisciplinary ionic liquids community. More broadly, our work provides a previously unidentified way of envisioning highly concentrated electrolytes, with implications for diverse areas of inquiry, ranging from designing electrochemical devices to rationalizing electrostatic interactions in biological systems. PMID:26040001

Polarizable Force Fields for CO2 and CH4 Adsorption in M-MOF-74

PubMed Central

2017-01-01

The family of M-MOF-74, with M = Co, Cr, Cu, Fe, Mg, Mn, Ni, Ti, V, and Zn, provides opportunities for numerous energy related gas separation applications. The pore structure of M-MOF-74 exhibits a high internal surface area and an exceptionally large adsorption capacity. The chemical environment of the adsorbate molecule in M-MOF-74 can be tuned by exchanging the metal ion incorporated in the structure. To optimize materials for a given separation process, insights into how the choice of the metal ion affects the interaction strength with adsorbate molecules and how to model these interactions are essential. Here, we quantitatively highlight the importance of polarization by comparing the proposed polarizable force field to orbital interaction energies from DFT calculations. Adsorption isotherms and heats of adsorption are computed for CO2, CH4, and their mixtures in M-MOF-74 with all 10 metal ions. The results are compared to experimental data, and to previous simulation results using nonpolarizable force fields derived from quantum mechanics. To the best of our knowledge, the developed polarizable force field is the only one so far trying to cover such a large set of possible metal ions. For the majority of metal ions, our simulations are in good agreement with experiments, demonstrating the effectiveness of our polarizable potential and the transferability of the adopted approach. PMID:28286598

Incorporation of the statistical multi-fragmentation model in PHITS and its application for simulation of fragmentation by heavy ions and protons

NASA Astrophysics Data System (ADS)

Ogawa, Tatsuhiko; Sato, Tatsuhiko; Hashimoto, Shintaro; Niita, Koji

2014-06-01

The fragmentation reactions of relativistic-energy nucleus-nucleus and proton-nucleus collisions were simulated using the Statistical Multi-fragmentation Model (SMM) incorporated with the Particle and Heavy Ion Transport code System (PHITS). The comparisons of calculated cross-sections with literature data showed that PHITS-SMM predicts the fragmentation cross-sections of heavy nuclei up to two orders of magnitude more accurately than PHITS for heavy-ion-induced reactions. For proton-induced reactions, noticeable improvements are observed for interactions of the heavy target with protons at an energy greater than 1 GeV. Therefore, consideration for multi-fragmentation reactions is necessary for the accurate simulation of energetic fragmentation reactions of heavy nuclei.

Additional application of the NASCAP code. Volume 2: SEPS, ion thruster neutralization and electrostatic antenna model

NASA Technical Reports Server (NTRS)

Katz, I.; Cassidy, J. J.; Mandell, M. J.; Parks, D. E.; Schnuelle, G. W.; Stannard, P. R.; Steen, P. G.

1981-01-01

The interactions of spacecraft systems with the surrounding plasma environment were studied analytically for three cases of current interest: calculating the impact of spacecraft generated plasmas on the main power system of a baseline solar electric propulsion stage (SEPS), modeling the physics of the neutralization of an ion thruster beam by a plasma bridge, and examining the physical and electrical effects of orbital ambient plasmas on the operation of an electrostatically controlled membrane mirror. In order to perform these studies, the NASA charging analyzer program (NASCAP) was used as well as several other computer models and analytical estimates. The main result of the SEPS study was to show how charge exchange ion expansion can create a conducting channel between the thrusters and the solar arrays. A fluid-like model was able to predict plasma potentials and temperatures measured near the main beam of an ion thruster and in the vicinity of a hollow cathode neutralizer. Power losses due to plasma currents were shown to be substantial for several proposed electrostatic antenna designs.

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+).

Si amorphization by focused ion beam milling: Point defect model with dynamic BCA simulation and experimental validation.

PubMed

Huang, J; Loeffler, M; Muehle, U; Moeller, W; Mulders, J J L; Kwakman, L F Tz; Van Dorp, W F; Zschech, E

2018-01-01

A Ga focused ion beam (FIB) is often used in transmission electron microscopy (TEM) analysis sample preparation. In case of a crystalline Si sample, an amorphous near-surface layer is formed by the FIB process. In order to optimize the FIB recipe by minimizing the amorphization, it is important to predict the amorphous layer thickness from simulation. Molecular Dynamics (MD) simulation has been used to describe the amorphization, however, it is limited by computational power for a realistic FIB process simulation. On the other hand, Binary Collision Approximation (BCA) simulation is able and has been used to simulate ion-solid interaction process at a realistic scale. In this study, a Point Defect Density approach is introduced to a dynamic BCA simulation, considering dynamic ion-solid interactions. We used this method to predict the c-Si amorphization caused by FIB milling on Si. To validate the method, dedicated TEM studies are performed. It shows that the amorphous layer thickness predicted by the numerical simulation is consistent with the experimental data. In summary, the thickness of the near-surface Si amorphization layer caused by FIB milling can be well predicted using the Point Defect Density approach within the dynamic BCA model. Copyright © 2017 Elsevier B.V. All rights reserved.

Structure factor of liquid alkali metals using a classical-plasma reference system

NASA Astrophysics Data System (ADS)

Pastore, G.; Tosi, M. P.

1984-06-01

This paper presents calculations of the liquid structure factor of the alkali metals near freezing, starting from the classical plasma of bare ions as reference liquid. The indirect ion-ion interaction arising from electronic screening is treated by an optimized random phase approximation (ORPA), imposing physical requirements as in the original ORPA scheme developed by Weeks, Chandler and Andersen for liquids with strongly repulsive core potentials. A comparison of the results with computer simulation data for a model of liquid rubidium shows that the present approach overcomes the well-known difficulties met in applying to these metals the standard ORPA based on a reference liquid of neutral hard spheres. The optimization scheme is also shown to be equivalent to a reduction of the range of the indirect interaction in momentum space, as proposed empirically in an earlier work. Comparison with experiment for the other alkalis shows that a good overall representation of the data can be obtained for sodium, potassium and cesium, but not for lithium, when one uses a very simple form of the electron-ion potential adjusted to the liquid compressibility. The small-angle scattering region is finally examined more carefully in the light of recent data of Waseda, with a view to possible refinements of the pseudopotential model.

Probing interactions of thermal Sr Rydberg atoms using simultaneous optical and ion detection

NASA Astrophysics Data System (ADS)

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

2017-06-01

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

Mechanism of Amido-Thiourea Catalyzed Enantioselective Imine Hydrocyanation: Transition State Stabilization via Multiple Non-Covalent Interactions

PubMed Central

Zuend, Stephan J.

2009-01-01

An experimental and computational investigation of amido-thiourea promoted imine hydrocyanation has revealed a new and unexpected mechanism of catalysis. Rather than direct activation of the imine by the thiourea, as had been proposed previously in related systems, the data are consistent with a mechanism involving catalyst-promoted proton transfer from hydrogen isocyanide to imine to generate diastereomeric iminium/cyanide ion pairs that are bound to catalyst through multiple non-covalent interactions; these ion pairs collapse to form the enantiomeric α-aminonitrile products. This mechanistic proposal is supported by the observation of a statistically significant correlation between experimental and calculated enantioselectivities induced by eight different catalysts (P ≪ 0.01). The computed models reveal a basis for enantioselectivity that involves multiple stabilizing and destabilizing interactions between substrate and catalyst, including thiourea-cyanide and amide-iminium interactions. PMID:19778044

Dependence of Photochemical Escape of Oxygen at Mars on Solar Radiation and Solar Wind Interaction

NASA Astrophysics Data System (ADS)

Cravens, T.; Rahmati, A.; Lillis, R. J.; Fox, J. L.; Bougher, S. W.; Jakosky, B. M.

2016-12-01

The evolution of the atmosphere of Mars and the loss of volatiles over the life of the solar system is a key topic in planetary science. An important loss process in the ionosphere is photochemical escape. In particular, dissociative recombination of O2+ ions (the major ion species) produces fast oxygen atoms, some of which can escape from the planet. Several theoretical models have been constructed over the years to study hot oxygen and its escape from Mars. These model have a number of uncertainties, particularly for the elastic cross sections of O collisions with target neutral species. Recently, the Mars Atmosphere and Volatile Evolution Mission (MAVEN) mission has been rapidly improving our understanding of the upper atmosphere and ionosphere of Mars and its interaction with the external environment (e.g., the solar wind). The purpose of the current paper is to take a simple analytical approach to the oxygen escape problem in order to: (1) study the role that solar flux and solar wind variations have on escape and (2) isolate the effects of uncertainties in oxygen cross sections on the derived oxygen escape rates. Not surprisingly, we find, in agreement with more elaborate numerical models, that the escape flux is directly proportional to the incident solar extreme ultraviolet irradiance and is inversely proportional to the backscatter elastic cross section. The role for atmospheric loss that ion transport plays in the topside ionosphere and how the solar wind interaction drives this will also be discussed.

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.

Multi-species analysis of ion distributions at Mars

NASA Astrophysics Data System (ADS)

Curry, S.; Liemohn, M. W.; Fang, X.; Ma, Y.; Johnson, B.; Bougher, S. W.; Dong, C.

2012-12-01

This study focuses on using the Mars Test Particle simulation to compare observations with virtual detections of O+, O2+, CO2+, and H+ in an orbital configuration in the Mars space environment. These planetary pick-up ions are formed when the solar wind directly interacts with the neutral atmosphere, causing the ions to be accelerated by the background convective electric field. The subsequent mass loading and ion escape are still the subject of great interest, specifically with respect to which species dominates ion loss from Mars. Modeling efforts and observations have found different results; some conclude that O+ is the most dominant escaping ion while others conclude that O2+ has the larger total loss rate. Furthermore, mass loss might actually favor CO2+ because of its tri-atomic structure. To address this unresolved issue, this study will present velocity space distributions for different species and discuss fluxes and escape rates using different modeling parameters. The simulation will also illustrate individual particle traces, which reveal the origin and trajectories of the different ion species. Finally, results from different solar conditions will be presented with respect to ion fluxes and energies as well as overall escape in order to robustly describe the physical processes controlling planetary ion distributions and atmospheric escape.

Ion properties in a Hall current thruster operating at high voltage

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

Garrigues, L., E-mail: laurent.garrigues@laplace.univ-tlse.fr

2016-04-28

Operation of a 5 kW-class Hall current Thruster for various voltages from 400 V to 800 V and a xenon mass flow rate of 6 mg s{sup −1} have been studied with a quasi-neutral hybrid model. In this model, anomalous electron transport is fitted from ion mean velocity measurements, and energy losses due to electron–wall interactions are used as a tuned parameter to match expected electron temperature strength for same class of thruster. Doubly charged ions production has been taken into account and detailed collisions between heavy species included. As the electron temperature increases, the main channel of Xe{sup 2+} ion production becomes stepwisemore » ionization of Xe{sup +} ions. For an applied voltage of 800 V, the mass utilization efficiency is in the range of 0.8–1.1, and the current fraction of doubly charged ions varies between 0.1 and 0.2. Results show that the region of ion production of each species is located at the same place inside the thruster channel. Because collision processes mean free path is larger than the acceleration region, each type of ions experiences same potential drop, and ion energy distributions of singly and doubly charged are very similar.« less

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.

Modeling of annexin A2-Membrane interactions by molecular dynamics simulations.

PubMed

Hakobyan, Davit; Gerke, Volker; Heuer, Andreas

2017-01-01

The annexins are a family of Ca2+-regulated phospholipid binding proteins that are involved in membrane domain organization and membrane trafficking. Although they are widely studied and crystal structures are available for several soluble annexins their mode of membrane association has never been studied at the molecular level. Here we obtained molecular information on the annexin-membrane interaction that could serve as paradigm for the peripheral membrane association of cytosolic proteins by Molecular Dynamics simulations. We analyzed systems containing the monomeric annexin A2 (AnxA2), a membrane with negatively charged phosphatidylserine (POPS) lipids as well as Ca2+ ions. On the atomic level we identify the AnxA2 orientations and the respective residues which display the strongest interaction with Ca2+ ions and the membrane. The simulation results fully agree with earlier experimental findings concerning the positioning of bound Ca2+ ions. Furthermore, we identify for the first time a significant interaction between lysine residues of the protein and POPS lipids that occurs independently of Ca2+ suggesting that AnxA2-membrane interactions can also occur in a low Ca2+ environment. Finally, by varying Ca2+ concentrations and lipid composition in our simulations we observe a calcium-induced negative curvature of the membrane as well as an AnxA2-induced lipid ordering.

Comparisons between GRNTRN simulations and beam measurements of proton lateral broadening distributions

NASA Astrophysics Data System (ADS)

Mertens, Christopher; Moyers, Michael; Walker, Steven; Tweed, John

Recent developments in NASA's High Charge and Energy Transport (HZETRN) code have included lateral broadening of primary ion beams due to small-angle multiple Coulomb scattering, and coupling of the ion-nuclear scattering interactions with energy loss and straggling. The new version of HZETRN based on Green function methods, GRNTRN, is suitable for modeling transport with both space environment and laboratory boundary conditions. Multiple scattering processes are a necessary extension to GRNTRN in order to accurately model ion beam experiments, to simulate the physical and biological-effective radiation dose, and to develop new methods and strategies for light ion radiation therapy. In this paper we compare GRNTRN simulations of proton lateral scattering distributions with beam measurements taken at Loma Linda Medical University. The simulated and measured lateral proton distributions will be compared for a 250 MeV proton beam on aluminum, polyethylene, polystyrene, bone, iron, and lead target materials.

On rotational dynamics of an NH4+ ion in water

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

Chang, Tsun-Mei; Dang, Liem X.

2003-05-15

We used molecular dynamics simulations to characterize the rotational dynamics of the NH4+ ion in liquid water. The polarizable potential models were to describe the ion-water and water-water interactions. This study complements the work of Karim and Haymet (J. Chem. Phys., 93, 5961, 1990), who employed effective pir potential models. The computed rotational diffusion coefficients of the NH4+ ion in water, which were determined from the angular momentum autocorrelation function and the angular mean-square displacement, are 0.093 x 1012 rad2/s and 0.067 x 1012 rad2/s, repectively. These results are in good agreement with the 0.075 x 1012 rad2/s value determinedmore » from the nuclear magnetic resonance (NMR) spectroscopy studies of Perrin and Gipe (J. Am. Chem. Soc., 108, 1088, 1986; Science, 238, 1393, 1987).« less

Interpretation with a Donnan-based concept of the influence of simple salt concentration on the apparent binding of divalent ions to the polyelectrolytes polystyrenesulfonate and dextran sulfate

USGS Publications Warehouse

Marinsky, J.A.; Baldwin, Robert F.; Reddy, M.M.

1985-01-01

It has been shown that the apparent enhancement of divalent metal ion binding to polyions such as polystyrenesulfonate (PSS) and dextran sulfate (DS) by decreasing the ionic strength of these mixed counterion systems (M2+, M+, X-, polyion) can be anticipated with the Donnan-based model developed by one of us (J.A.M.). Ion-exchange distribution methods have been employed to measure the removal by the polyion of trace divalent metal ion from simple salt (NaClO4)-polyion (NaPSS) mixtures. These data and polyion interaction data published earlier by Mattai and Kwak for the mixed counterion systems MgCl2-LiCl-DS and MgCl2-CsCl-DS have been shown to be amenable to rather precise analysis by this model. ?? 1985 American Chemical Society.

Multi-fluid MHD Study of the Solar Wind Interaction with Mars' Upper Atmosphere during the 2015 March 8th ICME Event

NASA Astrophysics Data System (ADS)

Dong, C.; Ma, Y.; Bougher, S. W.; Toth, G.; Nagy, A. F.; Halekas, J. S.; Dong, Y.; Curry, S.; Luhmann, J. G.; Brain, D. A.; Connerney, J. E. P.; Espley, J. R.; Mahaffy, P. R.; Benna, M.; McFadden, J. P.; Mitchell, D. L.; DiBraccio, G. A.; Lillis, R. J.; Jakosky, B. M.; Grebowsky, J. M.

2015-12-01

The 3-D Mars multi-fluid BATS-R-US MHD code is used to study the solar wind interaction with the Martian upper atmosphere during the 2015 March 8th interplanetary coronal mass ejection (ICME). We studied four steady-state cases, corresponding to three major ICME phases: pre-ICME phase (Case 1), sheath phase (Cases 2--3), and ejecta phase (Case 4). Detailed data-model comparisons demonstrate that the simulation results are in good agreement with Mars Atmosphere and Volatile EvolutioN (MAVEN) measurements, indicating that the multi-fluid MHD model can reproduce most of the features observed by MAVEN, thus providing confidence in the estimate of ion escape rates from its calculation. The total ion escape rate is increased by an order of magnitude, from 2.05×1024 s-1 (pre-ICME phase) to 2.25×1025 s-1 (ICME sheath phase), during this time period. The calculated ion escape rates were used to examine the relative importance of the two major ion loss channels from the planet: energetic pickup ion loss through the dayside plume and cold ionospheric ion loss through the nightside plasma wake region. We found that the energetic pickup ions escaping from the dayside plume could be as much as ~23% of the total ion loss prior to the ICME arrival. Interestingly, the tailward ion escape rate is significantly increased at the ejecta phase, leading to a reduction of the dayside ion escape to ~5% of the total ion loss. Under such circumstance, the cold ionospheric ions escaping from the plasma wake comprise the majority of the ion loss from the planet. Furthermore, by comparing four simulation results along the same MAVEN orbit, we note that there is no significant variation in the Martian lower ionosphere. Finally, both bow shock and magnetic pileup boundary (BS, MPB) locations are decreased from (1.2 RMars, 1.57 RMars) at the pre-ICME phase to (1.16 RMars, 1.47 RMars) respectively during the sheath phase along the dayside Sun-Mars line. MAVEN has provided a great opportunity to study the evolution of the Martian atmosphere and climate over its history. A large quantity of useful data has been returned for future studies. These kinds of data-model comparisons can help the community to better understand the Martian upper atmosphere response to the (extreme) variation in the solar wind and its interplanetary environment from a global perspective.

Dynamical discrete/continuum linear response shells theory of solvation: convergence test for NH4+ and OH- ions in water solution using DFT and DFTB methods.

PubMed

de Lima, Guilherme Ferreira; Duarte, Hélio Anderson; Pliego, Josefredo R

2010-12-09

A new dynamical discrete/continuum solvation model was tested for NH(4)(+) and OH(-) ions in water solvent. The method is similar to continuum solvation models in a sense that the linear response approximation is used. However, different from pure continuum models, explicit solvent molecules are included in the inner shell, which allows adequate treatment of specific solute-solvent interactions present in the first solvation shell, the main drawback of continuum models. Molecular dynamics calculations coupled with SCC-DFTB method are used to generate the configurations of the solute in a box with 64 water molecules, while the interaction energies are calculated at the DFT level. We have tested the convergence of the method using a variable number of explicit water molecules and it was found that even a small number of waters (as low as 14) are able to produce converged values. Our results also point out that the Born model, often used for long-range correction, is not reliable and our method should be applied for more accurate calculations.

Synthesis of nanoscale copper nitride thin film and modification of the surface under high electronic excitation.

PubMed

Ghosh, S; Tripathi, A; Ganesan, V; Avasthi, D K

2008-05-01

Nanoscale (approximately 90 nm) Copper nitride (Cu3N) films are deposited on borosilicate glass and Si substrates by RF sputtering technique in the reactive environment of nitrogen gas. These films are irradiated with 200 MeV Au15+ ions from Pelletron accelerator in order to modify the surface by high electronic energy deposition of heavy ions. Due to irradiation (i) at incident ion fluence of 1 x 10(12) ions/cm2 enhancement of grains, (ii) at 5 x 10912) ions/cm2 mass transport on the films surface, (iii) at 2 x 10(13) ions/cm2 line-like features on Cu3N/glass and nanometallic structures on Cu3N/Si surface are observed. The surface morphology is examined by atomic force microscope (AFM). All results are explained on the basis of a thermal spike model of ion-solid interaction.

Anomalous X-Ray Reflectivity Characterization of Ion Distribution at Biomimetic Membranes

NASA Astrophysics Data System (ADS)

Vaknin, David; Krüger, Peter; Lösche, Mathias

2003-05-01

Anomalous x-ray reflectivity measurements provides detailed information on ion binding to biomembrane surfaces. Using a monochromatic beam tuned to various x-ray energies at the Argonne National Laboratory Advanced Photon Source and utilizing a newly commissioned x-ray liquid surfaces reflectometer, measurements at and away from ion absorption edges allow determination of the distribution of these ions as they accumulate near lipid membranes. As a model, the interaction of Ba2+ ions with DMPA- (1,2-dimyristoyl-sn-glycero-3-phosphatidic acid) monolayers at the aqueous surface is studied. We find an unexpectedly large concentration of barium at the interface, ≈1.5 per DMPA-, forming a Stern layer of bound ions and a cloud of less densely bound ions near the lipid headgroups. This result can be understood only if one assumes that bound cations are partially speciated, e.g., as BaOH+.

Time-implicit fluid/particle hybrid simulations of the anode plasma dynamics in ion diodes

NASA Astrophysics Data System (ADS)

Pointon, T. D.; Boine-Frankenheim, O.; Mehlhorn, T. A.

1997-04-01

Applied-B ion diode experiments with Li+1 ion sources on the PBFA II and SABRE ion accelerators show that early in the pulse the beam is essentially pure Li+1, but is rapidly overwhelmed by impurity ions, called the `parasitic load'. Furthermore, the increasing parasitic current rapidly drops the diode voltage, limiting the accelerator power that can be coupled into the beam. This `impedance collapse' is believed to arise from the desorption of impurity neutrals from the anode surface. These neutrals charge-exchange with the ions, rapidly expanding into the anode-cathode gap where they are ionized by beam ions or secondary electrons. In order to model these processes we are developing a 1 1/2 D electrostatic multifluid/PIC (hybrid) code, designed to self-consistently simulate collisional plasma/neutral systems with an arbitrary number of interacting species, over greatly varying density regimes and together with applied electric and magnetic fields.

An ion displacement membrame model.

PubMed

Hladky, S B; Harris, J D

1967-09-01

The usual assumption in treating the diffusion of ions in an electric field has been that the movement of each ion is independent of the movement of the others. The resulting equation for diffusion by a succession of spontaneous jumps has been well stated by Parlin and Eyring. This paper will consider one simple case in which a different assumption is reasonable. Diffusion of monovalent positive ions is considered as a series of jumps from one fixed negative site to another. The sites are assumed to be full (electrical neutrality). Interaction occurs by the displacement of one ion by another. An ion leaves a site if and only if another ion, not necessarily of the same species, attempts to occupy the same site. Flux ratios and net fluxes are given as functions of the electrical potential, concentration ratios, and number of sites encountered in crossing the membrane. Quantitative comparisons with observations of Hodgkin and Keynes are presented.

Ion/Neutral, Ion/Electron, Ion/Photon, and Ion/Ion Interactions in Tandem Mass Spectrometry: Do we need them all? Are they enough?

PubMed Central

McLuckey, Scott A.; Mentinova, Marija

2011-01-01

A range of strategies and tools has been developed to facilitate the determination of primary structures of analyte molecules of interest via tandem mass spectrometry (MS/MS). The two main factors that determine the primary structural information present in an MS/MS spectrum are the type of ion generated from the analyte molecule and the dissociation method. The ion-type subjected to dissociation is determined by the ionization method/conditions and ion transformation processes that might take place after initial gas-phase ion formation. Furthermore, the range of analyte-related ion types can be expanded via derivatization reactions prior to mass spectrometry. Dissociation methods include those that simply alter the population of internal states of the mass-selected ion (i.e., activation methods like collision-induced dissociation) as well as processes that rely on transformation of the ion-type prior to dissociation (e.g., electron capture dissociation). A variety of ionic interactions has been studied for the purpose of ion dissociation and ion transformation that include ion/neutral, ion/photon, ion/electron, and ion/ion interactions. A wide range of phenomena has been observed, many of which have been explored/developed as means for structural analysis. The techniques arising from these phenomena are discussed within the context of the elements of structure determination in tandem mass spectrometry, viz., ion-type definition and dissociation. Unique aspects of the various ion interactions are emphasized along with any barriers to widespread implementation. PMID:21472539

Metal ion binding to iron oxides

NASA Astrophysics Data System (ADS)

Ponthieu, M.; Juillot, F.; Hiemstra, T.; van Riemsdijk, W. H.; Benedetti, M. F.

2006-06-01

The biogeochemistry of trace elements (TE) is largely dependent upon their interaction with heterogeneous ligands including metal oxides and hydrous oxides of iron. The modeling of TE interactions with iron oxides has been pursued using a variety of chemical models. The objective of this work is to show that it is possible to model the adsorption of protons and TE on a crystallized oxide (i.e., goethite) and on an amorphous oxide (HFO) in an identical way. Here, we use the CD-MUSIC approach in combination with valuable and reliable surface spectroscopy information about the nature of surface complexes of the TE. The other objective of this work is to obtain generic parameters to describe the binding of the following elements (Cd, Co, Cu, Ni, Pb, and Zn) onto both iron oxides for the CD-MUSIC approach. The results show that a consistent description of proton and metal ion binding is possible for goethite and HFO with the same set of model parameters. In general a good prediction of almost all the collected experimental data sets corresponding to metal ion binding to HFO is obtained. Moreover, dominant surface species are in agreement with the recently published surface complexes derived from X-ray absorption spectroscopy (XAS) data. Until more detailed information on the structure of the two iron oxides is available, the present option seems a reasonable approximation and can be used to describe complex geochemical systems. To improve our understanding and modeling of multi-component systems we need more data obtained at much lower metal ion to iron oxide ratios in order to be able to account eventually for sites that are not always characterized in spectroscopic studies.

The influence of self-assembling supramolecular structures on the passive membrane transport of ion-paired molecules.

PubMed

Benaouda, F; Brown, M B; Shah, B; Martin, G P; Jones, S A

2012-12-15

Weak ion-ion interactions, such as those associated with ion-pair formation, are difficult to isolate and characterise in the liquid state, but they have the potential to alter significantly the physicochemical behaviour of molecules in solution. The aim of this work was to gain a better understanding of how ion-ion interactions influenced passive membrane transport. The test system was composed of propylene (PG) glycol, water and diclofenac diethylamine (DDEA). Infrared spectroscopy was employed to determine the nature of the DDEA ion-pair interactions and the drug-vehicle association. Passive transport was assessed using homogeneous synthetic membranes. Solution-state analysis demonstrated that the ion-pair was unperturbed by vehicle composition changes, but the solvent-DDEA interactions were modified. DDEA-PG/water hydrogen bonding influenced the ion-pair solubility (X(dev)) and the solvent interactions slowed transport rate in PG-rich vehicles (0.84±0.05 μg cm(-2) h(-1), at ln(X(dev))=0.57). In water-rich co-solvents, the presence of strong water structuring facilitated a significant increase (p<0.05) in transmembrane penetration rate (e.g. 4.33±0.92 μg cm(-2) h(-1), at ln(X(dev))=-0.13). The data demonstrates that weak ion-ion interactions can result in the embedding of polar entities within a stable solvent complex and spontaneous supramolecular assembly should be considered when interpreting transmembrane transport processes of ionic molecules. Copyright © 2012 Elsevier B.V. All rights reserved.

Multi-charge-state molecular dynamics and self-diffusion coefficient in the warm dense matter regime

NASA Astrophysics Data System (ADS)

Fu, Yongsheng; Hou, Yong; Kang, Dongdong; Gao, Cheng; Jin, Fengtao; Yuan, Jianmin

2018-01-01

We present a multi-ion molecular dynamics (MIMD) simulation and apply it to calculating the self-diffusion coefficients of ions with different charge-states in the warm dense matter (WDM) regime. First, the method is used for the self-consistent calculation of electron structures of different charge-state ions in the ion sphere, with the ion-sphere radii being determined by the plasma density and the ion charges. The ionic fraction is then obtained by solving the Saha equation, taking account of interactions among different charge-state ions in the system, and ion-ion pair potentials are computed using the modified Gordon-Kim method in the framework of temperature-dependent density functional theory on the basis of the electron structures. Finally, MIMD is used to calculate ionic self-diffusion coefficients from the velocity correlation function according to the Green-Kubo relation. A comparison with the results of the average-atom model shows that different statistical processes will influence the ionic diffusion coefficient in the WDM regime.

Interaction of minor ions with fast and slow shocks

NASA Technical Reports Server (NTRS)

Whang, Y. C.

1990-01-01

The coronal slow shock was predicted to exist embedded in large coronal holes at 4 to 10 solar radii. A three-fluid model was used to study the jumps in minor ions propertes across the coronal slow shock. The jump conditions were formulated in the de Hoffmann-Teller frame of reference. The Rankine-Hugoniot solution determines the MHD flow and the magnetic field across the shocks. For each minor ion species, the fluid equations for the conservation of mass, momentum, and energy can be solved to determine the velocity and the temperature of the ions across the shock. A simularity solution was also obtained for heavy ions. The results show that on the downstream side of the coronal slow shock the ion temperatures are nearly proportional to the ion masses for He, O, Si, and Fe in agreement with observed ion temperatures in the inner solar wind. This indicates that the possibly existing coronal slow shock can be responsible for the observed heating of minor ions in the solar wind.

Research in pulsed power plasma physics

NASA Astrophysics Data System (ADS)

Hinshelwood, David; Rose, David

1993-11-01

The research was conducted in support of light-ion-driven inertial confinement fusion (ICF) for the Department of Energy (DOE), and nuclear weapon effects simulation (NWES) for the Defense Nuclear Agency (DNA). Accomplishments related to ion beams include: development of a practical backup approach to ion beam transport; the first studies of ion-beam interaction with a neutral gas; initial investigations of a promising industrial application of ion beam technology; and detailed theoretical evaluation of several different ion beam transport schemes. Major accomplishments relating to opening switches include: the first direct measurement of the electron density in an opening switch; detailed studies of switch conduction-time scaling; evaluation of several different switch plasma sources; and extensive studies of switch performance into diode loads, leading to the development of a new (and now generally accepted) model of switch behavior.

Sensitivity of electrospray molecular dynamics simulations to long-range Coulomb interaction models

NASA Astrophysics Data System (ADS)

Mehta, Neil A.; Levin, Deborah A.

2018-03-01

Molecular dynamics (MD) electrospray simulations of 1-ethyl-3-methylimidazolium tetrafluoroborate (EMIM-BF4) ion liquid were performed with the goal of evaluating the influence of long-range Coulomb models on ion emission characteristics. The direct Coulomb (DC), shifted force Coulomb sum (SFCS), and particle-particle particle-mesh (PPPM) long-range Coulomb models were considered in this work. The DC method with a sufficiently large cutoff radius was found to be the most accurate approach for modeling electrosprays, but, it is computationally expensive. The Coulomb potential energy modeled by the DC method in combination with the radial electric fields were found to be necessary to generate the Taylor cone. The differences observed between the SFCS and the DC in terms of predicting the total ion emission suggest that the former should not be used in MD electrospray simulations. Furthermore, the common assumption of domain periodicity was observed to be detrimental to the accuracy of the capillary-based electrospray simulations.

Sensitivity of electrospray molecular dynamics simulations to long-range Coulomb interaction models.

PubMed

Mehta, Neil A; Levin, Deborah A

2018-03-01

Molecular dynamics (MD) electrospray simulations of 1-ethyl-3-methylimidazolium tetrafluoroborate (EMIM-BF_{4}) ion liquid were performed with the goal of evaluating the influence of long-range Coulomb models on ion emission characteristics. The direct Coulomb (DC), shifted force Coulomb sum (SFCS), and particle-particle particle-mesh (PPPM) long-range Coulomb models were considered in this work. The DC method with a sufficiently large cutoff radius was found to be the most accurate approach for modeling electrosprays, but, it is computationally expensive. The Coulomb potential energy modeled by the DC method in combination with the radial electric fields were found to be necessary to generate the Taylor cone. The differences observed between the SFCS and the DC in terms of predicting the total ion emission suggest that the former should not be used in MD electrospray simulations. Furthermore, the common assumption of domain periodicity was observed to be detrimental to the accuracy of the capillary-based electrospray simulations.

Gas-phase study of new organozinc reagents by IRMPD-spectroscopy, computational modelling and tandem-MS.

PubMed

Massah, Ahmad R; Dreiocker, Frank; Jackson, Richard F W; Pickup, Barry T; Oomens, Jos; Meijer, Anthony J H M; Schäfer, Mathias

2011-08-07

An extensive set of organozinc iodides, useful for Negishi-type cross-coupling reactions, are investigated as respective cations after formal loss of iodide in the gas phase. Firstly, two new alkylzinc compounds derived from Tyrosine (Tyr) and Tryptophan (Trp) are closely examined. Secondly, the influence of specific protecting groups on the subtle balance between intra- and intermolecular coordination of zinc in these reagents is probed through trifluoroacetyl (TFA)-derivatized alkylzinc compounds. Finally, the influence of the strongly coordinating bidentate ligand N,N,N',N'-tetramethylethylenediamine (TMEDA) on the structure of alkylzinc cations is further explored in order to better understand the stability of the respective complexes towards water. A combination of electrospray (ESI)-MS/MS, accurate ion mass measurements, infrared multiple-photon dissociation (IRMPD) spectroscopy and computational modelling allowed the full characterisation of all dimethylformamide (DMF)-solvated and TMEDA-coordinated alkylzinc cations in the gas phase. The calculations indicate that the zinc cation in gas-phase alkylzinc-DMF or TMEDA-complex ions preferentially adopts a tetrahedral coordination sphere with four ligands. Additionally, conformers with only three binding partners bound to zinc but with effectively combined hydrogen-bond interactions are also found. Collision induced dissociation (CID) patterns demonstrate that the zinc-DMF interaction in tetrahedral four-coordinate mono-DMF-zinc complex ions as well as the interaction between TMEDA and zinc in the corresponding complex ions is even stronger than typical covalent bonds. In most cases, all major features of the IRMPD spectra are consistent with only a single major isomer, allowing secured identification and assignment. This journal is © the Owner Societies 2011

Application of linear pH gradients for the modeling of ion exchange chromatography: Separation of monoclonal antibody monomer from aggregates.

PubMed

Kluters, Simon; Wittkopp, Felix; Jöhnck, Matthias; Frech, Christian

2016-02-01

The mobile phase pH is a key parameter of every ion exchange chromatography process. However, mechanistic insights into the pH influence on the ion exchange chromatography equilibrium are rare. This work describes a mechanistic model capturing salt and pH influence in ion exchange chromatography. The pH dependence of the characteristic protein charge and the equilibrium constant is introduced to the steric mass action model based on a protein net charge model considering the number of amino acids interacting with the stationary phase. This allows the description of the adsorption equilibrium of the chromatographed proteins as a function of pH. The model parameters were determined for a monoclonal antibody monomer, dimer, and a higher aggregated species based on a manageable set of pH gradient experiments. Without further modification of the model parameters the transfer to salt gradient elution at fixed pH is demonstrated. A lumped rate model was used to predict the separation of the monoclonal antibody monomer/aggregate mixture in pH gradient elution and for a pH step elution procedure-also at increased protein loadings up to 48 g/L packed resin. The presented model combines both salt and pH influence and may be useful for the development and deeper understanding of an ion exchange chromatography separation. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Insights on Li-TFSI diffusion in polyethylene oxide for battery applications

NASA Astrophysics Data System (ADS)

Molinari, Nicola; Mailoa, Jonathan; Kozinsky, Boris; Robert Bosch LLC Collaboration

Improving the energy density, safety and efficiency of lithium-ion (Li-ion) batteries is crucial for the future of energy storage and applications such as electric cars. A key step in the research of next-generation solid polymeric electrolyte materials is understanding the diffusion mechanism of Li-ion in polyethylene oxide (PEO) in order to guide the design of electrolytes materials with high Li-ion diffusion while, ideally, suppress counter-anion movement. In this work we use computer simulations to investigate this long-standing problem at a fundamental level. The system under study has Li-TFSI concentration and PEO chain length that are representative of practical application specifications; the interactions of the molecular model are described via the PCFF+ all-atom force-field. Validation of the model is performed by comparing trends against experiments for diffusivity and conductivity as a function of salt concentration. The analysis of Li-TFSI molecular dynamics trajectories reveals that 1. for high Li-TFSI concentration a significant fraction of Li-ion is coordinated by only TFSI and consistently move less than PEO-coordinated Li-ion, 2. PEO chain motion is key in enabling Li-ion movement. Robert Bosch LLC.

Discrimination of ionic species from broad-beam ion sources

NASA Technical Reports Server (NTRS)

Anderson, J. R.

1993-01-01

The performance of a broad-beam, three-grid, ion extraction system incorporating radio frequency (RF) mass discrimination was investigated experimentally. This testing demonstrated that the system, based on a modified single-stage Bennett mass spectrometer, can discriminate between ionic species having about a 2-to-1 mass ratio while producing a broad-beam of ions with low kinetic energy (less than 15 eV). Testing was conducted using either argon and krypton ions or atomic and diatomic oxygen ions. A simple one-dimensional model, which ignores magnetic field and space-charge effects, was developed to predict the species separation capabilities as well as the kinetic energies of the extracted ions. The experimental results correlated well with the model predictions. This RF mass discrimination system can be used in applications where both atomic and diatomic ions are produced, but a beam of only one of the species is desired. An example of such an application is a 5 eV atomic oxygen source. This source would produce a beam of atomic oxygen with 5 eV kinetic energy, which would be directed onto a material specimen, to simulate the interaction between the surface of a satellite and the rarefied atmosphere encountered in low-Earth orbit.

A large ion beam device for laboratory solar wind studies

NASA Astrophysics Data System (ADS)

Ulibarri, Zach; Han, Jia; Horányi, Mihály; Munsat, Tobin; Wang, Xu; Whittall-Scherfee, Guy; Yeo, Li Hsia

2017-11-01

The Colorado Solar Wind Experiment is a new device constructed at the Institute for Modeling Plasma, Atmospheres, and Cosmic Dust at the University of Colorado. A large cross-sectional Kaufman ion source is used to create steady state plasma flow to model the solar wind in an experimental vacuum chamber. The plasma beam has a diameter of 12 cm at the source, ion energies of up to 1 keV, and ion flows of up to 0.1 mA/cm2. Chamber pressure can be reduced to 4 × 10-5 Torr under operating conditions to suppress ion-neutral collisions and create a monoenergetic ion beam. The beam profile has been characterized by a Langmuir probe and an ion energy analyzer mounted on a two-dimensional translation stage. The beam profile meets the requirements for planned experiments that will study solar wind interaction with lunar magnetic anomalies, the charging and dynamics of dust in the solar wind, plasma wakes and refilling, and the wakes of topographic features such as craters or boulders. This article describes the technical details of the device, initial operation and beam characterization, and the planned experiments.

The characteristics of RF modulated plasma boundary sheaths: An analysis of the standard sheath model

NASA Astrophysics Data System (ADS)

Naggary, Schabnam; Brinkmann, Ralf Peter

2015-09-01

The characteristics of radio frequency (RF) modulated plasma boundary sheaths are studied on the basis of the so-called ``standard sheath model.'' This model assumes that the applied radio frequency ωRF is larger than the plasma frequency of the ions but smaller than that of the electrons. It comprises a phase-averaged ion model - consisting of an equation of continuity (with ionization neglected) and an equation of motion (with collisional ion-neutral interaction taken into account) - a phase-resolved electron model - consisting of an equation of continuity and the assumption of Boltzmann equilibrium -, and Poisson's equation for the electrical field. Previous investigations have studied the standard sheath model under additional approximations, most notably the assumption of a step-like electron front. This contribution presents an investigation and parameter study of the standard sheath model which avoids any further assumptions. The resulting density profiles and overall charge-voltage characteristics are compared with those of the step-model based theories. The authors gratefully acknowledge Efe Kemaneci for helpful comments and fruitful discussions.

Kinetic response of ionospheric ions to onset of auroral electric fields

NASA Technical Reports Server (NTRS)

Chiu, Y. T.; Kan, J. R.

1981-01-01

By examining the exact analytic solution of a kinetic model of collisional interaction of ionospheric ions with atmospheric neutrals in the Bhatnagar-Gross-Krook approximation, we show that the onset of intense auroral electric fields in the topside ionosphere can produce the following kinetic effects: (1) heat the bulk ionospheric ions to approximately 2 eV, thus driving them up to higher altitudes where they can be subjected to collisionless plasma processes; (2) produce a non-Maxwellian superthermal tail in the distribution function; and (3) cause the ion distribution function to be anisotropic with respect to the magnetic field with the perpendicular average thermal energy exceeding the parallel thermal energy.

Fast semi-analytical method for precise prediction of ion energy distribution functions and sheath electric field in multi-frequency capacitively coupled plasmas

NASA Astrophysics Data System (ADS)

Chen, Wencong; Zhang, Xi; Diao, Dongfeng

2018-05-01

We propose a fast semi-analytical method to predict ion energy distribution functions and sheath electric field in multi-frequency capacitively coupled plasmas, which are difficult to measure in commercial plasma reactors. In the intermediate frequency regime, the ion density within the sheath is strongly modulated by the low-frequency sheath electric field, making the time-independent ion density assumption employed in conventional models invalid. Our results are in a good agreement with experimental measurements and computer simulations. The application of this method will facilitate the understanding of ion–material interaction mechanisms and development of new-generation plasma etching devices.

On the role of Fe ions on magnetic properties of doped TiO2 nanoparticles

NASA Astrophysics Data System (ADS)

Tolea, F.; Grecu, M. N.; Kuncser, V.; Constantinescu, S. Gr.; Ghica, D.

2015-04-01

The role of iron doping on magnetic properties of hydrothermal anatase TiO2:57Fe (0-1 at. %) nanoparticles is investigated by combining superconducting quantum interference device magnetometry with Mössbauer and electron paramagnetic resonance techniques. The results on both as-prepared and thermally treated samples in reduced air atmosphere reveal complexity of magnetic interactions, in connection to certain iron ion electron configurations and defects (oxygen vacancies, F-center, and Ti3+ ions). The distribution of iron ions is predominantly at nanoparticle surface layers. Formation of weak ferromagnetic domains up to 380 K is mainly related to defects, supporting the bound magnetic polaron model.

Solvation behavior of carbonate-based electrolytes in sodium ion batteries.

PubMed

Cresce, Arthur V; Russell, Selena M; Borodin, Oleg; Allen, Joshua A; Schroeder, Marshall A; Dai, Michael; Peng, Jing; Gobet, Mallory P; Greenbaum, Steven G; Rogers, Reginald E; Xu, Kang

2016-12-21

Sodium ion batteries are on the cusp of being a commercially available technology. Compared to lithium ion batteries, sodium ion batteries can potentially offer an attractive dollar-per-kilowatt-hour value, though at the penalty of reduced energy density. As a materials system, sodium ion batteries present a unique opportunity to apply lessons learned in the study of electrolytes for lithium ion batteries; specifically, the behavior of the sodium ion in an organic carbonate solution and the relationship of ion solvation with electrode surface passivation. In this work the Li + and Na + -based solvates were characterized using electrospray mass spectrometry, infrared and Raman spectroscopy, 17 O, 23 Na and pulse field gradient double-stimulated-echo pulse sequence nuclear magnetic resonance (NMR), and conductivity measurements. Spectroscopic evidence demonstrate that the Li + and Na + cations share a number of similar ion-solvent interaction trends, such as a preference in the gas and liquid phase for a solvation shell rich in cyclic carbonates over linear carbonates and fluorinated carbonates. However, quite different IR spectra due to the PF 6 - anion interactions with the Na + and Li + cations were observed and were rationalized with the help of density functional theory (DFT) calculations that were also used to examine the relative free energies of solvates using cluster - continuum models. Ion-solvent distances for Na + were longer than Li + , and Na + had a greater tendency towards forming contact pairs compared to Li + in linear carbonate solvents. In tests of hard carbon Na-ion batteries, performance was not well correlated to Na + solvent preference, leading to the possibility that Na + solvent preference may play a reduced role in the passivation of anode surfaces and overall Na-ion battery performance.

Sequential water molecule binding enthalpies for aqueous nanodrops containing a mono-, di- or trivalent ion and between 20 and 500 water molecules† †Electronic supplementary information (ESI) available: Detailed description of the experimental and computational modeling methods. Isolation, BIRD and UVPD sequence for [Ru(NH3)6]3+·(H2O)169–171, nanoESI spectra for 2+ and 3+ ions. Detailed description of the isotope distribution simulation program. Comparison between experimental and simulated 1+, 2+ and 3+ ion isotope distributions. Wavelength dependence of the deduced sequential binding enthalpies. Comparison of experimental UVPD binding enthalpies to the liquid drop model at different temperatures. Complete list of binding enthalpies and average number of water molecules lost upon UVPD. See DOI: 10.1039/c6sc04957e Click here for additional data file.

PubMed Central

Heiles, Sven; Cooper, Richard J.; DiTucci, Matthew J.

2017-01-01

Sequential water molecule binding enthalpies, ΔH n,n–1, are important for a detailed understanding of competitive interactions between ions, water and solute molecules, and how these interactions affect physical properties of ion-containing nanodrops that are important in aerosol chemistry. Water molecule binding enthalpies have been measured for small clusters of many different ions, but these values for ion-containing nanodrops containing more than 20 water molecules are scarce. Here, ΔH n,n–1 values are deduced from high-precision ultraviolet photodissociation (UVPD) measurements as a function of ion identity, charge state and cluster size between 20–500 water molecules and for ions with +1, +2 and +3 charges. The ΔH n,n–1 values are obtained from the number of water molecules lost upon photoexcitation at a known wavelength, and modeling of the release of energy into the translational, rotational and vibrational motions of the products. The ΔH n,n–1 values range from 36.82 to 50.21 kJ mol–1. For clusters containing more than ∼250 water molecules, the binding enthalpies are between the bulk heat of vaporization (44.8 kJ mol–1) and the sublimation enthalpy of bulk ice (51.0 kJ mol–1). These values depend on ion charge state for clusters with fewer than 150 water molecules, but there is a negligible dependence at larger size. There is a minimum in the ΔH n,n–1 values that depends on the cluster size and ion charge state, which can be attributed to the competing effects of ion solvation and surface energy. The experimental ΔH n,n–1 values can be fit to the Thomson liquid drop model (TLDM) using bulk ice parameters. By optimizing the surface tension and temperature change of the logarithmic partial pressure for the TLDM, the experimental sequential water molecule binding enthalpies can be fit with an accuracy of ±3.3 kJ mol–1 over the entire range of cluster sizes. PMID:28451364

Safety focused modeling of lithium-ion batteries: A review

NASA Astrophysics Data System (ADS)

Abada, S.; Marlair, G.; Lecocq, A.; Petit, M.; Sauvant-Moynot, V.; Huet, F.

2016-02-01

Safety issues pertaining to Li-ion batteries justify intensive testing all along their value chain. However, progress in scientific knowledge regarding lithium based battery failure modes, as well as remarkable technologic breakthroughs in computing science, now allow for development and use of prediction tools to assist designers in developing safer batteries. Subsequently, this paper offers a review of significant modeling works performed in the area with a focus on the characterization of the thermal runaway hazard and their relating triggering events. Progress made in models aiming at integrating battery ageing effect and related physics is also discussed, as well as the strong interaction with modeling-focused use of testing, and the main achievements obtained towards marketing safer systems. Current limitations and new challenges or opportunities that are expected to shape future modeling activity are also put in perspective. According to market trends, it is anticipated that safety may still act as a restraint in the search for acceptable compromise with overall performance and cost of lithium-ion based and post lithium-ion rechargeable batteries of the future. In that context, high-throughput prediction tools capable of screening adequate new components properties allowing access to both functional and safety related aspects are highly desirable.

Theory of Alike Selectivity in Biological Channels

NASA Technical Reports Server (NTRS)

Luchinsky, Dmitry G.; Gibby, Will A. T.; Kaufman, Igor Kh.; Eisenberg, Robert S.; McClintock, Peter V. E.

2016-01-01

We introduce a statistical mechanical model of the selectivity filter that accounts for the interaction between ions within the channel and derive Eisenman equation of the filter selectivity directly from the condition of barrier-less conduction.

Complete devil's staircase and crystal-superfluid transitions in a dipolar XXZ spin chain: a trapped ion quantum simulation

NASA Astrophysics Data System (ADS)

Hauke, Philipp; Cucchietti, Fernando M.; Müller-Hermes, Alexander; Bañuls, Mari-Carmen; Cirac, J. Ignacio; Lewenstein, Maciej

2010-11-01

Systems with long-range interactions show a variety of intriguing properties: they typically accommodate many metastable states, they can give rise to spontaneous formation of supersolids, and they can lead to counterintuitive thermodynamic behavior. However, the increased complexity that comes with long-range interactions strongly hinders theoretical studies. This makes a quantum simulator for long-range models highly desirable. Here, we show that a chain of trapped ions can be used to quantum simulate a one-dimensional (1D) model of hard-core bosons with dipolar off-site interaction and tunneling, equivalent to a dipolar XXZ spin-1/2 chain. We explore the rich phase diagram of this model in detail, employing perturbative mean-field theory, exact diagonalization and quasi-exact numerical techniques (density-matrix renormalization group and infinite time-evolving block decimation). We find that the complete devil's staircase—an infinite sequence of crystal states existing at vanishing tunneling—spreads to a succession of lobes similar to the Mott lobes found in Bose-Hubbard models. Investigating the melting of these crystal states at increased tunneling, we do not find (contrary to similar 2D models) clear indications of supersolid behavior in the region around the melting transition. However, we find that inside the insulating lobes there are quasi-long-range (algebraic) correlations, as opposed to models with nearest-neighbor tunneling, that show exponential decay of correlations.

Interaction between Silver Nanoparticles and Spinach Leaf

NASA Astrophysics Data System (ADS)

Tian, Y.; Li, H.; Zhang, Y.; Riser, E.; He, S.; Zhang, W.

2013-12-01

Interactions of engineered nanoparticles (ENPs) with plant surfaces are critical to assessing the bioavailability of ENPs to edible plants and to further evaluating impacts of ENPs on ecological health and food safety. Silver nanoparticles (i.e., nanoAg) could enter the agroecosystems either as an active ingredient in pesticides or from other industrial and consumer applications. Thus, in the events of pesticide application, rainfall, and irrigation, vegetable leaves could become in contact and then interact with nanoAg. The present study was to assess whether the interaction of nanoAg with spinach leaves can be described by classical sorption models and to what extent it depends on and varies with dispersion methods, environmental temperature, and ion release. We investigated the stability and ion release of nanoAg dispersed by sodium dodecyl sulfate (SDS, 1%) and humic acid (HA, 10 mg C/L) solutions, as well as sorption and desorption of nanoAg on and from the fresh spinach leaf. Results showed SDS-nanoAg released about 2%-8% more Ag ion than HA-nanoAg. The sorption of Ag ion, described by the Freundlich model in the initial concentration range of 0.6-50 mg/L, was 2-4 times higher than that of nanoAg. The sorption of nanoAg on spinach leaf can be fitted by the Langmuir model, and the maximum sorption amount of HA-nanoAg and SDS-nanoAg was 0.21 and 0.41 mg/g, respectively. The higher sorption of SDS-nanoAg relative to that of HA-nanoAg could be partially resulted from the higher release of Ag ion from the former. The maximum desorption amount of HA-nanoAg and SDS-nanoAg in 1% SDS solution was 0.08 and 0.10 mg/g, respectively. NanoAg attachment on and its penetration to the spinach leaf was visualized by the Scanning Electron Microscope equipped with an Energy Dispersive Spectrometer (SEM-EDS). It is equally important that the less sorption of nanoAg under low environmental temperature could be partially due to the closure of stomata, as verified by SEM-EDS. CytoViva Hyperspectral Imaging System was also employed to map the distribution of nanoAg in the leaf profile. Significant sorption of nanoAg on spinach leaf should urge the precaution with potential widespread use of ENPs in agriculture.

Densities and apparent molar volumes of atmospherically important electrolyte solutions. 2. The systems H(+)-HSO4(-)-SO4(2-)-H2O from 0 to 3 mol kg(-1) as a function of temperature and H(+)-NH4(+)-HSO4(-)-SO4)2-)-H2O from 0 to 6 mol kg(-1) at 25 °C using a Pitzer ion interaction model, and NH4HSO4-H2O and (NH4)3H(SO4)2-H2O over the entire concentration range.

PubMed

Clegg, S L; Wexler, A S

2011-04-21

A Pitzer ion interaction model has been applied to the systems H(2)SO(4)-H(2)O (0-3 mol kg(-1), 0-55 °C) and H(2)SO(4)-(NH(4))(2)SO(4)-H(2)O (0-6 mol kg(-1), 25 °C) for the calculation of apparent molar volume and density. The dissociation reaction HSO(4)(-)((aq)) ↔ H(+)((aq)) + SO(4)(2-)((aq)) is treated explicitly. Apparent molar volumes of the SO(4)(2-) ion at infinite dilution were obtained from part 1 of this work, (1) and the value for the bisulfate ion was determined in this study from 0 to 55 °C. In dilute solutions of both systems, the change in the degree of dissociation of the HSO(4)(-) ion with concentration results in much larger variations of the apparent molar volumes of the solutes than for conventional strong (fully dissociated) electrolytes. Densities and apparent molar volumes are tabulated. Apparent molar volumes calculated using the model are combined with other data for the solutes NH(4)HSO(4) and (NH(4))(3)H(SO(4))(2) at 25 °C to obtain apparent molar volumes and densities over the entire concentration range (including solutions supersaturated with respect to the salts).

Dynamical thermalization in isolated quantum dots and black holes

NASA Astrophysics Data System (ADS)

Kolovsky, Andrey R.; Shepelyansky, Dima L.

2017-01-01

We study numerically a model of quantum dot with interacting fermions. At strong interactions with small conductance the model is reduced to the Sachdev-Ye-Kitaev black-hole model while at weak interactions and large conductance it describes a Landau-Fermi liquid in a regime of quantum chaos. We show that above the Åberg threshold for interactions there is an onset of dynamical themalization with the Fermi-Dirac distribution describing the eigenstates of an isolated dot. At strong interactions in the isolated black-hole regime there is also the onset of dynamical thermalization with the entropy described by the quantum Gibbs distribution. This dynamical thermalization takes place in an isolated system without any contact with a thermostat. We discuss the possible realization of these regimes with quantum dots of 2D electrons and cold ions in optical lattices.

Silver ions-mediated conformational switch: facile design of structure-controllable nucleic acid probes.

PubMed

Wang, Yongxiang; Li, Jishan; Wang, Hao; Jin, Jianyu; Liu, Jinhua; Wang, Kemin; Tan, Weihong; Yang, Ronghua

2010-08-01

Conformationally constraint nucleic acid probes were usually designed by forming an intramolecular duplex based on Watson-Crick hydrogen bonds. The disadvantages of these approaches are the inflexibility and instability in complex environment of the Watson-Crick-based duplex. We report that this hydrogen bonding pattern can be replaced by metal-ligation between specific metal ions and the natural bases. To demonstrate the feasibility of this principle, two linear oligonucleotides and silver ions were examined as models for DNA hybridization assay and adenosine triphosphate detection. The both nucleic acids contain target binding sequences in the middle and cytosine (C)-rich sequences at the lateral portions. The strong interaction between Ag(+) ions and cytosines forms stable C-Ag(+)-C structures, which promises the oligonucleotides to form conformationally constraint formations. In the presence of its target, interaction between the loop sequences and the target unfolds the C-Ag(+)-C structures, and the corresponding probes unfolding can be detected by a change in their fluorescence emission. We discuss the thermodynamic and kinetic opportunities that are provided by using Ag(+) ion complexes instead of traditional Watson-Crick-based duplex. In particular, the intrinsic feature of the metal-ligation motif facilitates the design of functional nucleic acids probes by independently varying the concentration of Ag(+) ions in the medium.

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.

Importance of Ambipolar Electric Field in the Ion Loss from Mars- Results from a Multi-fluid MHD Model with the Electron Pressure Equation Included

NASA Astrophysics Data System (ADS)

Ma, Y.; Dong, C.; van der Holst, B.; Nagy, A. F.; Bougher, S. W.; Toth, G.; Cravens, T.; Yelle, R. V.; Jakosky, B. M.

2017-12-01

The multi-fluid (MF) magnetohydrodynamic (MHD) model of Mars is further improved by solving an additional electron pressure equation. Through the electron pressure equation, the electron temperature is calculated based on the effects from various electrons related heating and cooling processes (e.g. photo-electron heating, electron-neutral collision and electron-ion collision), and thus the improved model is able to calculate the electron temperature and the electron pressure force self-consistently. Electron thermal conductivity is also considered in the calculation. Model results of a normal case with electron pressure equation included (MFPe) are compared in detail to an identical case using the regular MF model to identify the effect of the improved physics. We found that when the electron pressure equation is included, the general interaction patterns are similar to that of the case with no electron pressure equation. The model with electron pressure equation predicts that electron temperature is much larger than the ion temperature in the ionosphere, consistent with both Viking and MAVEN observations. The inclusion of electron pressure equation significantly increases the total escape fluxes predicted by the model, indicating the importance of the ambipolar electric field(electron pressure gradient) in driving the ion loss from Mars.

Hylleraas-Configuration Interaction study of the 1S ground state of the negative Li ion.

PubMed

Sims, James S

2017-12-28

In a previous work Sims and Hagstrom [J. Chem. Phys. 140, 224312 (2014)] reported Hylleraas-Configuration Interaction (Hy-CI) method variational calculations for the neutral atom and positive ion 1 S ground states of the beryllium isoelectronic sequence. The Li - ion, nominally the first member of this series, has a decidedly different electronic structure. This paper reports the results of a large, comparable calculation for the Li - ground state to explore how well the Hy-CI method can represent the more diffuse L shell of Li - which is representative of the Be(2sns) excited states as well. The best non-relativistic energy obtained was -7.500 776 596 hartree, indicating that 10 - 20 nh accuracy is attainable in Hy-CI and that convergence of the r 12 r 34 double cusp is fast and that this correlation type can be accurately represented within the Hy-CI model.

Experimental characterization of a transition from collisionless to collisional interaction between head-on-merging supersonic plasma jets

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

Moser, Auna L., E-mail: mosera@fusion.gat.com; Hsu, Scott C., E-mail: scotthsu@lanl.gov

We present results from experiments on the head-on merging of two supersonic plasma jets in an initially collisionless regime for the counter-streaming ions. The plasma jets are of either an argon/impurity or hydrogen/impurity mixture and are produced by pulsed-power-driven railguns. Based on time- and space-resolved fast-imaging, multi-chord interferometry, and survey-spectroscopy measurements of the overlapping region between the merging jets, we observe that the jets initially interpenetrate, consistent with calculated inter-jet ion collision lengths, which are long. As the jets interpenetrate, a rising mean-charge state causes a rapid decrease in the inter-jet ion collision length. Finally, the interaction becomes collisional andmore » the jets stagnate, eventually producing structures consistent with collisional shocks. These experimental observations can aid in the validation of plasma collisionality and ionization models for plasmas with complex equations of state.« less

Focused helium-ion-beam-induced deposition

NASA Astrophysics Data System (ADS)

Alkemade, P. F. A.; Miro, H.

2014-12-01

The recent introduction of the helium ion microscope (HIM) offers new possibilities for materials modification and fabrication with spatial resolution below 10 nm. In particular, the specific interaction of He+ ions in the tens of keV energy range with materials—i.e., minimal deflection and mainly energy loss via electronic excitations—renders the HIM a special tool for ion-beam-induced deposition. In this work, an overview is given of all studies of helium-ion-beam-induced deposition (He-IBID) that appeared in the literature before summer 2014. Continuum models that describe the deposition processes are presented in detail, with emphasis on precursor depletion and replenishment. In addition, a Monte Carlo model is discussed. Basic experimental He-IBID studies are critically examined. They show deposition rates of up to 0.1 nm3/ion. Analysis by means of a continuum model yields the precursor diffusion constant and the cross sections for beam-induced precursor decomposition and beam-induced desorption. Moreover, it is shown that deposition takes place only in a small zone around the beam impact point. Furthermore, the characterization of deposited materials is discussed in terms of microstructure and resistivity. It is shown that He-IBID material resembles more electron-beam-induced-deposition (EBID) material than Ga-ion-beam-induced-deposition (Ga-IBID) material. Nevertheless, the spatial resolution for He-IBID is in general better than for EBID and Ga-IBID; in particular, proximity effects are minimal.

Rydberg Excitation of a Single Trapped Ion.

PubMed

Feldker, T; Bachor, P; Stappel, M; Kolbe, D; Gerritsma, R; Walz, J; Schmidt-Kaler, F

2015-10-23

We demonstrate excitation of a single trapped cold (40)Ca(+) ion to Rydberg levels by laser radiation in the vacuum ultraviolet at a wavelength of 122 nm. Observed resonances are identified as 3d(2)D(3/2) to 51F, 52F and 3d(2)D(5/2) to 64F. We model the line shape and our results imply a large state-dependent coupling to the trapping potential. Rydberg ions are of great interest for future applications in quantum computing and simulation, in which large dipolar interactions are combined with the superb experimental control offered by Paul traps.

Positive ion temperature effect on the plasma-wall transition

NASA Astrophysics Data System (ADS)

Morales Crespo, R.

2018-06-01

This paper analyses the plasma-wall interaction of a plasma in contact with a conducting planar surface when the positive-ion temperature is not negligible compared with the electron one. The electric potential from the plasma to the wall is obtained by the appropriate formulation of the model as an initial-value problem as well as some features useful for experimental applications, such as the positive current-to-voltage characteristics, the saturation current density, the floating potential or an estimation of the sheath thickness. Finally, it is analysed how all these quantities depend on the ionization degree and the positive-ion temperature.

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

Omelchenko, Yuri A.

Global interactions of energetic ions with magnetoplasmas and neutral gases lie at the core of many space and laboratory plasma phenomena ranging from solar wind entry into and transport within planetary magnetospheres and exospheres to fast-ion driven instabilities in fusion devices to astrophysics-in-lab experiments. The ability of computational models to properly account for physical effects that underlie such interactions, namely ion kinetic, ion cyclotron, Hall, collisional and ionization processes is important for the success and planning of experimental research in plasma physics. Understanding the physics of energetic ions, in particular their nonlinear resonance interactions with Alfvén waves, is central tomore » improving the heating performance of magnetically confined plasmas for future energy generation. Fluid models are not adequate for high-beta plasmas as they cannot fully capture ion kinetic and cyclotron physics (e.g., ion behavior in the presence of magnetic nulls, shock structures, plasma interpenetration, etc.). Recent results from global reconnection simulations show that even in a MHD-like regime there may be significant differences between kinetic and MHD simulations. Therefore, kinetic modeling becomes essential for meeting modern day challenges in plasma physics. The hybrid approximation is an intermediate approximation between the fluid and fully kinetic approximations. It eliminates light waves, removes the electron inertial temporal and spatial scales from the problem and enables full-orbit ion kinetics. As a result, hybrid codes have become effective tools for exploring ion-scale driven phenomena associated with ion beams, shocks, reconnection and turbulence that control the large-scale behavior of laboratory and space magnetoplasmas. A number of numerical issues, however, make three-dimensional (3D) large-scale hybrid simulations of inhomogeneous magnetized plasmas prohibitively expensive or even impossible. To resolve these difficulties we have developed a novel Event-driven Multiscale Asynchronous Parallel Simulation (EMAPS) technology that replaces time stepping with self-adaptive update events. Local calculations are carried out only on an “as needed basis”. EMAPS (i) guarantees accurate and stable processing of physical variables in time accurate simulations, and (ii) eliminates unnecessary computation. Applying EMAPS to the hybrid model has resulted in the development of a unique parallel code, dimension-independent (compile-time-configurable) HYPERS (Hybrid Parallel Event-Resolved Simulator) that scales to hundreds of thousands of parallel processors. HYPERS advances electromagnetic fields and particles asynchronously on time scales determined by local physical laws and mesh properties. To achieve high computational accuracy in complex device geometries, HYPERS employs high-fidelity Cartesian grids with masked conductive cells. The HYPERS model includes multiple ion species, energy and momentum conserving ion-ion collisions, and provides a number of approximations for plasma resistivity and vacuum regions. Both local and periodic boundary conditions are allowed. The HYPERS solver preserves zero divergence of magnetic field. The project has demonstrated HYPERS capabilities on a number of applications of interest to fusion and astrophysical plasma physics applications listed below. 1. Theta-pinch formation of FRCs The formation, spontaneous spin-up, and stability of theta-pinch formed field-reversed configurations have been studied self-consistently in 3D. The end-to-end hybrid simulations reveal poloidal profiles of implosion-driven fast toroidal plasma rotation and demonstrate three discharge regimes as a function of experimental parameters: the decaying stable configuration, the tilt unstable configuration, and the nonlinear evolution of a fast growing tearing mode. 2. FRC collisions with magnetic mirrors Interactions of fast plasma streams and objects with magnetic obstacles (dipoles, mirrors, etc) lie at the core of many space and laboratory plasma phenomena ranging from magnetoshells and solar wind interactions with planetary magnetospheres to compact fusion plasmas. HYPERS simulations are compared with data from the MSX experiment (LANL) that focuses on the physics of magnetized collisionless shocks through the acceleration and subsequent stagnation of FRC plasmoids against a strong magnetic mirrors and flux-conserving boundaries. 3. Exploding magnetoplasmas Results from hybrid simulations of two experiments at the LAPD and Nevada Terawatt Facility are discussed where short-pulse lasers are used to ablate solid targets to produce plasmas that expand across external magnetic fields. The first simulation recreates flutelike density striations observed at the leading edge of a carbon plasma and predicts an early destruction of the magnetic cavity in agreement with experimental evidence. In the second simulation a polyethylene target is ablated into a mixture of protons and carbon ions. A mechanism is demonstrated that allows protons to penetrate the magnetic field in the form of a collimated flow. The results are compared to experimental data and single-fluid MHD simulations. The EMAPS framework has the potential for wide application in many other engineering and scientific fields, such as climate models, biological systems, electronic devices, seismic events, oil reservation simulators that all involve advancing solutions of partial differential equations in time where the rate of activity can be adapted widely over the spatial domain depending on locally space/time phenomena (“events”).« less

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.

Data Reduction and Analysis of Pioneer Venus Orbital Ion Mass Spectrometer

NASA Technical Reports Server (NTRS)

Cloutier, Paul A.

1996-01-01

Research was carried out on developing a flow field interaction model for both the dayside and nightside ionosphere of Venus. Specific topics related to the dayside ionosphere included: (1) wave particle mechanisms at the ionopause, (2) structure and dynamics of the Venus ionopause and Ionosphere, and (3) flows and fields in the Venus Ionosphere. The structure and dynamics of ion troughs was also studied in the nightside ionosphere of Venus.

Solar wind interaction with dusty plasmas produces instabilities and solitary structures

NASA Astrophysics Data System (ADS)

Saleem, H.; Ali, S.

2017-12-01

It is pointed out that the solar wind interaction with dusty magnetospheres of the planets can give rise to purely growing instabilities as well as nonlinear electric field structures. Linear dispersion relation of the low frequency electrostatic ion-acoustic wave (IAW) is modified in the presence of stationary dust and its frequency becomes larger than its frequency in usual electron ion plasma even if ion temperature is equal to the electron temperature. This dust-ion-acoustic wave (DIAW) either becomes a purely growing electrostatic instability or turns out to be the modified dust-ion-acoustic wave (mDIAW) depending upon the magnitude of shear flow scale length and its direction. Growth rate of shear flow-driven electrostatic instability in a plasma having negatively charged stationary dust is larger than the usual D'Angelo instability of electron-ion plasma. It is shown that shear modified dust ion acoustic wave (mDIAW) produces electrostatic solitons in the nonlinear regime. The fluid theory predicts the existence of electrostatic solitons in the dusty plasmas in those regions where the inhomogeneous solar wind flow is parallel to the planetary or cometary magnetic field lines. The amplitude and width of the solitary structure depends upon dust density and magnitude of shear in the flow. This is a general theoretical model which is applied to dusty plasma of Saturn's F-ring for illustration.

Cellulose Nanofibrils and Mechanism of their Mineralization in Biomimetic Synthesis of Hydroxyapatite/Native Bacterial Cellulose Nanocomposites: Molecular Dynamics Simulations.

PubMed

Lukasheva, N V; Tolmachev, D A

2016-01-12

Molecular dynamics (MD) simulation of a nanofibril of native bacterial cellulose (BC) in solutions of mineral ions is presented. The supersaturated calcium-phosphate (CP) solution with the ionic composition of hydroxyapatite and CaCl2 solutions with the concentrations below, equal to, and above the solubility limits are simulated. The influence of solvation models (TIP3P and TIP4P-ew water models) on structural characteristics of the simulated nanofibril and on the crystal nucleation process is assessed. The structural characteristics of cellulose nanofibrils (in particular, of the surface layer) are found to be nearly independent of the solvation models used in the simulation and on the presence of ions in the solutions. It is shown that ionic clusters are formed in the solution rather than on the fibril surface. The cluster sizes are slightly different for the two water models. The effect of the ion-ion interaction parameters on the results is discussed. The main conclusion is that the activity of hydroxyl groups on the BC fibril surface is not high enough to cause adsorption of Ca(2+) ions from the solution. Therefore, the nucleation of CP crystals takes place initially in solution, and then the crystallites formed can be adsorbed on BC nanofibril surfaces.

Deuterium charge exchange recombination spectroscopy from the top of the pedestal to the scrape off layer in H-mode plasmas

NASA Astrophysics Data System (ADS)

Haskey, S. R.; Grierson, B. A.; Stagner, L.; Burrell, K. H.; Chrystal, C.; Groebner, R. J.; Ashourvan, A.; Pablant, N. A.

2017-10-01

Recent completion of the thirty two channel main-ion (deuterium) charge exchange recombination spectroscopy (CER) diagnostic on DIII-D [J.L. Luxon, Nucl. Fusion 42 (2002) 614] enables detailed comparisons between impurity and main-ion temperature, density, and toroidal rotation. Sixteen sightlines cover the core of the plasma and another sixteen are densely packed towards the edge, providing high resolution measurements of the pedestal and steep gradient edge region of H-mode plasmas. The complexities of the Dα spectrum require fitting with a comprehensive model, as well as using iterative collisional radiative modeling to determine the underlying thermal deuterium ion properties. Large differences in the structure and magnitude of impurity (C6+) and main-ion (D+) toroidal rotation profiles are seen in the H-mode pedestal. Additionally the D+ temperature can be half the value of the C6+ temperature at the separatrix and shows more of a pedestal structure. Typically only the impurity properties are measured and the main-ion properties are either assumed to be the same, or inferred using neoclassical models, which require validation in the steep gradient region. These measured differences have implications for transport model validation, intrinsic rotation studies, pedestal stability, and the boundary conditions for scrape off layer and plasma material interactions studies.

Deuterium charge exchange recombination spectroscopy from the top of the pedestal to the scrape off layer in H-mode plasmas

DOE PAGES

Haskey, S. R.; Grierson, B. A.; Stagner, L.; ...

2017-10-25

Recent completion of the thirty two channel main-ion (deuterium) charge exchange recombination spectroscopy (CER) diagnostic on DIII-D enables detailed comparisons between impurity and main-ion temperature, density, and toroidal rotation. Sixteen sightlines cover the core of the plasma and another sixteen are densely packed towards the edge, providing high resolution measurements of the pedestal and steep gradient edge region of H-mode plasmas. The complexities of the D α spectrum require fitting with a comprehensive model, as well as using iterative collisional radiative modeling to determine the underlying thermal deuterium ion properties. Large differences in the structure and magnitude of impurity (Cmore » 6+) and main-ion (D +) toroidal rotation profiles are seen in the H-mode pedestal. Additionally the D + temperature can be half the value of the C 6+ temperature at the separatrix and shows more of a pedestal structure. Typically only the impurity properties are measured and the main-ion properties are either assumed to be the same, or inferred using neoclassical models, which require validation in the steep gradient region. Furthermore, these measured differences have implications for transport model validation, intrinsic rotation studies, pedestal stability, and the boundary conditions for scrape off layer and plasma material interactions studies.« less

Influence of nanoparticle-ion and nanoparticle-polymer interactions on ion transport and viscoelastic properties of polymer electrolytes

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

Mogurampelly, Santosh; Sethuraman, Vaidyanathan; Pryamitsyn, Victor

We use atomistic simulations to probe the ion conductivities and mechanical properties of polyethylene oxide electrolytes containing Al{sub 2}O{sub 3} nanoparticles. We specifically study the influence of repulsive polymer-nanoparticle and ion-nanoparticle interactions and compare the results with those reported for electrolytes containing the polymorph β-Al{sub 2}O{sub 3} nanoparticles. We observe that incorporating repulsive nanoparticle interactions generally results in increased ionic mobilities and decreased elastic moduli for the electrolyte. Our results indicate that both ion transport and mechanical properties are influenced by the polymer segmental dynamics in the interfacial zones of the nanoparticle in the ion-doped systems. Such effects were seenmore » to be determined by an interplay between the nanoparticle-polymer, nanoparticle-ion, and ion-polymer interactions. In addition, such interactions were also observed to influence the number of dissociated ions and the resulting conductivities. Within the perspective of the influence of nanoparticles on the polymer relaxation times in ion-doped systems, our results in the context of viscoelastic properties were consistent with the ionic mobilities. Overall, our results serve to highlight some issues that confront the efforts to use nanoparticle dispersions to simultaneously enhance the conductivity and the mechanical strength of polymer electrolyte.« less

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)

High pressure luminescence of Nd3+ in YAlO3 perovskite nanocrystals: A crystal-field analysis

NASA Astrophysics Data System (ADS)

Hernández-Rodríguez, Miguel A.; Muñoz-Santiuste, Juan E.; Lavín, Víctor; Lozano-Gorrín, Antonio D.; Rodríguez-Hernández, Plácida; Muñoz, Alfonso; Venkatramu, Vemula; Martín, Inocencio R.; Rodríguez-Mendoza, Ulises R.

2018-01-01

Pressure-induced energy blue- and red-shifts of the 4F3/2 → 4I9/2,11/2 near-infrared emission lines of Nd3+ ions in YAlO3 perovskite nano-particles have been measured from ambient conditions up to 29 GPa. Different positive and negative linear pressure coefficients have been calibrated for the emission lines and related to pressure-induced changes in the interactions between those Nd3+ ions and their twelve oxygen ligands at the yttrium site. Potentiality of the simple overlap model, combined with ab initio structural calculations, in the description of the effects of these interactions on the energy levels and luminescence properties of the optically active Nd3+ ion is emphasized. Simulations show how the energies of the 4f3 ground configuration and the barycenters of the multiplets increase with pressure, whereas the Coulomb interaction between f-electrons decreases and the crystal-field strength increases. All these effects combined explain the wavelength blue-shifts of some near-infrared emission lines of Nd3+ ions. Large pressure rates of various emission lines suggest that a YAlO3 perovskite nano-crystal can be a potential candidate for near-infrared optical pressure sensors.

The interplay of ion crosslinking, free ion content, and polymer mobility in PEO-based single-ion conductors

NASA Astrophysics Data System (ADS)

Lin, Kan-Ju; Maranas, Janna

2010-03-01

We use molecular dynamics simulation to study ion clustering and dynamics in ion containing polymers. This PEO based single-ion conducting ionomer serves as a model system for understanding cation transport in solid state polymer electrolytes (SPEs). Although small-angle x-ray scattering does not show an ionomer peak, we observer various cation-anion complexes in the simulation, suggesting ionomer backbones are crosslinked through ion complexes. These crosslinks reduce the adjacent PEO mobility resulting in a symmetric mobility gradient along the PEO chain. We vary the cation-anion interaction in the simulation to observe the interplay of cation-anion association, polymer mobility and cation motion. Cation-anion association controls the number of free ions, which is important in ionic conductivity when these materials are used as SPEs. Polymer mobility controls how fast the free ions are able to move through the SPE. High conductivity requires both a high free ion content and fast polymer motion. To understand the connection between the two, we ``tune'' the force field in order to manipulate the free ion content and observe the influence on PEO dynamics.

Analysis and modeling of proton beam loss and emittance growth in the Relativistic Heavy Ion Collider

DOE PAGES

Luo, Y.; Fischer, W.; White, S.

2016-02-04

The Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory has been operating since 2000. Over the past decade, thanks to the continuously increased bunch intensity and reduced β*s at the interaction points, the peak luminosity in the polarized proton operation has been increased by more than two orders of magnitude. In this article, we will present the operational observations at the routine proton physics stores. In addition, the mechanisms for the beam loss, transverse emittance growth, and bunch lengthening are analyzed. Lastly, numerical calculations and multiparticle tracking are used to model these observations.

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

CorAL is a software Library designed to aid in the analysis of femtoscipic data. Femtoscopic data are a class of measured quantities used in heavy-ion collisions to characterize particle emitting source sizes. The most common type of this data is two-particle correleations induced by the Hanbury-Brown/Twiss (HBT) Effect, but can also include correlations induced by final-state interactions between pairs of emitted particles in a heavy-ion collision. Because heavy-ion collisions are complex many particle systems, modeling hydrodynamical models or hybrid techniques. Using the CRAB module, CorAL can turn the output from these models into something that can be directley compared tomore » experimental data. CorAL can also take the raw experimentally measured correlation functions and image them by inverting the Koonin-Pratt equation to extract the space-time emission profile of the particle emitting source. This source function can be further analyzed or directly compared to theoretical calculations.« less

Cross-Beam Energy Transfer Driven by Incoherent Laser Beams with Frequency Detuning

NASA Astrophysics Data System (ADS)

Maximov, A.; Myatt, J. F.; Short, R. W.; Igumenshchev, I. V.; Seka, W.

2015-11-01

In the direct-drive method of the inertial confinement fusion (ICF), the coupling of laser energy to target plasmas is strongly influenced by the effect of cross-beam energy transfer (CBET) between multiple driving laser beams. The laser -plasma interaction (LPI) model of CBET is based on the nonparaxial laser light propagation coupled with the low-frequency ion-acoustic-domain plasma response. Common ion waves driven by multiple laser beams play a very important role in CBET. The effect of the frequency detuning (colors) in the driving laser beams is studied and it is shown to significantly reduce the level of common ion waves and therefore the level of CBET. The differences between the LPI-based CBET model and the ray-based CBET model used in hydrocodes are discussed. This material is based upon work supported by the Department of Energy National Nuclear Security Administration under Award Number DE-NA0001944.

Control of Chemical Effects in the Separation Process of a Differential Mobility / Mass Spectrometer System

PubMed Central

Schneider, Bradley B.; Coy, Stephen L.; Krylov, Evgeny V.; Nazarov, Erkinjon G.

2013-01-01

Differential mobility spectrometry (DMS) separates ions on the basis of the difference in their migration rates under high versus low electric fields. Several models describing the physical nature of this field mobility dependence have been proposed but emerging as a dominant effect is the clusterization model sometimes referred to as the dynamic cluster-decluster model. DMS resolution and peak capacity is strongly influenced by the addition of modifiers which results in the formation and dissociation of clusters. This process increases selectivity due to the unique chemical interactions that occur between an ion and neutral gas phase molecules. It is thus imperative to bring the parameters influencing the chemical interactions under control and find ways to exploit them in order to improve the analytical utility of the device. In this paper we describe three important areas that need consideration in order to stabilize and capitalize on the chemical processes that dominate a DMS separation. The first involves means of controlling the dynamic equilibrium of the clustering reactions with high concentrations of specific reagents. The second area involves a means to deal with the unwanted heterogeneous cluster ion populations emitted from the electrospray ionization process that degrade resolution and sensitivity. The third involves fine control of parameters that affect the fundamental collision processes, temperature and pressure. PMID:20065515

Formation of vortices in the presence of sheared electron flows in the earth's ionosphere

NASA Astrophysics Data System (ADS)

Farid, T.; Shukla, P. K.; Sakanaka, P. H.; Mirza, A. M.

2000-12-01

It is shown that sheared electron flows can generate long as well as short wavelength (in comparison with the ion gyroradius) electrostatic waves in a nonuniform magnetplasma. For this purpose, we derive dispersion relations by employing two-fluid and hybrid models; in the two-fluid model the dynamics of both the electrons and ions are governed by the hydrodynamic equations and the guiding center fluid drifts, whereas the hybrid model assumes kinetic ions and fluid electrons. Explicit expressions for the growth rates and thresholds are presented. Linearly excited waves attain finite amplitudes and start interacting among themselves. The interaction is governed by the nonlinear equations containing the Jacobian nonlinearities. Stationary solutions of the nonlinear mode coupling equations can be represented in the form of a dipolar vortex and a vortex street. Conditions under which the latter arise are given. Numerical results for the growth rates of linearly excited modes as well as for various types of vortices are displayed for the parameters that are relevant for the F-region of the Earth's ionosphere. It is suggested that the results of the present investigation are useful in understanding the properties of nonthermal electrostatic waves and associated nonlinear vortex structures in the Earth's ionosphere.

Development of a Thermodynamic Model for the Hanford Tank Waste Operations Simulator - 12193

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

Carter, Robert; Seniow, Kendra

The Hanford Tank Waste Operations Simulator (HTWOS) is the current tool used by the Hanford Tank Operations Contractor for system planning and assessment of different operational strategies. Activities such as waste retrievals in the Hanford tank farms and washing and leaching of waste in the Waste Treatment and Immobilization Plant (WTP) are currently modeled in HTWOS. To predict phase compositions during these activities, HTWOS currently uses simple wash and leach factors that were developed many years ago. To improve these predictions, a rigorous thermodynamic framework has been developed based on the multi-component Pitzer ion interaction model for use with severalmore » important chemical species in Hanford tank waste. These chemical species are those with the greatest impact on high-level waste glass production in the WTP and whose solubility depends on the processing conditions. Starting with Pitzer parameter coefficients and species chemical potential coefficients collated from open literature sources, reconciliation with published experimental data led to a self-consistent set of coefficients known as the HTWOS Pitzer database. Using Gibbs energy minimization with the Pitzer ion interaction equations in Microsoft Excel,1 a number of successful predictions were made for the solubility of simple mixtures of the chosen species. Currently, this thermodynamic framework is being programmed into HTWOS as the mechanism for determining the solid-liquid phase distributions for the chosen species, replacing their simple wash and leach factors. Starting from a variety of open literature sources, a collection of Pitzer parameters and species chemical potentials, as functions of temperature, was tested for consistency and accuracy by comparison with available experimental thermodynamic data (e.g., osmotic coefficients and solubility). Reconciliation of the initial set of parameter coefficients with the experimental data led to the development of the self-consistent set known as the HTWOS Pitzer database. Using Microsoft Excel to formulate the Gibbs energy minimization method and the multi-component Pitzer ion interaction equations, several predictions of the solubility of solute mixtures at various temperatures were made using the HTWOS Pitzer database coefficients. Examples of these predictions are shown in Figure 3 and Figure 4. A listing of the entire HTWOS Pitzer database can be found in RPP-RPT-50703. Currently, work is underway to install the Pitzer ion interaction model in HTWOS as the mechanism for determining the solid-liquid phase distributions of select waste constituents during tank retrievals and subsequent washing and leaching of the waste. Validation of the Pitzer ion interaction model in HTWOS will be performed with analytical laboratory data of actual tank waste. This change in HTWOS is expected to elicit shifts in mission criteria, such as mission end date and quantity of high-level waste glass produced by WTP, as predicted by HTWOS. These improvements to the speciation calculations in HTWOS, however, will establish a better planning basis and facilitate more effective and efficient future operations of the WTP. (authors)« less

Shear modulus of neutron star crust

NASA Astrophysics Data System (ADS)

Baiko, D. A.

2011-09-01

The shear modulus of solid neutron star crust is calculated by the thermodynamic perturbation theory, taking into account ion motion. At a given density, the crust is modelled as a body-centred cubic Coulomb crystal of fully ionized atomic nuclei of one type with a uniform charge-compensating electron background. Classic and quantum regimes of ion motion are considered. The calculations in the classic temperature range agree well with previous Monte Carlo simulations. At these temperatures, the shear modulus is given by the sum of a positive contribution due to the static lattice and a negative ∝ T contribution due to the ion motion. The quantum calculations are performed for the first time. The main result is that at low temperatures the contribution to the shear modulus due to the ion motion saturates at a constant value, associated with zero-point ion vibrations. Such behaviour is qualitatively similar to the zero-point ion motion contribution to the crystal energy. The quantum effects may be important for lighter elements at higher densities, where the ion plasma temperature is not entirely negligible compared to the typical Coulomb ion interaction energy. The results of numerical calculations are approximated by convenient fitting formulae. They should be used for precise neutron star oscillation modelling, a rapidly developing branch of stellar seismology.