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Sample records for continuum-solvent electrostatics calculation

  1. Histidine in Continuum Electrostatics Protonation State Calculations

    Science.gov (United States)

    Couch, Vernon; Stuchebruckhov, Alexei

    2014-01-01

    A modification to the standard continuum electrostatics approach to calculate protein pKas which allows for the decoupling of histidine tautomers within a two state model is presented. Histidine with four intrinsically coupled protonation states cannot be easily incorporated into a two state formalism because the interaction between the two protonatable sites of the imidazole ring is not purely electrostatic. The presented treatment, based on a single approximation of the interrelation between histidine’s charge states, allows for a natural separation of the two protonatable sites associated with the imidazole ring as well as the inclusion of all protonation states within the calculation. PMID:22072521

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

    Science.gov (United States)

    Bonthuis, Douwe Jan; Netz, Roland R

    2013-10-03

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

  3. PCE: web tools to compute protein continuum electrostatics

    Science.gov (United States)

    Miteva, Maria A.; Tufféry, Pierre; Villoutreix, Bruno O.

    2005-01-01

    PCE (protein continuum electrostatics) is an online service for protein electrostatic computations presently based on the MEAD (macroscopic electrostatics with atomic detail) package initially developed by D. Bashford [(2004) Front Biosci., 9, 1082–1099]. This computer method uses a macroscopic electrostatic model for the calculation of protein electrostatic properties, such as pKa values of titratable groups and electrostatic potentials. The MEAD package generates electrostatic energies via finite difference solution to the Poisson–Boltzmann equation. Users submit a PDB file and PCE returns potentials and pKa values as well as color (static or animated) figures displaying electrostatic potentials mapped on the molecular surface. This service is intended to facilitate electrostatics analyses of proteins and thereby broaden the accessibility to continuum electrostatics to the biological community. PCE can be accessed at . PMID:15980492

  4. Computing pKa Values in Different Solvents by Electrostatic Transformation.

    Science.gov (United States)

    Rossini, Emanuele; Netz, Roland R; Knapp, Ernst-Walter

    2016-07-12

    We introduce a method that requires only moderate computational effort to compute pKa values of small molecules in different solvents with an average accuracy of better than 0.7 pH units. With a known pKa value in one solvent, the electrostatic transform method computes the pKa value in any other solvent if the proton solvation energy is known in both considered solvents. To apply the electrostatic transform method to a molecule, the electrostatic solvation energies of the protonated and deprotonated molecular species are computed in the two considered solvents using a dielectric continuum to describe the solvent. This is demonstrated for 30 molecules belonging to 10 different molecular families by considering 77 measured pKa values in 4 different solvents: water, acetonitrile, dimethyl sulfoxide, and methanol. The electrostatic transform method can be applied to any other solvent if the proton solvation energy is known. It is exclusively based on physicochemical principles, not using any empirical fetch factors or explicit solvent molecules, to obtain agreement with measured pKa values and is therefore ready to be generalized to other solute molecules and solvents. From the computed pKa values, we obtained relative proton solvation energies, which agree very well with the proton solvation energies computed recently by ab initio methods, and used these energies in the present study.

  5. On calculation of the electrostatic potential of a phosphatidylinositol phosphate-containing phosphatidylcholine lipid membrane accounting for membrane dynamics.

    Directory of Open Access Journals (Sweden)

    Jonathan C Fuller

    Full Text Available Many signaling events require the binding of cytoplasmic proteins to cell membranes by recognition of specific charged lipids, such as phosphoinositol-phosphates. As a model for a protein-membrane binding site, we consider one charged phosphoinositol phosphate (PtdIns(3P embedded in a phosphatidylcholine bilayer. As the protein-membrane binding is driven by electrostatic interactions, continuum solvent models require an accurate representation of the electrostatic potential of the phosphoinositol phosphate-containing membrane. We computed and analyzed the electrostatic potentials of snapshots taken at regular intervals from molecular dynamics simulations of the bilayer. We observe considerable variation in the electrostatic potential of the bilayer both along a single simulation and between simulations performed with the GAFF or CHARMM c36 force fields. However, we find that the choice of GAFF or CHARMM c36 parameters has little effect on the electrostatic potential of a given configuration of the bilayer with a PtdIns(3P embedded in it. From our results, we propose a remedian averaging method for calculating the electrostatic potential of a membrane system that is suitable for simulations of protein-membrane binding with a continuum solvent model.

  6. Extending the Solvation-Layer Interface Condition Continum Electrostatic Model to a Linearized Poisson-Boltzmann Solvent.

    Science.gov (United States)

    Molavi Tabrizi, Amirhossein; Goossens, Spencer; Mehdizadeh Rahimi, Ali; Cooper, Christopher D; Knepley, Matthew G; Bardhan, Jaydeep P

    2017-06-13

    We extend the linearized Poisson-Boltzmann (LPB) continuum electrostatic model for molecular solvation to address charge-hydration asymmetry. Our new solvation-layer interface condition (SLIC)/LPB corrects for first-shell response by perturbing the traditional continuum-theory interface conditions at the protein-solvent and the Stern-layer interfaces. We also present a GPU-accelerated treecode implementation capable of simulating large proteins, and our results demonstrate that the new model exhibits significant accuracy improvements over traditional LPB models, while reducing the number of fitting parameters from dozens (atomic radii) to just five parameters, which have physical meanings related to first-shell water behavior at an uncharged interface. In particular, atom radii in the SLIC model are not optimized but uniformly scaled from their Lennard-Jones radii. Compared to explicit-solvent free-energy calculations of individual atoms in small molecules, SLIC/LPB is significantly more accurate than standard parametrizations (RMS error 0.55 kcal/mol for SLIC, compared to RMS error of 3.05 kcal/mol for standard LPB). On parametrizing the electrostatic model with a simple nonpolar component for total molecular solvation free energies, our model predicts octanol/water transfer free energies with an RMS error 1.07 kcal/mol. A more detailed assessment illustrates that standard continuum electrostatic models reproduce total charging free energies via a compensation of significant errors in atomic self-energies; this finding offers a window into improving the accuracy of Generalized-Born theories and other coarse-grained models. Most remarkably, the SLIC model also reproduces positive charging free energies for atoms in hydrophobic groups, whereas standard PB models are unable to generate positive charging free energies regardless of the parametrized radii. The GPU-accelerated solver is freely available online, as is a MATLAB implementation.

  7. Electrostatics of the photosynthetic bacterial reaction center. Protonation of Glu L 212 and Asp L 213 - A new method of calculation.

    Science.gov (United States)

    Ptushenko, Vasily V; Cherepanov, Dmitry A; Krishtalik, Lev I

    2015-12-01

    Continuum electrostatic calculation of the transfer energies of anions from water into aprotic solvents gives the figures erroneous by order of magnitude. This is due to the hydrogen bond disruption that suggests the necessity to reconsider the traditional approach of the purely electrostatic calculation of the transfer energy from water into protein. In this paper, the method combining the experimental estimates of the transfer energies from water into aprotic solvent and the electrostatic calculation of the transfer energies from aprotic solvent into protein is proposed. Hydrogen bonds between aprotic solvent and solute are taken into account by introducing an imaginary aprotic medium incapable to form hydrogen bonds with the solute. Besides, a new treatment of the heterogeneous intraprotein dielectric permittivity based on the microscopic protein structure and electrometric measurements is elaborated. The method accounts semi-quantitatively for the electrostatic effect of diverse charged amino acid substitutions in the donor and acceptor parts of the photosynthetic bacterial reaction center from Rhodobacter sphaeroides. Analysis of the volatile secondary acceptor site QB revealed that in the conformation with a minimal distance between quinone QB and Glu L 212 the proton uptake upon the reduction of QB is prompted by Glu L 212 in alkaline and by Asp L 213 in slightly acidic regions. This agrees with the pH dependences of protonation degrees and the proton uptake. The method of pK calculation was applied successfully also for dissociation of Asp 26 in bacterial thioredoxin. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. Bounding the electrostatic free energies associated with linear continuum models of molecular solvation.

    Science.gov (United States)

    Bardhan, Jaydeep P; Knepley, Matthew G; Anitescu, Mihai

    2009-03-14

    The importance of electrostatic interactions in molecular biology has driven extensive research toward the development of accurate and efficient theoretical and computational models. Linear continuum electrostatic theory has been surprisingly successful, but the computational costs associated with solving the associated partial differential equations (PDEs) preclude the theory's use in most dynamical simulations. Modern generalized-Born models for electrostatics can reproduce PDE-based calculations to within a few percent and are extremely computationally efficient but do not always faithfully reproduce interactions between chemical groups. Recent work has shown that a boundary-integral-equation formulation of the PDE problem leads naturally to a new approach called boundary-integral-based electrostatics estimation (BIBEE) to approximate electrostatic interactions. In the present paper, we prove that the BIBEE method can be used to rigorously bound the actual continuum-theory electrostatic free energy. The bounds are validated using a set of more than 600 proteins. Detailed numerical results are presented for structures of the peptide met-enkephalin taken from a molecular-dynamics simulation. These bounds, in combination with our demonstration that the BIBEE methods accurately reproduce pairwise interactions, suggest a new approach toward building a highly accurate yet computationally tractable electrostatic model.

  9. Bounding the electrostatic free energies associated with linear continuum models of molecular solvation.

    Energy Technology Data Exchange (ETDEWEB)

    Bardhan, J. P.; Knepley, M. G.; Anitescu, M. (Biosciences Division); ( MCS); (Rush Univ.)

    2009-03-01

    The importance of electrostatic interactions in molecular biology has driven extensive research toward the development of accurate and efficient theoretical and computational models. Linear continuum electrostatic theory has been surprisingly successful, but the computational costs associated with solving the associated partial differential equations (PDEs) preclude the theory's use in most dynamical simulations. Modern generalized-Born models for electrostatics can reproduce PDE-based calculations to within a few percent and are extremely computationally efficient but do not always faithfully reproduce interactions between chemical groups. Recent work has shown that a boundary-integral-equation formulation of the PDE problem leads naturally to a new approach called boundary-integral-based electrostatics estimation (BIBEE) to approximate electrostatic interactions. In the present paper, we prove that the BIBEE method can be used to rigorously bound the actual continuum-theory electrostatic free energy. The bounds are validated using a set of more than 600 proteins. Detailed numerical results are presented for structures of the peptide met-enkephalin taken from a molecular-dynamics simulation. These bounds, in combination with our demonstration that the BIBEE methods accurately reproduce pairwise interactions, suggest a new approach toward building a highly accurate yet computationally tractable electrostatic model.

  10. Benchmarking Continuum Solvent Models for Keto-Enol Tautomerizations.

    Science.gov (United States)

    McCann, Billy W; McFarland, Stuart; Acevedo, Orlando

    2015-08-13

    Experimental free energies of tautomerization, ΔGT, were used to benchmark the gas-phase predictions of 17 different quantum mechanical methods and eight basis sets for seven keto-enol tautomer pairs dominated by their enolic form. The G4 method and M06/6-31+G(d,p) yielded the most accurate results, with mean absolute errors (MAE's) of 0.95 and 0.71 kcal/mol, respectively. Using these two theory levels, the solution-phase ΔGT values for 23 unique tautomer pairs composed of aliphatic ketones, β-dicarbonyls, and heterocycles were computed in multiple protic and aprotic solvents. The continuum solvation models, namely, polarizable continuum model (PCM), polarizable conductor calculation model (CPCM), and universal solvation model (SMD), gave relatively similar MAE's of ∼1.6-1.7 kcal/mol for G4 and ∼1.9-2.0 kcal/mol with M06/6-31+G(d,p). Partitioning the tautomer pairs into their respective molecular types, that is, aliphatic ketones, β-dicarbonyls, and heterocycles, and separating out the aqueous versus nonaqueous results finds G4/PCM utilizing the UA0 cavity to be the overall most accurate combination. Free energies of activation, ΔG(‡), for the base-catalyzed keto-enol interconversion of 2-nitrocyclohexanone were also computed using six bases and five solvents. The M06/6-31+G(d,p) reproduced the ΔG(‡) with MAE's of 1.5 and 1.8 kcal/mol using CPCM and SMD, respectively, for all combinations of base and solvent. That specific enolization was previously proposed to proceed via a concerted mechanism in less polar solvents but shift to a stepwise mechanism in more polar solvents. However, the current calculations suggest that the stepwise mechanism operates in all solvents.

  11. Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

    Energy Technology Data Exchange (ETDEWEB)

    Rocklin, Gabriel J. [Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th St., San Francisco, California 94143-2550, USA and Biophysics Graduate Program, University of California San Francisco, 1700 4th St., San Francisco, California 94143-2550 (United States); Mobley, David L. [Departments of Pharmaceutical Sciences and Chemistry, University of California Irvine, 147 Bison Modular, Building 515, Irvine, California 92697-0001, USA and Department of Chemistry, University of New Orleans, 2000 Lakeshore Drive, New Orleans, Louisiana 70148 (United States); Dill, Ken A. [Laufer Center for Physical and Quantitative Biology, 5252 Stony Brook University, Stony Brook, New York 11794-0001 (United States); Hünenberger, Philippe H., E-mail: phil@igc.phys.chem.ethz.ch [Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zürich (Switzerland)

    2013-11-14

    The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the ligand is alchemically inserted into the system, both in the solvated protein and free in solution. The corresponding ligand-insertion free energies are typically calculated in nanoscale computational boxes simulated under periodic boundary conditions and considering electrostatic interactions defined by a periodic lattice-sum. This is distinct from the ideal bulk situation of a system of macroscopic size simulated under non-periodic boundary conditions with Coulombic electrostatic interactions. This discrepancy results in finite-size effects, which affect primarily the charging component of the insertion free energy, are dependent on the box size, and can be large when the ligand bears a net charge, especially if the protein is charged as well. This article investigates finite-size effects on calculated charging free energies using as a test case the binding of the ligand 2-amino-5-methylthiazole (net charge +1 e) to a mutant form of yeast cytochrome c peroxidase in water. Considering different charge isoforms of the protein (net charges −5, 0, +3, or +9 e), either in the absence or the presence of neutralizing counter-ions, and sizes of the cubic computational box (edges ranging from 7.42 to 11.02 nm), the potentially large magnitude of finite-size effects on the raw charging free energies (up to 17.1 kJ mol{sup −1}) is demonstrated. Two correction schemes are then proposed to eliminate these effects, a numerical and an analytical one. Both schemes are based on a continuum-electrostatics analysis and require performing Poisson-Boltzmann (PB) calculations on the protein-ligand system. While the numerical scheme requires PB calculations under both non-periodic and periodic boundary conditions, the latter at the box size considered in the MD simulations, the analytical scheme only requires three non

  12. Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

    Science.gov (United States)

    Rocklin, Gabriel J.; Mobley, David L.; Dill, Ken A.; Hünenberger, Philippe H.

    2013-11-01

    The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the ligand is alchemically inserted into the system, both in the solvated protein and free in solution. The corresponding ligand-insertion free energies are typically calculated in nanoscale computational boxes simulated under periodic boundary conditions and considering electrostatic interactions defined by a periodic lattice-sum. This is distinct from the ideal bulk situation of a system of macroscopic size simulated under non-periodic boundary conditions with Coulombic electrostatic interactions. This discrepancy results in finite-size effects, which affect primarily the charging component of the insertion free energy, are dependent on the box size, and can be large when the ligand bears a net charge, especially if the protein is charged as well. This article investigates finite-size effects on calculated charging free energies using as a test case the binding of the ligand 2-amino-5-methylthiazole (net charge +1 e) to a mutant form of yeast cytochrome c peroxidase in water. Considering different charge isoforms of the protein (net charges -5, 0, +3, or +9 e), either in the absence or the presence of neutralizing counter-ions, and sizes of the cubic computational box (edges ranging from 7.42 to 11.02 nm), the potentially large magnitude of finite-size effects on the raw charging free energies (up to 17.1 kJ mol-1) is demonstrated. Two correction schemes are then proposed to eliminate these effects, a numerical and an analytical one. Both schemes are based on a continuum-electrostatics analysis and require performing Poisson-Boltzmann (PB) calculations on the protein-ligand system. While the numerical scheme requires PB calculations under both non-periodic and periodic boundary conditions, the latter at the box size considered in the MD simulations, the analytical scheme only requires three non-periodic PB

  13. Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects.

    Science.gov (United States)

    Rocklin, Gabriel J; Mobley, David L; Dill, Ken A; Hünenberger, Philippe H

    2013-11-14

    The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the ligand is alchemically inserted into the system, both in the solvated protein and free in solution. The corresponding ligand-insertion free energies are typically calculated in nanoscale computational boxes simulated under periodic boundary conditions and considering electrostatic interactions defined by a periodic lattice-sum. This is distinct from the ideal bulk situation of a system of macroscopic size simulated under non-periodic boundary conditions with Coulombic electrostatic interactions. This discrepancy results in finite-size effects, which affect primarily the charging component of the insertion free energy, are dependent on the box size, and can be large when the ligand bears a net charge, especially if the protein is charged as well. This article investigates finite-size effects on calculated charging free energies using as a test case the binding of the ligand 2-amino-5-methylthiazole (net charge +1 e) to a mutant form of yeast cytochrome c peroxidase in water. Considering different charge isoforms of the protein (net charges -5, 0, +3, or +9 e), either in the absence or the presence of neutralizing counter-ions, and sizes of the cubic computational box (edges ranging from 7.42 to 11.02 nm), the potentially large magnitude of finite-size effects on the raw charging free energies (up to 17.1 kJ mol(-1)) is demonstrated. Two correction schemes are then proposed to eliminate these effects, a numerical and an analytical one. Both schemes are based on a continuum-electrostatics analysis and require performing Poisson-Boltzmann (PB) calculations on the protein-ligand system. While the numerical scheme requires PB calculations under both non-periodic and periodic boundary conditions, the latter at the box size considered in the MD simulations, the analytical scheme only requires three non-periodic PB

  14. Modelos contínuos do solvente: fundamentos Continuum solvation models: fundamentals

    Directory of Open Access Journals (Sweden)

    Josefredo R. Pliego Jr

    2006-06-01

    Full Text Available Continuum solvation models are nowadays widely used in the modeling of solvent effects and the range of applications goes from the calculation of partition coefficients to chemical reactions in solution. The present work presents a detailed explanation of the physical foundations of continuum models. We discuss the polarization of a dielectric and its representation through the volume and surface polarization charges. The Poisson equation for a dielectric was obtained and we have also derived and discuss the apparent surface charge method and its application for free energy of solvation calculations.

  15. Ionic Solution: What Goes Right and Wrong with Continuum Solvation Modeling.

    Science.gov (United States)

    Wang, Changhao; Ren, Pengyu; Luo, Ray

    2017-12-14

    Solvent-mediated electrostatic interactions were well recognized to be important in the structure and function of molecular systems. Ionic interaction is an important component in electrostatic interactions, especially in highly charged molecules, such as nucleic acids. Here, we focus on the quality of the widely used Poisson-Boltzmann surface area (PBSA) continuum models in modeling ionic interactions by comparing with both explicit solvent simulations and the experiment. In this work, the molality-dependent chemical potentials for sodium chloride (NaCl) electrolyte were first simulated in the SPC/E explicit solvent. Our high-quality simulation agrees well with both the previous study and the experiment. Given the free-energy simulations in SPC/E as the benchmark, we used the same sets of snapshots collected in the SPC/E solvent model for PBSA free-energy calculations in the hope to achieve the maximum consistency between the two solvent models. Our comparative analysis shows that the molality-dependent chemical potentials of NaCl were reproduced well with both linear PB and nonlinear PB methods, although nonlinear PB agrees better with SPC/E and the experiment. Our free-energy simulations also show that the presence of salt increases the hydrophobic effect in a nonlinear fashion, in qualitative agreement with previous theoretical studies of Onsager and Samaras. However, the lack of molality-dependency in the nonelectrostatics continuum models dramatically reduces the overall quality of PBSA methods in modeling salt-dependent energetics. These analyses point to further improvements needed for more robust modeling of solvent-mediated interactions by the continuum solvation frameworks.

  16. Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins

    Energy Technology Data Exchange (ETDEWEB)

    Gunner, Marilyn R.; Baker, Nathan A.

    2016-06-20

    Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions are dominated by solvation and electrostatic energies and modulated by protein conformational relaxation in response to the ionization state changes. Although computational methods for calculating these interactions can provide very powerful tools for predicting protein charge states, they include several critical approximations of which users should be aware. This chapter discusses the strengths, weaknesses, and approximations of popular computational methods for predicting charge states and understanding their underlying electrostatic interactions. The goal of this chapter is to inform users about applications and potential caveats of these methods as well as outline directions for future theoretical and computational research.

  17. Nonlocal continuum electrostatic theory predicts surprisingly small energetic penalties for charge burial in proteins.

    Science.gov (United States)

    Bardhan, Jaydeep P

    2011-09-14

    We study the energetics of burying charges, ion pairs, and ionizable groups in a simple protein model using nonlocal continuum electrostatics. Our primary finding is that the nonlocal response leads to markedly reduced solvent screening, comparable to the use of application-specific protein dielectric constants. Employing the same parameters as used in other nonlocal studies, we find that for a sphere of radius 13.4 Å containing a single +1e charge, the nonlocal solvation free energy varies less than 18 kcal/mol as the charge moves from the surface to the center, whereas the difference in the local Poisson model is ∼35 kcal/mol. Because an ion pair (salt bridge) generates a comparatively more rapidly varying Coulomb potential, energetics for salt bridges are even more significantly reduced in the nonlocal model. By varying the central parameter in nonlocal theory, which is an effective length scale associated with correlations between solvent molecules, nonlocal-model energetics can be varied from the standard local results to essentially zero; however, the existence of the reduction in charge-burial penalties is quite robust to variations in the protein dielectric constant and the correlation length. Finally, as a simple exploratory test of the implications of nonlocal response, we calculate glutamate pK(a) shifts and find that using standard protein parameters (ε(protein) = 2-4), nonlocal results match local-model predictions with much higher dielectric constants. Nonlocality may, therefore, be one factor in resolving discrepancies between measured protein dielectric constants and the model parameters often used to match titration experiments. Nonlocal models may hold significant promise to deepen our understanding of macromolecular electrostatics without substantially increasing computational complexity. © 2011 American Institute of Physics

  18. Conformational analysis of glutamic acid: a density functional approach using implicit continuum solvent model.

    Science.gov (United States)

    Turan, Başak; Selçuki, Cenk

    2014-09-01

    Amino acids are constituents of proteins and enzymes which take part almost in all metabolic reactions. Glutamic acid, with an ability to form a negatively charged side chain, plays a major role in intra and intermolecular interactions of proteins, peptides, and enzymes. An exhaustive conformational analysis has been performed for all eight possible forms at B3LYP/cc-pVTZ level. All possible neutral, zwitterionic, protonated, and deprotonated forms of glutamic acid structures have been investigated in solution by using polarizable continuum model mimicking water as the solvent. Nine families based on the dihedral angles have been classified for eight glutamic acid forms. The electrostatic effects included in the solvent model usually stabilize the charged forms more. However, the stability of the zwitterionic form has been underestimated due to the lack of hydrogen bonding between the solute and solvent; therefore, it is observed that compact neutral glutamic acid structures are more stable in solution than they are in vacuum. Our calculations have shown that among all eight possible forms, some are not stable in solution and are immediately converted to other more stable forms. Comparison of isoelectronic glutamic acid forms indicated that one of the structures among possible zwitterionic and anionic forms may dominate over the other possible forms. Additional investigations using explicit solvent models are necessary to determine the stability of charged forms of glutamic acid in solution as our results clearly indicate that hydrogen bonding and its type have a major role in the structure and energy of conformers.

  19. Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins.

    Science.gov (United States)

    Gunner, M R; Baker, N A

    2016-01-01

    Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions is dominated by solvation and electrostatic energies and modulated by protein conformational relaxation in response to the ionization state changes. Although computational methods for calculating these interactions can provide very powerful tools for predicting protein charge states, they include several critical approximations of which users should be aware. This chapter discusses the strengths, weaknesses, and approximations of popular computational methods for predicting charge states and understanding the underlying electrostatic interactions. The goal of this chapter is to inform users about applications and potential caveats of these methods as well as outline directions for future theoretical and computational research. © 2016 Elsevier Inc. All rights reserved.

  20. Improving the treatment of coarse-grain electrostatics: CVCEL

    Energy Technology Data Exchange (ETDEWEB)

    Ceres, N.; Lavery, R., E-mail: richard.lavery@ibcp.fr [Bioinformatics: Structures and Interactions, Institut de Biologie et Chimie des Protéines, BMSSI UMR CNRS 5086/Université Lyon I, 7 Passage du Vercors, Lyon 69367 (France)

    2015-12-28

    We propose an analytic approach for calculating the electrostatic energy of proteins or protein complexes in aqueous solution. This method, termed CVCEL (Circular Variance Continuum ELectrostatics), is fitted to Poisson calculations and is able to reproduce the corresponding energies for different choices of solute dielectric constant. CVCEL thus treats both solute charge interactions and charge self-energies, and it can also deal with salt solutions. Electrostatic damping notably depends on the degree of solvent exposure of the charges, quantified here in terms of circular variance, a measure that reflects the vectorial distribution of the neighbors around a given center. CVCEL energies can be calculated rapidly and have simple analytical derivatives. This approach avoids the need for calculating effective atomic volumes or Born radii. After describing how the method was developed, we present test results for coarse-grain proteins of different shapes and sizes, using different internal dielectric constants and different salt concentrations and also compare the results with those from simple distance-dependent models. We also show that the CVCEL approach can be used successfully to calculate the changes in electrostatic energy associated with changes in protein conformation or with protein-protein binding.

  1. Improving the treatment of coarse-grain electrostatics: CVCEL

    International Nuclear Information System (INIS)

    Ceres, N.; Lavery, R.

    2015-01-01

    We propose an analytic approach for calculating the electrostatic energy of proteins or protein complexes in aqueous solution. This method, termed CVCEL (Circular Variance Continuum ELectrostatics), is fitted to Poisson calculations and is able to reproduce the corresponding energies for different choices of solute dielectric constant. CVCEL thus treats both solute charge interactions and charge self-energies, and it can also deal with salt solutions. Electrostatic damping notably depends on the degree of solvent exposure of the charges, quantified here in terms of circular variance, a measure that reflects the vectorial distribution of the neighbors around a given center. CVCEL energies can be calculated rapidly and have simple analytical derivatives. This approach avoids the need for calculating effective atomic volumes or Born radii. After describing how the method was developed, we present test results for coarse-grain proteins of different shapes and sizes, using different internal dielectric constants and different salt concentrations and also compare the results with those from simple distance-dependent models. We also show that the CVCEL approach can be used successfully to calculate the changes in electrostatic energy associated with changes in protein conformation or with protein-protein binding

  2. Improving the treatment of coarse-grain electrostatics: CVCEL.

    Science.gov (United States)

    Ceres, N; Lavery, R

    2015-12-28

    We propose an analytic approach for calculating the electrostatic energy of proteins or protein complexes in aqueous solution. This method, termed CVCEL (Circular Variance Continuum ELectrostatics), is fitted to Poisson calculations and is able to reproduce the corresponding energies for different choices of solute dielectric constant. CVCEL thus treats both solute charge interactions and charge self-energies, and it can also deal with salt solutions. Electrostatic damping notably depends on the degree of solvent exposure of the charges, quantified here in terms of circular variance, a measure that reflects the vectorial distribution of the neighbors around a given center. CVCEL energies can be calculated rapidly and have simple analytical derivatives. This approach avoids the need for calculating effective atomic volumes or Born radii. After describing how the method was developed, we present test results for coarse-grain proteins of different shapes and sizes, using different internal dielectric constants and different salt concentrations and also compare the results with those from simple distance-dependent models. We also show that the CVCEL approach can be used successfully to calculate the changes in electrostatic energy associated with changes in protein conformation or with protein-protein binding.

  3. Influence of solvent polarization and non-uniform ion size on electrostatic properties between charged surfaces in an electrolyte solution

    Science.gov (United States)

    Sin, Jun-Sik

    2017-12-01

    In this paper, we study electrostatic properties between two similar or oppositely charged surfaces immersed in an electrolyte solution by using the mean-field approach accounting for solvent polarization and non-uniform size effects. Applying a free energy formalism accounting for unequal ion sizes and orientational ordering of water dipoles, we derive coupled and self-consistent equations to calculate electrostatic properties between charged surfaces. Electrostatic properties for similarly charged surfaces depend on the counterion size but not on the coion size. Moreover, electrostatic potential and osmotic pressure between similarly charged surfaces are found to be increased with increasing counterion size. On the other hand, the corresponding ones between oppositely charged surfaces are related to both sizes of positive and negative ions. For oppositely charged surfaces, the electrostatic potential, number density of solvent molecules, and relative permittivity of an electrolyte having unequal ion sizes are not symmetric about the centerline between the charged surfaces. For either case, the consideration of solvent polarization results in a decrease in the electrostatic potential and the osmotic pressure compared to the case without the effect.

  4. Continuum electrostatics for ionic solutions with non-uniform ionic sizes

    International Nuclear Information System (INIS)

    Li Bo

    2009-01-01

    This work concerns electrostatic properties of an ionic solution with multiple ionic species of possibly different ionic sizes. Such properties are described by the minimization of an electrostatic free-energy functional of ionic concentrations. Bounds are obtained for ionic concentrations with low electrostatic free energies. Such bounds are used to show that there exists a unique set of equilibrium ionic concentrations that minimizes the free-energy functional. The equilibrium ionic concentrations are found to depend sorely on the equilibrium electrostatic potential, resembling the classical Boltzmann distributions that relate the equilibrium ionic concentrations to the equilibrium electrostatic potential. Unless all the ionic and solvent molecular sizes are assumed to be the same, explicit formulae of such dependence are, however, not available in general. It is nevertheless proved that in equilibrium the ionic charge density is a decreasing function of the electrostatic potential. This determines a variational principle with a convex functional for the electrostatic potential

  5. Prediction of Reduction Potentials of Copper Proteins with Continuum Electrostatics and Density Functional Theory.

    Science.gov (United States)

    Fowler, Nicholas J; Blanford, Christopher F; Warwicker, Jim; de Visser, Sam P

    2017-11-02

    Blue copper proteins, such as azurin, show dramatic changes in Cu 2+ /Cu + reduction potential upon mutation over the full physiological range. Hence, they have important functions in electron transfer and oxidation chemistry and have applications in industrial biotechnology. The details of what determines these reduction potential changes upon mutation are still unclear. Moreover, it has been difficult to model and predict the reduction potential of azurin mutants and currently no unique procedure or workflow pattern exists. Furthermore, high-level computational methods can be accurate but are too time consuming for practical use. In this work, a novel approach for calculating reduction potentials of azurin mutants is shown, based on a combination of continuum electrostatics, density functional theory and empirical hydrophobicity factors. Our method accurately reproduces experimental reduction potential changes of 30 mutants with respect to wildtype within experimental error and highlights the factors contributing to the reduction potential change. Finally, reduction potentials are predicted for a series of 124 new mutants that have not yet been investigated experimentally. Several mutants are identified that are located well over 10 Å from the copper center that change the reduction potential by more than 85 mV. The work shows that secondary coordination sphere mutations mostly lead to long-range electrostatic changes and hence can be modeled accurately with continuum electrostatics. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  6. Exploring a multi-scale method for molecular simulation in continuum solvent model: Explicit simulation of continuum solvent as an incompressible fluid.

    Science.gov (United States)

    Xiao, Li; Luo, Ray

    2017-12-07

    We explored a multi-scale algorithm for the Poisson-Boltzmann continuum solvent model for more robust simulations of biomolecules. In this method, the continuum solvent/solute interface is explicitly simulated with a numerical fluid dynamics procedure, which is tightly coupled to the solute molecular dynamics simulation. There are multiple benefits to adopt such a strategy as presented below. At this stage of the development, only nonelectrostatic interactions, i.e., van der Waals and hydrophobic interactions, are included in the algorithm to assess the quality of the solvent-solute interface generated by the new method. Nevertheless, numerical challenges exist in accurately interpolating the highly nonlinear van der Waals term when solving the finite-difference fluid dynamics equations. We were able to bypass the challenge rigorously by merging the van der Waals potential and pressure together when solving the fluid dynamics equations and by considering its contribution in the free-boundary condition analytically. The multi-scale simulation method was first validated by reproducing the solute-solvent interface of a single atom with analytical solution. Next, we performed the relaxation simulation of a restrained symmetrical monomer and observed a symmetrical solvent interface at equilibrium with detailed surface features resembling those found on the solvent excluded surface. Four typical small molecular complexes were then tested, both volume and force balancing analyses showing that these simple complexes can reach equilibrium within the simulation time window. Finally, we studied the quality of the multi-scale solute-solvent interfaces for the four tested dimer complexes and found that they agree well with the boundaries as sampled in the explicit water simulations.

  7. The effect of macromolecular crowding on the electrostatic component of barnase-barstar binding: a computational, implicit solvent-based study.

    Directory of Open Access Journals (Sweden)

    Helena W Qi

    Full Text Available Macromolecular crowding within the cell can impact both protein folding and binding. Earlier models of cellular crowding focused on the excluded volume, entropic effect of crowding agents, which generally favors compact protein states. Recently, other effects of crowding have been explored, including enthalpically-related crowder-protein interactions and changes in solvation properties. In this work, we explore the effects of macromolecular crowding on the electrostatic desolvation and solvent-screened interaction components of protein-protein binding. Our simple model enables us to focus exclusively on the electrostatic effects of water depletion on protein binding due to crowding, providing us with the ability to systematically analyze and quantify these potentially intuitive effects. We use the barnase-barstar complex as a model system and randomly placed, uncharged spheres within implicit solvent to model crowding in an aqueous environment. On average, we find that the desolvation free energy penalties incurred by partners upon binding are lowered in a crowded environment and solvent-screened interactions are amplified. At a constant crowder density (fraction of total available volume occupied by crowders, this effect generally increases as the radius of model crowders decreases, but the strength and nature of this trend can depend on the water probe radius used to generate the molecular surface in the continuum model. In general, there is huge variation in desolvation penalties as a function of the random crowder positions. Results with explicit model crowders can be qualitatively similar to those using a lowered "effective" solvent dielectric to account for crowding, although the "best" effective dielectric constant will likely depend on multiple system properties. Taken together, this work systematically demonstrates, quantifies, and analyzes qualitative intuition-based insights into the effects of water depletion due to crowding on the

  8. Titration Behavior of Residues at the Entrance of the D-Pathway of Cytochrome c Oxidase from Paracoccus denitrificans Investigated by Continuum Electrostatic Calculations

    International Nuclear Information System (INIS)

    Olkhova, Elena; Helms, Volkhard H.; Michel, Hartmut

    2005-01-01

    Continuum electrostatic calculations were employed to investigate the titration curves of the fully oxidized state of wild type and several variants of cytochrome c oxidase from Paracoccus denitrificans (N131D, N131C, N131V, and D124N) for different values of the dielectric constant of the protein. The effects of the mutations at the entrance of the D-proton transfer pathway were found to be quite localized to their immediate surroundings. The results can be well interpreted in the light of the available biochemical and structural data and help understanding the effects of mutations on proton conductivity. The mutations of aspartic acid Asp-I-124 to a neutral residue resulted in a decreased pKa value of His-I-28 suggesting that the mutation of His-I-28 may have a significant influence on the coupling of electron and proton transfer in cytochrome c oxidase. We also investigated the effect of the mutations N131D, N131C, and N131V on the residue Glu-I-278 in terms of its pKa value and electrostatic interaction energies

  9. Estimate of electrostatic solvation free energy of electron in various polar solvents by using modified born equation

    International Nuclear Information System (INIS)

    Yamashita, Kazuo; Kitamura, Mitsutaka; Imai, Hideo

    1976-01-01

    The modified Born equation was tentatively applied to estimate the electrostatic free energies of solvation of the electron in various polar solvents. The related data of halide ions and a datum of the hydration free energy of the electron obtained by radiation chemical studies were used for the numerical calculations. (auth.)

  10. Understanding and Manipulating Electrostatic Fields at the Protein-Protein Interface Using Vibrational Spectroscopy and Continuum Electrostatics Calculations.

    Science.gov (United States)

    Ritchie, Andrew W; Webb, Lauren J

    2015-11-05

    Biological function emerges in large part from the interactions of biomacromolecules in the complex and dynamic environment of the living cell. For this reason, macromolecular interactions in biological systems are now a major focus of interest throughout the biochemical and biophysical communities. The affinity and specificity of macromolecular interactions are the result of both structural and electrostatic factors. Significant advances have been made in characterizing structural features of stable protein-protein interfaces through the techniques of modern structural biology, but much less is understood about how electrostatic factors promote and stabilize specific functional macromolecular interactions over all possible choices presented to a given molecule in a crowded environment. In this Feature Article, we describe how vibrational Stark effect (VSE) spectroscopy is being applied to measure electrostatic fields at protein-protein interfaces, focusing on measurements of guanosine triphosphate (GTP)-binding proteins of the Ras superfamily binding with structurally related but functionally distinct downstream effector proteins. In VSE spectroscopy, spectral shifts of a probe oscillator's energy are related directly to that probe's local electrostatic environment. By performing this experiment repeatedly throughout a protein-protein interface, an experimental map of measured electrostatic fields generated at that interface is determined. These data can be used to rationalize selective binding of similarly structured proteins in both in vitro and in vivo environments. Furthermore, these data can be used to compare to computational predictions of electrostatic fields to explore the level of simulation detail that is necessary to accurately predict our experimental findings.

  11. Performance test of multicomponent quantum mechanical calculation with polarizable continuum model for proton chemical shift.

    Science.gov (United States)

    Kanematsu, Yusuke; Tachikawa, Masanori

    2015-05-21

    Multicomponent quantum mechanical (MC_QM) calculations with polarizable continuum model (PCM) have been tested against liquid (1)H NMR chemical shifts for a test set of 80 molecules. Improvement from conventional quantum mechanical calculations was achieved for MC_QM calculations. The advantage of the multicomponent scheme could be attributed to the geometrical change from the equilibrium geometry by the incorporation of the hydrogen nuclear quantum effect, while that of PCM can be attributed to the change of the electronic structure according to the polarization by solvent effects.

  12. STABILITY OF A CYLINDRICAL SOLUTE-SOLVENT INTERFACE: EFFECT OF GEOMETRY, ELECTROSTATICS, AND HYDRODYNAMICS.

    Science.gov (United States)

    Li, B O; Sun, Hui; Zhou, Shenggao

    The solute-solvent interface that separates biological molecules from their surrounding aqueous solvent characterizes the conformation and dynamics of such molecules. In this work, we construct a solvent fluid dielectric boundary model for the solvation of charged molecules and apply it to study the stability of a model cylindrical solute-solvent interface. The motion of the solute-solvent interface is defined to be the same as that of solvent fluid at the interface. The solvent fluid is assumed to be incompressible and is described by the Stokes equation. The solute is modeled simply by the ideal-gas law. All the viscous force, hydrostatic pressure, solute-solvent van der Waals interaction, surface tension, and electrostatic force are balanced at the solute-solvent interface. We model the electrostatics by Poisson's equation in which the solute-solvent interface is treated as a dielectric boundary that separates the low-dielectric solute from the high-dielectric solvent. For a cylindrical geometry, we find multiple cylindrically shaped equilibrium interfaces that describe polymodal (e.g., dry and wet) states of hydration of an underlying molecular system. These steady-state solutions exhibit bifurcation behavior with respect to the charge density. For their linearized systems, we use the projection method to solve the fluid equation and find the dispersion relation. Our asymptotic analysis shows that, for large wavenumbers, the decay rate is proportional to wavenumber with the proportionality half of the ratio of surface tension to solvent viscosity, indicating that the solvent viscosity does affect the stability of a solute-solvent interface. Consequences of our analysis in the context of biomolecular interactions are discussed.

  13. Numerical Integration Techniques for Curved-Element Discretizations of Molecule–Solvent Interfaces

    Science.gov (United States)

    Bardhan, Jaydeep P.; Altman, Michael D.; Willis, David J.; Lippow, Shaun M.; Tidor, Bruce; White, Jacob K.

    2012-01-01

    Surface formulations of biophysical modeling problems offer attractive theoretical and computational properties. Numerical simulations based on these formulations usually begin with discretization of the surface under consideration; often, the surface is curved, possessing complicated structure and possibly singularities. Numerical simulations commonly are based on approximate, rather than exact, discretizations of these surfaces. To assess the strength of the dependence of simulation accuracy on the fidelity of surface representation, we have developed methods to model several important surface formulations using exact surface discretizations. Following and refining Zauhar’s work (J. Comp.-Aid. Mol. Des. 9:149-159, 1995), we define two classes of curved elements that can exactly discretize the van der Waals, solvent-accessible, and solvent-excluded (molecular) surfaces. We then present numerical integration techniques that can accurately evaluate nonsingular and singular integrals over these curved surfaces. After validating the exactness of the surface discretizations and demonstrating the correctness of the presented integration methods, we present a set of calculations that compare the accuracy of approximate, planar-triangle-based discretizations and exact, curved-element-based simulations of surface-generalized-Born (sGB), surface-continuum van der Waals (scvdW), and boundary-element method (BEM) electrostatics problems. Results demonstrate that continuum electrostatic calculations with BEM using curved elements, piecewise-constant basis functions, and centroid collocation are nearly ten times more accurate than planartriangle BEM for basis sets of comparable size. The sGB and scvdW calculations give exceptional accuracy even for the coarsest obtainable discretized surfaces. The extra accuracy is attributed to the exact representation of the solute–solvent interface; in contrast, commonly used planar-triangle discretizations can only offer improved

  14. Accurate Solution of Multi-Region Continuum Biomolecule Electrostatic Problems Using the Linearized Poisson-Boltzmann Equation with Curved Boundary Elements

    Science.gov (United States)

    Altman, Michael D.; Bardhan, Jaydeep P.; White, Jacob K.; Tidor, Bruce

    2009-01-01

    We present a boundary-element method (BEM) implementation for accurately solving problems in biomolecular electrostatics using the linearized Poisson–Boltzmann equation. Motivating this implementation is the desire to create a solver capable of precisely describing the geometries and topologies prevalent in continuum models of biological molecules. This implementation is enabled by the synthesis of four technologies developed or implemented specifically for this work. First, molecular and accessible surfaces used to describe dielectric and ion-exclusion boundaries were discretized with curved boundary elements that faithfully reproduce molecular geometries. Second, we avoided explicitly forming the dense BEM matrices and instead solved the linear systems with a preconditioned iterative method (GMRES), using a matrix compression algorithm (FFTSVD) to accelerate matrix-vector multiplication. Third, robust numerical integration methods were employed to accurately evaluate singular and near-singular integrals over the curved boundary elements. Finally, we present a general boundary-integral approach capable of modeling an arbitrary number of embedded homogeneous dielectric regions with differing dielectric constants, possible salt treatment, and point charges. A comparison of the presented BEM implementation and standard finite-difference techniques demonstrates that for certain classes of electrostatic calculations, such as determining absolute electrostatic solvation and rigid-binding free energies, the improved convergence properties of the BEM approach can have a significant impact on computed energetics. We also demonstrate that the improved accuracy offered by the curved-element BEM is important when more sophisticated techniques, such as non-rigid-binding models, are used to compute the relative electrostatic effects of molecular modifications. In addition, we show that electrostatic calculations requiring multiple solves using the same molecular geometry

  15. Combining MOSCED with molecular simulation free energy calculations or electronic structure calculations to develop an efficient tool for solvent formulation and selection

    Science.gov (United States)

    Cox, Courtney E.; Phifer, Jeremy R.; Ferreira da Silva, Larissa; Gonçalves Nogueira, Gabriel; Ley, Ryan T.; O'Loughlin, Elizabeth J.; Pereira Barbosa, Ana Karolyne; Rygelski, Brett T.; Paluch, Andrew S.

    2017-02-01

    Solubility parameter based methods have long been a valuable tool for solvent formulation and selection. Of these methods, the MOdified Separation of Cohesive Energy Density (MOSCED) has recently been shown to correlate well the equilibrium solubility of multifunctional non-electrolyte solids. However, before it can be applied to a novel solute, a limited amount of reference solubility data is required to regress the necessary MOSCED parameters. Here we demonstrate for the solutes methylparaben, ethylparaben, propylparaben, butylparaben, lidocaine and ephedrine how conventional molecular simulation free energy calculations or electronic structure calculations in a continuum solvent, here the SMD or SM8 solvation model, can instead be used to generate the necessary reference data, resulting in a predictive flavor of MOSCED. Adopting the melting point temperature and enthalpy of fusion of these compounds from experiment, we are able to predict equilibrium solubilities. We find the method is able to well correlate the (mole fraction) equilibrium solubility in non-aqueous solvents over four orders of magnitude with good quantitative agreement.

  16. Electronic excitations in a dielectric continuum solvent with quantum Monte Carlo: Acrolein in water

    International Nuclear Information System (INIS)

    Floris, Franca Maria; Amovilli, Claudio; Filippi, Claudia

    2014-01-01

    We investigate here the vertical n → π * and π → π * transitions of s-trans-acrolein in aqueous solution by means of a polarizable continuum model (PCM) we have developed for the treatment of the solute at the quantum Monte Carlo (QMC) level of the theory. We employ the QMC approach which allows us to work with highly correlated electronic wave functions for both the solute ground and excited states and, to study the vertical transitions in the solvent, adopt the commonly used scheme of considering fast and slow dielectric polarization. To perform calculations in a non-equilibrium solvation regime for the solute excited state, we add a correction to the global dielectric polarization charge density, obtained self consistently with the solute ground-state wave function by assuming a linear-response scheme. For the solvent polarization in the field of the solute in the ground state, we use the static dielectric constant while, for the electronic dielectric polarization, we employ the solvent refractive index evaluated at the same frequency of the photon absorbed by the solute for the transition. This choice is shown to be better than adopting the most commonly used value of refractive index measured in the region of visible radiation. Our QMC calculations show that, for standard cavities, the solvatochromic shifts obtained with the PCM are underestimated, even though of the correct sign, for both transitions of acrolein in water. Only by reducing the size of the cavity to values where more than one electron is escaped to the solvent region, we regain the experimental shift for the n → π * case and also improve considerably the shift for the π → π * transition

  17. Electronic excitations in a dielectric continuum solvent with quantum Monte Carlo: Acrolein in water

    Science.gov (United States)

    Floris, Franca Maria; Filippi, Claudia; Amovilli, Claudio

    2014-01-01

    We investigate here the vertical n → π* and π → π* transitions of s-trans-acrolein in aqueous solution by means of a polarizable continuum model (PCM) we have developed for the treatment of the solute at the quantum Monte Carlo (QMC) level of the theory. We employ the QMC approach which allows us to work with highly correlated electronic wave functions for both the solute ground and excited states and, to study the vertical transitions in the solvent, adopt the commonly used scheme of considering fast and slow dielectric polarization. To perform calculations in a non-equilibrium solvation regime for the solute excited state, we add a correction to the global dielectric polarization charge density, obtained self consistently with the solute ground-state wave function by assuming a linear-response scheme. For the solvent polarization in the field of the solute in the ground state, we use the static dielectric constant while, for the electronic dielectric polarization, we employ the solvent refractive index evaluated at the same frequency of the photon absorbed by the solute for the transition. This choice is shown to be better than adopting the most commonly used value of refractive index measured in the region of visible radiation. Our QMC calculations show that, for standard cavities, the solvatochromic shifts obtained with the PCM are underestimated, even though of the correct sign, for both transitions of acrolein in water. Only by reducing the size of the cavity to values where more than one electron is escaped to the solvent region, we regain the experimental shift for the n → π* case and also improve considerably the shift for the π → π* transition.

  18. Electronic excitations in a dielectric continuum solvent with quantum Monte Carlo: Acrolein in water

    Energy Technology Data Exchange (ETDEWEB)

    Floris, Franca Maria, E-mail: floris@dcci.unipi.it; Amovilli, Claudio [Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa (Italy); Filippi, Claudia [MESA Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands)

    2014-01-21

    We investigate here the vertical n → π{sup *} and π → π{sup *} transitions of s-trans-acrolein in aqueous solution by means of a polarizable continuum model (PCM) we have developed for the treatment of the solute at the quantum Monte Carlo (QMC) level of the theory. We employ the QMC approach which allows us to work with highly correlated electronic wave functions for both the solute ground and excited states and, to study the vertical transitions in the solvent, adopt the commonly used scheme of considering fast and slow dielectric polarization. To perform calculations in a non-equilibrium solvation regime for the solute excited state, we add a correction to the global dielectric polarization charge density, obtained self consistently with the solute ground-state wave function by assuming a linear-response scheme. For the solvent polarization in the field of the solute in the ground state, we use the static dielectric constant while, for the electronic dielectric polarization, we employ the solvent refractive index evaluated at the same frequency of the photon absorbed by the solute for the transition. This choice is shown to be better than adopting the most commonly used value of refractive index measured in the region of visible radiation. Our QMC calculations show that, for standard cavities, the solvatochromic shifts obtained with the PCM are underestimated, even though of the correct sign, for both transitions of acrolein in water. Only by reducing the size of the cavity to values where more than one electron is escaped to the solvent region, we regain the experimental shift for the n → π{sup *} case and also improve considerably the shift for the π → π{sup *} transition.

  19. Discrete and continuum modeling of solvent effects in a twisted intramolecular charge transfer system: The 4-N,N-dimethylaminobenzonitrile (DMABN) molecule.

    Science.gov (United States)

    Modesto-Costa, Lucas; Borges, Itamar

    2018-08-05

    The 4-N,N-dimethylaminobenzonitrile (DMABN) molecule is a prototypical system displaying twisted intramolecular (TICT) charge transfer effects. The ground and the first four electronic excited states (S 1 -S 4 ) in gas phase and upon solvation were studied. Charge transfer values as function of the torsion angle between the donor group (dimethylamine) and the acceptor moiety (benzonitrile) were explicitly computed. Potential energy curves were also obtained. The algebraic diagrammatic construction method at the second-order [ADC(2)] ab initio wave function was employed. Three solvents of increased polarities (benzene, DMSO and water) were investigated using discrete (average solvent electrostatic configuration - ASEC) and continuum (conductor-like screening model - COSMO) models. The results for the S 3 and S 4 excited states and the S 1 -S 4 charge transfer curves were not previously available in the literature. Electronic gas phase and solvent vertical spectra are in good agreement with previous theoretical and experimental results. In the twisted (90°) geometry the optical oscillator strengths have negligible values even for the S 2 bright state. Potential energy curves show two distinct pairs of curves intersecting at decreasing angles or not crossing in the more polar solvents. Charge transfer and electric dipole values allowed the rationalization of these results. The former effects are mostly independent of the solvent model and polarity. Although COSMO and ASEC solvent models mostly lead to similar results, there is an important difference: some crossings of the excitation energy curves appear only in the ASEC solvation model, which has important implications to the photochemistry of DMABN. Copyright © 2018 Elsevier B.V. All rights reserved.

  20. Reformulation of Maxwell's equations to incorporate near-solute solvent structure.

    Science.gov (United States)

    Yang, Pei-Kun; Lim, Carmay

    2008-09-04

    Maxwell's equations, which treat electromagnetic interactions between macroscopic charged objects in materials, have explained many phenomena and contributed to many applications in our lives. Derived in 1861 when no methods were available to determine the atomic structure of macromolecules, Maxwell's equations assume the solvent to be a structureless continuum. However, near-solute solvent molecules are highly structured, unlike far-solute bulk solvent molecules. Current methods cannot treat both the near-solute solvent structure and time-dependent electromagnetic interactions in a macroscopic system. Here, we derive "microscopic" electrodynamics equations that can treat macroscopic time-dependent electromagnetic field problems like Maxwell's equations and reproduce the solvent molecular and dipole density distributions observed in molecular dynamics simulations. These equations greatly reduce computational expense by not having to include explicit solvent molecules, yet they treat the solvent electrostatic and van der Waals effects more accurately than continuum models. They provide a foundation to study electromagnetic interactions between molecules in a macroscopic system that are ubiquitous in biology, bioelectromagnetism, and nanotechnology. The general strategy presented herein to incorporate the near-solute solvent structure would enable studies on how complex cellular protein-ligand interactions are affected by electromagnetic radiation, which could help to prevent harmful electromagnetic spectra or find potential therapeutic applications.

  1. Electronic excitation of molecules in solution calculated using the symmetry-adapted cluster–configuration interaction method in the polarizable continuum model

    International Nuclear Information System (INIS)

    Fukuda, Ryoichi; Ehara, Masahiro

    2015-01-01

    The effects from solvent environment are specific to the electronic states; therefore, a computational scheme for solvent effects consistent with the electronic states is necessary to discuss electronic excitation of molecules in solution. The PCM (polarizable continuum model) SAC (symmetry-adapted cluster) and SAC-CI (configuration interaction) methods are developed for such purposes. The PCM SAC-CI adopts the state-specific (SS) solvation scheme where solvent effects are self-consistently considered for every ground and excited states. For efficient computations of many excited states, we develop a perturbative approximation for the PCM SAC-CI method, which is called corrected linear response (cLR) scheme. Our test calculations show that the cLR PCM SAC-CI is a very good approximation of the SS PCM SAC-CI method for polar and nonpolar solvents

  2. Membrane Protein Properties Revealed through Data-Rich Electrostatics Calculations.

    Science.gov (United States)

    Marcoline, Frank V; Bethel, Neville; Guerriero, Christopher J; Brodsky, Jeffrey L; Grabe, Michael

    2015-08-04

    The electrostatic properties of membrane proteins often reveal many of their key biophysical characteristics, such as ion channel selectivity and the stability of charged membrane-spanning segments. The Poisson-Boltzmann (PB) equation is the gold standard for calculating protein electrostatics, and the software APBSmem enables the solution of the PB equation in the presence of a membrane. Here, we describe significant advances to APBSmem, including full automation of system setup, per-residue energy decomposition, incorporation of PDB2PQR, calculation of membrane-induced pKa shifts, calculation of non-polar energies, and command-line scripting for large-scale calculations. We highlight these new features with calculations carried out on a number of membrane proteins, including the recently solved structure of the ion channel TRPV1 and a large survey of 1,614 membrane proteins of known structure. This survey provides a comprehensive list of residues with large electrostatic penalties for being embedded in the membrane, potentially revealing interesting functional information. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes.

    Science.gov (United States)

    Gkionis, Konstantinos; Kruse, Holger; Šponer, Jiří

    2016-04-12

    Modern dispersion-corrected DFT methods have made it possible to perform reliable QM studies on complete nucleic acid (NA) building blocks having hundreds of atoms. Such calculations, although still limited to investigations of potential energy surfaces, enhance the portfolio of computational methods applicable to NAs and offer considerably more accurate intrinsic descriptions of NAs than standard MM. However, in practice such calculations are hampered by the use of implicit solvent environments and truncation of the systems. Conventional QM optimizations are spoiled by spurious intramolecular interactions and severe structural deformations. Here we compare two approaches designed to suppress such artifacts: partially restrained continuum solvent QM and explicit solvent QM/MM optimizations. We report geometry relaxations of a set of diverse double-quartet guanine quadruplex (GQ) DNA stems. Both methods provide neat structures without major artifacts. However, each one also has distinct weaknesses. In restrained optimizations, all errors in the target geometries (i.e., low-resolution X-ray and NMR structures) are transferred to the optimized geometries. In QM/MM, the initial solvent configuration causes some heterogeneity in the geometries. Nevertheless, both approaches represent a decisive step forward compared to conventional optimizations. We refine earlier computations that revealed sizable differences in the relative energies of GQ stems computed with AMBER MM and QM. We also explore the dependence of the QM/MM results on the applied computational protocol.

  4. Electrostatic interactions in aqueous solutions of polyelectrolyte

    International Nuclear Information System (INIS)

    Belloni, Luc

    1982-01-01

    In this study, the structure, equilibrium and transport properties of poly-electrolytes solutions are reported. These dissymmetric systems are studied in the context of a primitive model (Charged hard spheres and rods in a solvent continuum). The first phenomenon studied is the strong electrostatic attractive interaction of counterions on the poly-ion surface. The model used considers the poly-ions on a matrix and the different concentrations are calculated using the P.B. equation. Auto-diffusion coefficients obtained give a good description of experimental slowing down of the counterions. The model allows a correlation between the theoretical limits represented by Bjerrum's and Manning's models and gives a physical significance to the concept of condensation. In the second part, the complete structure is calculated using only slightly restrictive H.N.C. approximation. This theory enables all the pair correlation functions to be calculated as well as thermodynamic data and structure factors. The last part of this study treats transport phenomena. Quasi-elastic light scattering gives information on the autocorrelation function of the scattered light intensity. Analysis using cumulants leads to an effective diffusion coefficient which is theoretically related to the structure factor and the hydrodynamic interactions. A crude approximation of the last contribution allows to fit the experimental data. (author) [fr

  5. Nonlocal and nonlinear electrostatics of a dipolar Coulomb fluid.

    Science.gov (United States)

    Sahin, Buyukdagli; Ralf, Blossey

    2014-07-16

    We study a model Coulomb fluid consisting of dipolar solvent molecules of finite extent which generalizes the point-like dipolar Poisson-Boltzmann model (DPB) previously introduced by Coalson and Duncan (1996 J. Phys. Chem. 100 2612) and Abrashkin et al (2007 Phys. Rev. Lett. 99 077801). We formulate a nonlocal Poisson-Boltzmann equation (NLPB) and study both linear and nonlinear dielectric response in this model for the case of a single plane geometry. Our results shed light on the relevance of nonlocal versus nonlinear effects in continuum models of material electrostatics.

  6. 3D RISM theory with fast reciprocal-space electrostatics

    Energy Technology Data Exchange (ETDEWEB)

    Heil, Jochen; Kast, Stefan M., E-mail: stefan.kast@tu-dortmund.de [Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 6, 44227 Dortmund (Germany)

    2015-03-21

    The calculation of electrostatic solute-solvent interactions in 3D RISM (“three-dimensional reference interaction site model”) integral equation theory is recast in a form that allows for a computational treatment analogous to the “particle-mesh Ewald” formalism as used for molecular simulations. In addition, relations that connect 3D RISM correlation functions and interaction potentials with thermodynamic quantities such as the chemical potential and average solute-solvent interaction energy are reformulated in a way that calculations of expensive real-space electrostatic terms on the 3D grid are completely avoided. These methodical enhancements allow for both, a significant speedup particularly for large solute systems and a smoother convergence of predicted thermodynamic quantities with respect to box size, as illustrated for several benchmark systems.

  7. 3D RISM theory with fast reciprocal-space electrostatics.

    Science.gov (United States)

    Heil, Jochen; Kast, Stefan M

    2015-03-21

    The calculation of electrostatic solute-solvent interactions in 3D RISM ("three-dimensional reference interaction site model") integral equation theory is recast in a form that allows for a computational treatment analogous to the "particle-mesh Ewald" formalism as used for molecular simulations. In addition, relations that connect 3D RISM correlation functions and interaction potentials with thermodynamic quantities such as the chemical potential and average solute-solvent interaction energy are reformulated in a way that calculations of expensive real-space electrostatic terms on the 3D grid are completely avoided. These methodical enhancements allow for both, a significant speedup particularly for large solute systems and a smoother convergence of predicted thermodynamic quantities with respect to box size, as illustrated for several benchmark systems.

  8. 3D RISM theory with fast reciprocal-space electrostatics

    International Nuclear Information System (INIS)

    Heil, Jochen; Kast, Stefan M.

    2015-01-01

    The calculation of electrostatic solute-solvent interactions in 3D RISM (“three-dimensional reference interaction site model”) integral equation theory is recast in a form that allows for a computational treatment analogous to the “particle-mesh Ewald” formalism as used for molecular simulations. In addition, relations that connect 3D RISM correlation functions and interaction potentials with thermodynamic quantities such as the chemical potential and average solute-solvent interaction energy are reformulated in a way that calculations of expensive real-space electrostatic terms on the 3D grid are completely avoided. These methodical enhancements allow for both, a significant speedup particularly for large solute systems and a smoother convergence of predicted thermodynamic quantities with respect to box size, as illustrated for several benchmark systems

  9. APBSmem: a graphical interface for electrostatic calculations at the membrane.

    Directory of Open Access Journals (Sweden)

    Keith M Callenberg

    2010-09-01

    Full Text Available Electrostatic forces are one of the primary determinants of molecular interactions. They help guide the folding of proteins, increase the binding of one protein to another and facilitate protein-DNA and protein-ligand binding. A popular method for computing the electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB equation, and there are several easy-to-use software packages available that solve the PB equation for soluble proteins. Here we present a freely available program, called APBSmem, for carrying out these calculations in the presence of a membrane. The Adaptive Poisson-Boltzmann Solver (APBS is used as a back-end for solving the PB equation, and a Java-based graphical user interface (GUI coordinates a set of routines that introduce the influence of the membrane, determine its placement relative to the protein, and set the membrane potential. The software Jmol is embedded in the GUI to visualize the protein inserted in the membrane before the calculation and the electrostatic potential after completing the computation. We expect that the ease with which the GUI allows one to carry out these calculations will make this software a useful resource for experimenters and computational researchers alike. Three examples of membrane protein electrostatic calculations are carried out to illustrate how to use APBSmem and to highlight the different quantities of interest that can be calculated.

  10. NMR investigation and theoretical calculations of the effect of solvent on the conformational analysis of 4',7-di-hydroxy-8-prenylflavan

    Directory of Open Access Journals (Sweden)

    Alcântara Antônio Flávio de Carvalho

    2004-01-01

    Full Text Available The NMR conformational study of 4',7-di-hydroxy-8-prenylflavan 1 was carried out in acetone-d6, DMSO-d6 and CDCl3 which enabled the proposition of three conformations, namely 1a, 1b and 1c, differing in the position of the prenyl group. Geometry optimizations performed using AM1 method showed that 1a (deltaHf = -86.2 kcal/mol is as stable as 1b (deltaHf = -85.1 kcal/mol and 1c (deltaHf = -85.4 kcal/mol. When the solvent was included, the calculations showed that the solute-solvent interactions could be explained either in the light of the electronic intermolecular delocalization or the electrostatic character between solute and solvent. Theoretical calculations (HF/6-31G*, deltaFT/BLYP/6-31G*, and deltaFT/B3LYP/6-31G* showed that the combination of these types of interactions present in each solute-solvent system, dependent on the chemical properties of the solvent, lead to different spatial arrangements of the prenyl group, which in turn determined the conformation of 1.

  11. Analyzed method for calculating the distribution of electrostatic field

    International Nuclear Information System (INIS)

    Lai, W.

    1981-01-01

    An analyzed method for calculating the distribution of electrostatic field under any given axial gradient in tandem accelerators is described. This method possesses satisfactory accuracy compared with the results of numerical calculation

  12. Electrostatic frequency maps for amide-I mode of β-peptide: Comparison of molecular mechanics force field and DFT calculations

    Science.gov (United States)

    Cai, Kaicong; Zheng, Xuan; Du, Fenfen

    2017-08-01

    The spectroscopy of amide-I vibrations has been widely utilized for the understanding of dynamical structure of polypeptides. For the modeling of amide-I spectra, two frequency maps were built for β-peptide analogue (N-ethylpropionamide, NEPA) in a number of solvents within different schemes (molecular mechanics force field based, GM map; DFT calculation based, GD map), respectively. The electrostatic potentials on the amide unit that originated from solvents and peptide backbone were correlated to the amide-I frequency shift from gas phase to solution phase during map parameterization. GM map is easier to construct with negligible computational cost since the frequency calculations for the samples are purely based on force field, while GD map utilizes sophisticated DFT calculations on the representative solute-solvent clusters and brings insight into the electronic structures of solvated NEPA and its chemical environments. The results show that the maps' predicted amide-I frequencies present solvation environmental sensitivities and exhibit their specific characters with respect to the map protocols, and the obtained vibrational parameters are in satisfactory agreement with experimental amide-I spectra of NEPA in solution phase. Although different theoretical schemes based maps have their advantages and disadvantages, the present maps show their potentials in interpreting the amide-I spectra for β-peptides, respectively.

  13. Continuum model of non-equilibrium solvation and solvent effect on ultra-fast processes

    International Nuclear Information System (INIS)

    Li Xiangyuan; Fu Kexiang; Zhu Quan

    2006-01-01

    In the past 50 years, non-equilibrium solvation theory for ultra-fast processes such as electron transfer and light absorption/emission has attracted particular interest. A great deal of research efforts was made in this area and various models which give reasonable qualitative descriptions for such as solvent reorganization energy in electron transfer and spectral shift in solution, were developed within the framework of continuous medium theory. In a series of publications by the authors, we clarified that the expression of the non-equilibrium electrostatic free energy that is at the dominant position of non-equilibrium solvation and serves as the basis of various models, however, was incorrectly formulated. In this work, the authors argue that reversible charging work integration was inappropriately applied in the past to an irreversible path linking the equilibrium or the non-equilibrium state. Because the step from the equilibrium state to the nonequilibrium state is factually thermodynamically irreversible, the conventional expression for non-equilibrium free energy that was deduced in different ways is unreasonable. Here the authors derive the non-equilibrium free energy to a quite different form according to Jackson integral formula. Such a difference throws doubts to the models including the famous Marcus two-sphere model for solvent reorganization energy of electron transfer and the Lippert-Mataga equation for spectral shift. By introducing the concept of 'spring energy' arising from medium polarizations, the energy constitution of the non-equilibrium state is highlighted. For a solute-solvent system, the authors separate the total electrostatic energy into different components: the self-energies of solute charge and polarized charge, the interaction energy between them and the 'spring energy' of the solvent polarization. With detailed reasoning and derivation, our formula for non-equilibrium free energy can be reached through different ways. Based on the

  14. Comparative Assessment of Nonlocal Continuum Solvent Models Exhibiting Overscreening

    Directory of Open Access Journals (Sweden)

    Ren Baihua

    2017-01-01

    Full Text Available Nonlocal continua have been proposed to offer a more realistic model for the electrostatic response of solutions such as the electrolyte solvents prominent in biology and electrochemistry. In this work, we review three nonlocal models based on the Landau-Ginzburg framework which have been proposed but not directly compared previously, due to different expressions of the nonlocal constitutive relationship. To understand the relationships between these models and the underlying physical insights from which they are derive, we situate these models into a single, unified Landau-Ginzburg framework. One of the models offers the capacity to interpret how temperature changes affect dielectric response, and we note that the variations with temperature are qualitatively reasonable even though predictions at ambient temperatures are not quantitatively in agreement with experiment. Two of these models correctly reproduce overscreening (oscillations between positive and negative polarization charge densities, and we observe small differences between them when we simulate the potential between parallel plates held at constant potential. These computations require reformulating the two models as coupled systems of local partial differential equations (PDEs, and we use spectral methods to discretize both problems. We propose further assessments to discriminate between the models, particularly in regards to establishing boundary conditions and comparing to explicit-solvent molecular dynamics simulations.

  15. Efficient implementation of three-dimensional reference interaction site model self-consistent-field method: application to solvatochromic shift calculations.

    Science.gov (United States)

    Minezawa, Noriyuki; Kato, Shigeki

    2007-02-07

    The authors present an implementation of the three-dimensional reference interaction site model self-consistent-field (3D-RISM-SCF) method. First, they introduce a robust and efficient algorithm for solving the 3D-RISM equation. The algorithm is a hybrid of the Newton-Raphson and Picard methods. The Jacobian matrix is analytically expressed in a computationally useful form. Second, they discuss the solute-solvent electrostatic interaction. For the solute to solvent route, the electrostatic potential (ESP) map on a 3D grid is constructed directly from the electron density. The charge fitting procedure is not required to determine the ESP. For the solvent to solute route, the ESP acting on the solute molecule is derived from the solvent charge distribution obtained by solving the 3D-RISM equation. Matrix elements of the solute-solvent interaction are evaluated by the direct numerical integration. A remarkable reduction in the computational time is observed in both routes. Finally, the authors implement the first derivatives of the free energy with respect to the solute nuclear coordinates. They apply the present method to "solute" water and formaldehyde in aqueous solvent using the simple point charge model, and the results are compared with those from other methods: the six-dimensional molecular Ornstein-Zernike SCF, the one-dimensional site-site RISM-SCF, and the polarizable continuum model. The authors also calculate the solvatochromic shifts of acetone, benzonitrile, and nitrobenzene using the present method and compare them with the experimental and other theoretical results.

  16. Nonlocal Electrostatics in Spherical Geometries Using Eigenfunction Expansions of Boundary-Integral Operators.

    Science.gov (United States)

    Bardhan, Jaydeep P; Knepley, Matthew G; Brune, Peter

    2015-01-01

    In this paper, we present an exact, infinite-series solution to Lorentz nonlocal continuum electrostatics for an arbitrary charge distribution in a spherical solute. Our approach relies on two key steps: (1) re-formulating the PDE problem using boundary-integral equations, and (2) diagonalizing the boundary-integral operators using the fact that their eigenfunctions are the surface spherical harmonics. To introduce this uncommon approach for calculations in separable geometries, we first re-derive Kirkwood's classic results for a protein surrounded concentrically by a pure-water ion-exclusion (Stern) layer and then a dilute electrolyte, which is modeled with the linearized Poisson-Boltzmann equation. The eigenfunction-expansion approach provides a computationally efficient way to test some implications of nonlocal models, including estimating the reasonable range of the nonlocal length-scale parameter λ. Our results suggest that nonlocal solvent response may help to reduce the need for very high dielectric constants in calculating pH-dependent protein behavior, though more sophisticated nonlocal models are needed to resolve this question in full. An open-source MATLAB implementation of our approach is freely available online.

  17. A Multi-Scale Method for Dynamics Simulation in Continuum Solvent Models I: Finite-Difference Algorithm for Navier-Stokes Equation.

    Science.gov (United States)

    Xiao, Li; Cai, Qin; Li, Zhilin; Zhao, Hongkai; Luo, Ray

    2014-11-25

    A multi-scale framework is proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent. This article reports our initial efforts to formulate the physical concepts necessary for coupling the two mechanics and develop a 3D numerical algorithm to simulate the solvent fluid via the Navier-Stokes equation. The numerical algorithm was validated with multiple test cases. The validation shows that the algorithm is effective and stable, with observed accuracy consistent with our design.

  18. Phase-shift calculation using continuum-discretized states

    International Nuclear Information System (INIS)

    Suzuki, Y.; Horiuchi, W.; Arai, K.

    2009-01-01

    We present a method for calculating scattering phase shifts which utilizes continuum-discretized states obtained in a bound-state type calculation. The wrong asymptotic behavior of the discretized state is remedied by means of the Green's function formalism. Test examples confirm the accuracy of the method. The α+n scattering is described using realistic nucleon-nucleon potentials. The 3/2 - and 1/2 - phase shifts obtained in a single-channel calculation are too small in comparison with experiment. The 1/2 + phase shifts are in reasonable agreement with experiment, and gain contributions both from the tensor and central components of the nucleon-nucleon potential.

  19. Solvent effects on the excited-state double proton transfer mechanism in the 7-azaindole dimer: a TDDFT study with the polarizable continuum model.

    Science.gov (United States)

    Yu, Xue-Fang; Yamazaki, Shohei; Taketsugu, Tetsuya

    2017-08-30

    Solvent effects on the excited-state double proton transfer (ESDPT) mechanism in the 7-azaindole (7AI) dimer were investigated using the time-dependent density functional theory (TDDFT) method. Excited-state potential energy profiles along the reaction paths in a locally excited (LE) state and a charge transfer (CT) state were calculated using the polarizable continuum model (PCM) to include the solvent effect. A series of non-polar and polar solvents with different dielectric constants were used to examine the polarity effect on the ESDPT mechanism. The present results suggest that in a non-polar solvent and a polar solvent with a small dielectric constant, ESDPT follows a concerted mechanism, similar to the case in the gas phase. In a polar solvent with a relatively large dielectric constant, however, ESDPT is likely to follow a stepwise mechanism via a stable zwitterionic intermediate in the LE state on the adiabatic potential energy surface, although inclusion of zero-point vibrational energy (ZPE) corrections again suggests the concerted mechanism. In the meantime, the stepwise reaction path involving the CT state with neutral intermediates is also examined, and is found to be less competitive than the concerted or stepwise path in the LE state in both non-polar and polar solvents. The present study provides a new insight into the experimental controversy of the ESDPT mechanism of the 7AI dimer in a solution.

  20. DelPhiForce web server: electrostatic forces and energy calculations and visualization.

    Science.gov (United States)

    Li, Lin; Jia, Zhe; Peng, Yunhui; Chakravorty, Arghya; Sun, Lexuan; Alexov, Emil

    2017-11-15

    Electrostatic force is an essential component of the total force acting between atoms and macromolecules. Therefore, accurate calculations of electrostatic forces are crucial for revealing the mechanisms of many biological processes. We developed a DelPhiForce web server to calculate and visualize the electrostatic forces at molecular level. DelPhiForce web server enables modeling of electrostatic forces on individual atoms, residues, domains and molecules, and generates an output that can be visualized by VMD software. Here we demonstrate the usage of the server for various biological problems including protein-cofactor, domain-domain, protein-protein, protein-DNA and protein-RNA interactions. The DelPhiForce web server is available at: http://compbio.clemson.edu/delphi-force. delphi@clemson.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  1. Solvent effects on the magnetic shielding of tertiary butyl alcohol

    African Journals Online (AJOL)

    )4 and tetramethyl ammonium cation N(CH3)4(+) have also been presented. KEY WORDS: Solvent effects, Magnetic shielding, Tertiary butyl alcohol, Tertiary butyl amine, Continuum solvation calculations, Chemical shift estimation methods

  2. MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations.

    Science.gov (United States)

    Vergara-Perez, Sandra; Marucho, Marcelo

    2016-01-01

    One of the most used and efficient approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation. There are several software packages available that solve the PB equation for molecules in aqueous electrolyte solutions. Most of these software packages are useful for scientists with specialized training and expertise in computational biophysics. However, the user is usually required to manually take several important choices, depending on the complexity of the biological system, to successfully obtain the numerical solution of the PB equation. This may become an obstacle for researchers, experimentalists, even students with no special training in computational methodologies. Aiming to overcome this limitation, in this article we present MPBEC, a free, cross-platform, open-source software that provides non-experts in the field an easy and efficient way to perform biomolecular electrostatic calculations on single processor computers. MPBEC is a Matlab script based on the Adaptative Poisson Boltzmann Solver, one of the most popular approaches used to solve the PB equation. MPBEC does not require any user programming, text editing or extensive statistical skills, and comes with detailed user-guide documentation. As a unique feature, MPBEC includes a useful graphical user interface (GUI) application which helps and guides users to configure and setup the optimal parameters and approximations to successfully perform the required biomolecular electrostatic calculations. The GUI also incorporates visualization tools to facilitate users pre- and post- analysis of structural and electrical properties of biomolecules.

  3. MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations

    Science.gov (United States)

    Vergara-Perez, Sandra; Marucho, Marcelo

    2016-01-01

    One of the most used and efficient approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation. There are several software packages available that solve the PB equation for molecules in aqueous electrolyte solutions. Most of these software packages are useful for scientists with specialized training and expertise in computational biophysics. However, the user is usually required to manually take several important choices, depending on the complexity of the biological system, to successfully obtain the numerical solution of the PB equation. This may become an obstacle for researchers, experimentalists, even students with no special training in computational methodologies. Aiming to overcome this limitation, in this article we present MPBEC, a free, cross-platform, open-source software that provides non-experts in the field an easy and efficient way to perform biomolecular electrostatic calculations on single processor computers. MPBEC is a Matlab script based on the Adaptative Poisson-Boltzmann Solver, one of the most popular approaches used to solve the PB equation. MPBEC does not require any user programming, text editing or extensive statistical skills, and comes with detailed user-guide documentation. As a unique feature, MPBEC includes a useful graphical user interface (GUI) application which helps and guides users to configure and setup the optimal parameters and approximations to successfully perform the required biomolecular electrostatic calculations. The GUI also incorporates visualization tools to facilitate users pre- and post-analysis of structural and electrical properties of biomolecules.

  4. Nonlocal Electrostatics in Spherical Geometries Using Eigenfunction Expansions of Boundary-Integral Operators

    Science.gov (United States)

    Bardhan, Jaydeep P.; Knepley, Matthew G.; Brune, Peter

    2015-01-01

    In this paper, we present an exact, infinite-series solution to Lorentz nonlocal continuum electrostatics for an arbitrary charge distribution in a spherical solute. Our approach relies on two key steps: (1) re-formulating the PDE problem using boundary-integral equations, and (2) diagonalizing the boundary-integral operators using the fact that their eigenfunctions are the surface spherical harmonics. To introduce this uncommon approach for calculations in separable geometries, we first re-derive Kirkwood’s classic results for a protein surrounded concentrically by a pure-water ion-exclusion (Stern) layer and then a dilute electrolyte, which is modeled with the linearized Poisson–Boltzmann equation. The eigenfunction-expansion approach provides a computationally efficient way to test some implications of nonlocal models, including estimating the reasonable range of the nonlocal length-scale parameter λ. Our results suggest that nonlocal solvent response may help to reduce the need for very high dielectric constants in calculating pH-dependent protein behavior, though more sophisticated nonlocal models are needed to resolve this question in full. An open-source MATLAB implementation of our approach is freely available online. PMID:26273581

  5. Massive calculations of electrostatic potentials and structure maps of biopolymers in a distributed computing environment

    International Nuclear Information System (INIS)

    Akishina, T.P.; Ivanov, V.V.; Stepanenko, V.A.

    2013-01-01

    Among the key factors determining the processes of transcription and translation are the distributions of the electrostatic potentials of DNA, RNA and proteins. Calculations of electrostatic distributions and structure maps of biopolymers on computers are time consuming and require large computational resources. We developed the procedures for organization of massive calculations of electrostatic potentials and structure maps for biopolymers in a distributed computing environment (several thousands of cores).

  6. Continuum variational and diffusion quantum Monte Carlo calculations

    International Nuclear Information System (INIS)

    Needs, R J; Towler, M D; Drummond, N D; Lopez RIos, P

    2010-01-01

    This topical review describes the methodology of continuum variational and diffusion quantum Monte Carlo calculations. These stochastic methods are based on many-body wavefunctions and are capable of achieving very high accuracy. The algorithms are intrinsically parallel and well suited to implementation on petascale computers, and the computational cost scales as a polynomial in the number of particles. A guide to the systems and topics which have been investigated using these methods is given. The bulk of the article is devoted to an overview of the basic quantum Monte Carlo methods, the forms and optimization of wavefunctions, performing calculations under periodic boundary conditions, using pseudopotentials, excited-state calculations, sources of calculational inaccuracy, and calculating energy differences and forces. (topical review)

  7. Calculations of time-of-flight aberrations in practical electrostatic electron lenses using the differential algebraic method

    International Nuclear Information System (INIS)

    Kang, Yongfeng; Zhao, Jingyi; Tang, Tiantong

    2013-01-01

    The high order time-of-flight (TOF) aberrations in a practical electrostatic electron lens are calculated using the differential algebraic (DA) method. The electrostatic fields of the electrostatic lens, which are calculated by the FEM methods, are in the form of discrete arrays. Thus, the proposed DA method is applicable for engineering designs, and programs are written to compute up to fifth order TOF aberrations of practical electrostatic electron lenses. An example is given, and TOF aberrations up to the fifth order are calculated. It is proven that the numerical results for the electrostatic fields in the form of discrete arrays have a good accuracy compared with the theoretical solutions. The accuracy is limited only by the accuracy of the numerical computation of the fields and the numerical computation algorithms for interpolation and integration. Finally, a practical electrostatic electron lens is analysed and discussed as an example.

  8. Electrostatics of proteins in dielectric solvent continua. I. An accurate and efficient reaction field description.

    Science.gov (United States)

    Bauer, Sebastian; Mathias, Gerald; Tavan, Paul

    2014-03-14

    We present a reaction field (RF) method which accurately solves the Poisson equation for proteins embedded in dielectric solvent continua at a computational effort comparable to that of an electrostatics calculation with polarizable molecular mechanics (MM) force fields. The method combines an approach originally suggested by Egwolf and Tavan [J. Chem. Phys. 118, 2039 (2003)] with concepts generalizing the Born solution [Z. Phys. 1, 45 (1920)] for a solvated ion. First, we derive an exact representation according to which the sources of the RF potential and energy are inducible atomic anti-polarization densities and atomic shielding charge distributions. Modeling these atomic densities by Gaussians leads to an approximate representation. Here, the strengths of the Gaussian shielding charge distributions are directly given in terms of the static partial charges as defined, e.g., by standard MM force fields for the various atom types, whereas the strengths of the Gaussian anti-polarization densities are calculated by a self-consistency iteration. The atomic volumes are also described by Gaussians. To account for covalently overlapping atoms, their effective volumes are calculated by another self-consistency procedure, which guarantees that the dielectric function ε(r) is close to one everywhere inside the protein. The Gaussian widths σ(i) of the atoms i are parameters of the RF approximation. The remarkable accuracy of the method is demonstrated by comparison with Kirkwood's analytical solution for a spherical protein [J. Chem. Phys. 2, 351 (1934)] and with computationally expensive grid-based numerical solutions for simple model systems in dielectric continua including a di-peptide (Ac-Ala-NHMe) as modeled by a standard MM force field. The latter example shows how weakly the RF conformational free energy landscape depends on the parameters σ(i). A summarizing discussion highlights the achievements of the new theory and of its approximate solution particularly by

  9. Electrostatics of proteins in dielectric solvent continua. I. An accurate and efficient reaction field description

    Energy Technology Data Exchange (ETDEWEB)

    Bauer, Sebastian; Mathias, Gerald; Tavan, Paul, E-mail: paul.tavan@physik.uni-muenchen.de [Lehrstuhl für BioMolekulare Optik, Ludwig–Maximilians Universität München, Oettingenstr. 67, 80538 München (Germany)

    2014-03-14

    We present a reaction field (RF) method which accurately solves the Poisson equation for proteins embedded in dielectric solvent continua at a computational effort comparable to that of an electrostatics calculation with polarizable molecular mechanics (MM) force fields. The method combines an approach originally suggested by Egwolf and Tavan [J. Chem. Phys. 118, 2039 (2003)] with concepts generalizing the Born solution [Z. Phys. 1, 45 (1920)] for a solvated ion. First, we derive an exact representation according to which the sources of the RF potential and energy are inducible atomic anti-polarization densities and atomic shielding charge distributions. Modeling these atomic densities by Gaussians leads to an approximate representation. Here, the strengths of the Gaussian shielding charge distributions are directly given in terms of the static partial charges as defined, e.g., by standard MM force fields for the various atom types, whereas the strengths of the Gaussian anti-polarization densities are calculated by a self-consistency iteration. The atomic volumes are also described by Gaussians. To account for covalently overlapping atoms, their effective volumes are calculated by another self-consistency procedure, which guarantees that the dielectric function ε(r) is close to one everywhere inside the protein. The Gaussian widths σ{sub i} of the atoms i are parameters of the RF approximation. The remarkable accuracy of the method is demonstrated by comparison with Kirkwood's analytical solution for a spherical protein [J. Chem. Phys. 2, 351 (1934)] and with computationally expensive grid-based numerical solutions for simple model systems in dielectric continua including a di-peptide (Ac-Ala-NHMe) as modeled by a standard MM force field. The latter example shows how weakly the RF conformational free energy landscape depends on the parameters σ{sub i}. A summarizing discussion highlights the achievements of the new theory and of its approximate solution

  10. Numerical solution of boundary-integral equations for molecular electrostatics.

    Science.gov (United States)

    Bardhan, Jaydeep P

    2009-03-07

    Numerous molecular processes, such as ion permeation through channel proteins, are governed by relatively small changes in energetics. As a result, theoretical investigations of these processes require accurate numerical methods. In the present paper, we evaluate the accuracy of two approaches to simulating boundary-integral equations for continuum models of the electrostatics of solvation. The analysis emphasizes boundary-element method simulations of the integral-equation formulation known as the apparent-surface-charge (ASC) method or polarizable-continuum model (PCM). In many numerical implementations of the ASC/PCM model, one forces the integral equation to be satisfied exactly at a set of discrete points on the boundary. We demonstrate in this paper that this approach to discretization, known as point collocation, is significantly less accurate than an alternative approach known as qualocation. Furthermore, the qualocation method offers this improvement in accuracy without increasing simulation time. Numerical examples demonstrate that electrostatic part of the solvation free energy, when calculated using the collocation and qualocation methods, can differ significantly; for a polypeptide, the answers can differ by as much as 10 kcal/mol (approximately 4% of the total electrostatic contribution to solvation). The applicability of the qualocation discretization to other integral-equation formulations is also discussed, and two equivalences between integral-equation methods are derived.

  11. Effect of electrostatic interaction on thermochemical behavior of 12-crown-4 ether in various polar solvents

    International Nuclear Information System (INIS)

    Barannikov, Vladimir P.; Guseynov, Sabir S.; Vyugin, Anatoliy I.

    2010-01-01

    The enthalpies of solution of 12-crown-4 ether have been measured in chloroform, ethyl acetate, acetone, pyridine, acetonitrile and methanol at 298.15 K. The values of enthalpy of solvation and solute-solvent interaction were determined from the obtained results and similar literature data for 12-crown-4 in solvents of various polarities. It was shown that the certain correlation is observed between the enthalpy of solute-solvent interaction and the squared dipole moment of the solvent molecules for solutions in tetrachlormethane, ethyl acetate, pyridine, acetonitrile, DMF, DMSO and propylene carbonate. This means that the electrostatic interaction of 12-crown-4 with polar solvent molecules contributes significantly to the exothermic effect of solvation. The understated negative value was found for the enthalpy of interaction of 12-crown-4 with acetone that can be connected with domination of low polar conformer of the crown ether in acetone medium. The most negative values of enthalpy of solvation are observed for solutions in chloroform and water because of hydrogen bonding between O-atoms of crown ether and molecules of the indicated solvents. This effect is not observed for methanol. The negative coefficient of pairwise solute-solute interaction in methanol indicates that the effects of solvophobic solute-solute interaction and H-bonding of the ether molecule with chain associates of methanol are not evinced in the thermochemical behavior of 12-crown-4.

  12. Embedding beyond electrostatics

    DEFF Research Database (Denmark)

    Nåbo, Lina J.; Olsen, Jógvan Magnus Haugaard; Holmgaard List, Nanna

    2016-01-01

    We study excited states of cholesterol in solution and show that, in this specific case, solute wave-function confinement is the main effect of the solvent. This is rationalized on the basis of the polarizable density embedding scheme, which in addition to polarizable embedding includes non-electrostatic...... repulsion that effectively confines the solute wave function to its cavity. We illustrate how the inclusion of non-electrostatic repulsion results in a successful identification of the intense π → π∗ transition, which was not possible using an embedding method that only includes electrostatics....... This underlines the importance of non-electrostatic repulsion in quantum-mechanical embedding-based methods....

  13. Nonlocal Poisson-Fermi model for ionic solvent.

    Science.gov (United States)

    Xie, Dexuan; Liu, Jinn-Liang; Eisenberg, Bob

    2016-07-01

    We propose a nonlocal Poisson-Fermi model for ionic solvent that includes ion size effects and polarization correlations among water molecules in the calculation of electrostatic potential. It includes the previous Poisson-Fermi models as special cases, and its solution is the convolution of a solution of the corresponding nonlocal Poisson dielectric model with a Yukawa-like kernel function. The Fermi distribution is shown to be a set of optimal ionic concentration functions in the sense of minimizing an electrostatic potential free energy. Numerical results are reported to show the difference between a Poisson-Fermi solution and a corresponding Poisson solution.

  14. Web servers and services for electrostatics calculations with APBS and PDB2PQR

    Science.gov (United States)

    Unni, Samir; Huang, Yong; Hanson, Robert; Tobias, Malcolm; Krishnan, Sriram; Li, Wilfred W.; Nielsen, Jens E.; Baker, Nathan A.

    2011-01-01

    APBS and PDB2PQR are widely utilized free software packages for biomolecular electrostatics calculations. Using the Opal toolkit, we have developed a Web services framework for these software packages that enables the use of APBS and PDB2PQR by users who do not have local access to the necessary amount of computational capabilities. This not only increases accessibility of the software to a wider range of scientists, educators, and students but it also increases the availability of electrostatics calculations on portable computing platforms. Users can access this new functionality in two ways. First, an Opal-enabled version of APBS is provided in current distributions, available freely on the web. Second, we have extended the PDB2PQR web server to provide an interface for the setup, execution, and visualization electrostatics potentials as calculated by APBS. This web interface also uses the Opal framework which ensures the scalability needed to support the large APBS user community. Both of these resources are available from the APBS/PDB2PQR website: http://www.poissonboltzmann.org/. PMID:21425296

  15. Effects of dielectric inhomogeneity on electrostatic twist rigidity of a helical biomolecule in Debye-Hückel regime

    Science.gov (United States)

    Rezaie-Dereshgi, Amir; Mohammad-Rafiee, Farshid

    2018-04-01

    The electrostatic interactions play a crucial role in biological systems. Here we consider an impermeable dielectric molecule in the solvent with a different dielectric constant. The electrostatic free energy in the problem is studied in the Debye-Hückel regime using the analytical Green function that is calculated in the paper. Using this electrostatic free energy, we study the electrostatic contribution to the twist rigidity of a double stranded helical molecule such as a DNA and an actin filament. The dependence of the electrostatic twist rigidity of the molecule to the dielectric inhomogeneity, structural parameters, and the salt concentration is studied. It is shown that, depending on the parameters, the electrostatic twist rigidity could be positive or negative.

  16. Continuous development of schemes for parallel computing of the electrostatics in biological systems: implementation in DelPhi.

    Science.gov (United States)

    Li, Chuan; Petukh, Marharyta; Li, Lin; Alexov, Emil

    2013-08-15

    Due to the enormous importance of electrostatics in molecular biology, calculating the electrostatic potential and corresponding energies has become a standard computational approach for the study of biomolecules and nano-objects immersed in water and salt phase or other media. However, the electrostatics of large macromolecules and macromolecular complexes, including nano-objects, may not be obtainable via explicit methods and even the standard continuum electrostatics methods may not be applicable due to high computational time and memory requirements. Here, we report further development of the parallelization scheme reported in our previous work (Li, et al., J. Comput. Chem. 2012, 33, 1960) to include parallelization of the molecular surface and energy calculations components of the algorithm. The parallelization scheme utilizes different approaches such as space domain parallelization, algorithmic parallelization, multithreading, and task scheduling, depending on the quantity being calculated. This allows for efficient use of the computing resources of the corresponding computer cluster. The parallelization scheme is implemented in the popular software DelPhi and results in speedup of several folds. As a demonstration of the efficiency and capability of this methodology, the electrostatic potential, and electric field distributions are calculated for the bovine mitochondrial supercomplex illustrating their complex topology, which cannot be obtained by modeling the supercomplex components alone. Copyright © 2013 Wiley Periodicals, Inc.

  17. Theoretical Calculation and Validation of the Water Vapor Continuum Absorption

    Science.gov (United States)

    Ma, Qiancheng; Tipping, Richard H.

    1998-01-01

    The primary objective of this investigation is the development of an improved parameterization of the water vapor continuum absorption through the refinement and validation of our existing theoretical formalism. The chief advantage of our approach is the self-consistent, first principles, basis of the formalism which allows us to predict the frequency, temperature and pressure dependence of the continuum absorption as well as provide insights into the physical mechanisms responsible for the continuum absorption. Moreover, our approach is such that the calculated continuum absorption can be easily incorporated into satellite retrieval algorithms and climate models. Accurate determination of the water vapor continuum is essential for the next generation of retrieval algorithms which propose to use the combined constraints of multi-spectral measurements such as those under development for EOS data analysis (e.g., retrieval algorithms based on MODIS and AIRS measurements); current Pathfinder activities which seek to use the combined constraints of infrared and microwave (e.g., HIRS and MSU) measurements to improve temperature and water profile retrievals, and field campaigns which seek to reconcile spectrally-resolved and broad-band measurements such as those obtained as part of FIRE. Current widely used continuum treatments have been shown to produce spectrally dependent errors, with the magnitude of the error dependent on temperature and abundance which produces errors with a seasonal and latitude dependence. Translated into flux, current water vapor continuum parameterizations produce flux errors of order 10 W/ml, which compared to the 4 W/m' magnitude of the greenhouse gas forcing and the 1-2 W/m' estimated aerosol forcing is certainly climatologically significant and unacceptably large. While it is possible to tune the empirical formalisms, the paucity of laboratory measurements, especially at temperatures of interest for atmospheric applications, preclude tuning

  18. Brief note on the statistical calculation of final continuum reaction cross sections of light nuclides

    International Nuclear Information System (INIS)

    Murata, Toru

    2003-01-01

    The level density parameters are determined to reproduce level structure and/or resonance level spacing of the nucleus. In the statistical compound nucleus model, cross sections to discrete levels decrease abruptly, and continuum level cross section increase strongly above the energy point where the continuum levels switched on. In the present study, for the nucleus which level scheme were well determined up to higher excitation energy more than 10 MeV, discrete level cross sections were calculated and summed up and compared with the cross section to the assumed continuum level corresponding to the discrete levels above several MeV excitation energy. Calculation of the (n, n') cross sections were made with CASTHY code of Moldauer model option using level density parameters determined with former method. It is shown that the assumed continuum cross section is fairly large compared with the summed up cross section. Origins of the discrepancy were discussed. (J.P.N.)

  19. Comparative density functional study of the complexes [UO2(CO3)3]4- and [(UO2)3(CO3)6]6- in aqueous solution.

    Science.gov (United States)

    Schlosser, Florian; Moskaleva, Lyudmila V; Kremleva, Alena; Krüger, Sven; Rösch, Notker

    2010-06-28

    With a relativistic all-electron density functional method, we studied two anionic uranium(VI) carbonate complexes that are important for uranium speciation and transport in aqueous medium, the mononuclear tris(carbonato) complex [UO(2)(CO(3))(3)](4-) and the trinuclear hexa(carbonato) complex [(UO(2))(3)(CO(3))(6)](6-). Focusing on the structures in solution, we applied for the first time a full solvation treatment to these complexes. We approximated short-range effects by explicit aqua ligands and described long-range electrostatic interactions via a polarizable continuum model. Structures and vibrational frequencies of "gas-phase" models with explicit aqua ligands agree best with experiment. This is accidental because the continuum model of the solvent to some extent overestimates the electrostatic interactions of these highly anionic systems with the bulk solvent. The calculated free energy change when three mono-nuclear complexes associate to the trinuclear complex, agrees well with experiment and supports the formation of the latter species upon acidification of a uranyl carbonate solution.

  20. Calculations in solvent extraction of rare earth metals

    International Nuclear Information System (INIS)

    Sadanandam, R.; Sharma, A.K.; Fonseca, M.F.; Hubli, R.C.; Suri, A.K.; Singh, D.K.

    2010-01-01

    The paper deals with calculation of number of countercurrent stages in solvent extraction of rare earths both under total reflux and partial reflux conditions to achieve a given degree of purification and recovery. The use of Fenske's equation normally used for separation by distillation is proposed to calculate the number of stages required under total reflux, replacing relative volatility by separation factor. Kremser's equations for extraction and scrubbing are used to calculate the number of stages in extraction and scrubbing modules under partial reflux conditions. McCabe-Thiele's approach is also adopted to arrive at the number of scrubbing stages. (author)

  1. Influence of Solvent-Solvent and Solute-Solvent Interaction Properties on Solvent-Mediated Potential

    International Nuclear Information System (INIS)

    Zhou Shiqi

    2005-01-01

    A recently proposed universal calculational recipe for solvent-mediated potential is applied to calculate excess potential of mean force between two large Lennard-Jones (LJ) or hard core attractive Yukawa particles immersed in small LJ solvent bath at supercritical state. Comparison between the present prediction with a hypernetted chain approximation adopted for solute-solute correlation at infinitely dilute limit and existing simulation data shows high accuracy for the region with large separation, and qualitative reliability for the solute particle contact region. The calculational simplicity of the present recipe allows for a detailed investigation on the effect of the solute-solvent and solvent-solvent interaction details on the excess potential of mean force. The resultant conclusion is that gathering of solvent particles near a solute particle leads to repulsive excess PMF, while depletion of solvent particles away from the solute particle leads to attractive excess PMF, and minor change of the solvent-solvent interaction range has large influence on the excess PMF.

  2. Accuracy of local exchange in the calculation of continuum wavefunctions

    International Nuclear Information System (INIS)

    Biava, D A; Bartschat, K; Saha, H P; Madison, D H

    2002-01-01

    It is well known that electron exchange can play an important role in electron-impact elastic, inelastic and ionization scattering from atoms and molecules. The proper theoretical treatment of exchange yields an inhomogeneous differential equation with a non-local exchange operator. To simplify the calculation, a local approximation is often made for this non-local operator. In this paper, we examine the accuracy of this approximation for the calculation of elastic scattering continuum waves in the presence of an argon ion with a single vacancy in the p-shell. It is found that one can reliably use the local exchange approximation for ionization leading to s-state vacancies but not p-state vacancies

  3. Importance of self-consistency in relativistic continuum random-phase approximation calculations

    International Nuclear Information System (INIS)

    Yang Ding; Cao Ligang; Tian Yuan; Ma Zhongyu

    2010-01-01

    A fully consistent relativistic continuum random phase approximation (RCRPA) is constructed, where the contribution of the continuum spectrum to nuclear excitations is treated exactly by the single-particle Green's function technique. The full consistency of the calculations is achieved that the same effective Lagrangian is adopted for the ground state and the excited states. The negative energy states in the Dirac sea are also included in the single-particle Green's function in the no-sea approximation. The currents from the vector meson and photon exchanges and the Coulomb interaction in RCRPA are treated exactly. The spin-orbit interaction is included naturally in the relativistic frame. Numerical results of the RCRPA are checked with the constrained relativistic mean-field theory. We study the effects of the inconsistency, particularly the currents and Coulomb interaction in various collective multipole excitations.

  4. Time-dependent non-equilibrium dielectric response in QM/continuum approaches

    Energy Technology Data Exchange (ETDEWEB)

    Ding, Feizhi; Lingerfelt, David B.; Li, Xiaosong, E-mail: benedetta.mennucci@unipi.it, E-mail: li@chem.washington.edu [Department of Chemistry, University of Washington, Seattle, Washington 98195 (United States); Mennucci, Benedetta, E-mail: benedetta.mennucci@unipi.it, E-mail: li@chem.washington.edu [Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Risorgimento 35, 56126 Pisa (Italy)

    2015-01-21

    The Polarizable Continuum Models (PCMs) are some of the most inexpensive yet successful methods for including the effects of solvation in quantum-mechanical calculations of molecular systems. However, when applied to the electronic excitation process, these methods are restricted to dichotomously assuming either that the solvent has completely equilibrated with the excited solute charge density (infinite-time limit), or that it retains the configuration that was in equilibrium with the solute prior to excitation (zero-time limit). This renders the traditional PCMs inappropriate for resolving time-dependent solvent effects on non-equilibrium solute electron dynamics like those implicated in the instants following photoexcitation of a solvated molecular species. To extend the existing methods to this non-equilibrium regime, we herein derive and apply a new formalism for a general time-dependent continuum embedding method designed to be propagated alongside the solute’s electronic degrees of freedom in the time domain. Given the frequency-dependent dielectric constant of the solvent, an equation of motion for the dielectric polarization is derived within the PCM framework and numerically integrated simultaneously with the time-dependent Hartree fock/density functional theory equations. Results for small molecular systems show the anticipated dipole quenching and electronic state dephasing/relaxation resulting from out-of-phase charge fluctuations in the dielectric and embedded quantum system.

  5. Efficient Algorithms for Electrostatic Interactions Including Dielectric Contrasts

    Directory of Open Access Journals (Sweden)

    Christian Holm

    2013-10-01

    Full Text Available Coarse-grained models of soft matter are usually combined with implicit solvent models that take the electrostatic polarizability into account via a dielectric background. In biophysical or nanoscale simulations that include water, this constant can vary greatly within the system. Performing molecular dynamics or other simulations that need to compute exact electrostatic interactions between charges in those systems is computationally demanding. We review here several algorithms developed by us that perform exactly this task. For planar dielectric surfaces in partial periodic boundary conditions, the arising image charges can be either treated with the MMM2D algorithm in a very efficient and accurate way or with the electrostatic layer correction term, which enables the user to use his favorite 3D periodic Coulomb solver. Arbitrarily-shaped interfaces can be dealt with using induced surface charges with the induced charge calculation (ICC* algorithm. Finally, the local electrostatics algorithm, MEMD(Maxwell Equations Molecular Dynamics, even allows one to employ a smoothly varying dielectric constant in the systems. We introduce the concepts of these three algorithms and an extension for the inclusion of boundaries that are to be held fixed at a constant potential (metal conditions. For each method, we present a showcase application to highlight the importance of dielectric interfaces.

  6. Solvation effects on chemical shifts by embedded cluster integral equation theory.

    Science.gov (United States)

    Frach, Roland; Kast, Stefan M

    2014-12-11

    The accurate computational prediction of nuclear magnetic resonance (NMR) parameters like chemical shifts represents a challenge if the species studied is immersed in strongly polarizing environments such as water. Common approaches to treating a solvent in the form of, e.g., the polarizable continuum model (PCM) ignore strong directional interactions such as H-bonds to the solvent which can have substantial impact on magnetic shieldings. We here present a computational methodology that accounts for atomic-level solvent effects on NMR parameters by extending the embedded cluster reference interaction site model (EC-RISM) integral equation theory to the prediction of chemical shifts of N-methylacetamide (NMA) in aqueous solution. We examine the influence of various so-called closure approximations of the underlying three-dimensional RISM theory as well as the impact of basis set size and different treatment of electrostatic solute-solvent interactions. We find considerable and systematic improvement over reference PCM and gas phase calculations. A smaller basis set in combination with a simple point charge model already yields good performance which can be further improved by employing exact electrostatic quantum-mechanical solute-solvent interaction energies. A larger basis set benefits more significantly from exact over point charge electrostatics, which can be related to differences of the solvent's charge distribution.

  7. PowderSim: Lagrangian Discrete and Mesh-Free Continuum Simulation Code for Cohesive Soils

    Science.gov (United States)

    Johnson, Scott; Walton, Otis; Settgast, Randolph

    2013-01-01

    PowderSim is a calculation tool that combines a discrete-element method (DEM) module, including calibrated interparticle-interaction relationships, with a mesh-free, continuum, SPH (smoothed-particle hydrodynamics) based module that utilizes enhanced, calibrated, constitutive models capable of mimicking both large deformations and the flow behavior of regolith simulants and lunar regolith under conditions anticipated during in situ resource utilization (ISRU) operations. The major innovation introduced in PowderSim is to use a mesh-free method (SPH-based) with a calibrated and slightly modified critical-state soil mechanics constitutive model to extend the ability of the simulation tool to also address full-scale engineering systems in the continuum sense. The PowderSim software maintains the ability to address particle-scale problems, like size segregation, in selected regions with a traditional DEM module, which has improved contact physics and electrostatic interaction models.

  8. Interdomain electron transfer in cellobiose dehydrogenase is governed by surface electrostatics.

    Science.gov (United States)

    Kadek, Alan; Kavan, Daniel; Marcoux, Julien; Stojko, Johann; Felice, Alfons K G; Cianférani, Sarah; Ludwig, Roland; Halada, Petr; Man, Petr

    2017-02-01

    Cellobiose dehydrogenase (CDH) is a fungal extracellular oxidoreductase which fuels lytic polysaccharide monooxygenase with electrons during cellulose degradation. Interdomain electron transfer between the flavin and cytochrome domain in CDH, preceding the electron flow to lytic polysaccharide monooxygenase, is known to be pH dependent, but the exact mechanism of this regulation has not been experimentally proven so far. To investigate the structural aspects underlying the domain interaction in CDH, hydrogen/deuterium exchange (HDX-MS) with improved proteolytic setup (combination of nepenthesin-1 with rhizopuspepsin), native mass spectrometry with ion mobility and electrostatics calculations were used. HDX-MS revealed pH-dependent changes in solvent accessibility and hydrogen bonding at the interdomain interface. Electrostatics calculations identified these differences to result from charge neutralization by protonation and together with ion mobility pointed at higher electrostatic repulsion between CDH domains at neutral pH. In addition, we uncovered extensive O-glycosylation in the linker region and identified the long-unknown exact cleavage point in papain-mediated domain separation. Transition of CDH between its inactive (open) and interdomain electron transfer-capable (closed) state is shown to be governed by changes in the protein surface electrostatics at the domain interface. Our study confirms that the interdomain electrostatic repulsion is the key factor modulating the functioning of CDH. The results presented in this paper provide experimental evidence for the role of charge repulsion in the interdomain electron transfer in cellobiose dehydrogenases, which is relevant for exploiting their biotechnological potential in biosensors and biofuel cells. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. Linear response coupled cluster theory with the polarizable continuum model within the singles approximation for the solvent response

    Science.gov (United States)

    Caricato, Marco

    2018-04-01

    We report the theory and the implementation of the linear response function of the coupled cluster (CC) with the single and double excitations method combined with the polarizable continuum model of solvation, where the correlation solvent response is approximated with the perturbation theory with energy and singles density (PTES) scheme. The singles name is derived from retaining only the contribution of the CC single excitation amplitudes to the correlation density. We compare the PTES working equations with those of the full-density (PTED) method. We then test the PTES scheme on the evaluation of excitation energies and transition dipoles of solvated molecules, as well as of the isotropic polarizability and specific rotation. Our results show a negligible difference between the PTED and PTES schemes, while the latter affords a significantly reduced computational cost. This scheme is general and can be applied to any solvation model that includes mutual solute-solvent polarization, including explicit models. Therefore, the PTES scheme is a competitive approach to compute response properties of solvated systems using CC methods.

  10. Theoretical insight into the solvent effect of H2O and formamide on the cooperativity effect in HMX complex.

    Science.gov (United States)

    Meng, Rui-Hong; Cao, Xiong; Hu, Shuang-Qi; Hu, Li-Shuang

    2017-08-01

    The cooperativity effects of the H-bonding interactions in HMX (1,3,5,7-tetranitro-1,3,5,7-tetrazacyclooctane)∙∙∙HMX∙∙∙FA (formamide), HMX∙∙∙HMX∙∙∙H 2 O and HMX∙∙∙HMX∙∙∙HMX complexes involving the chair and chair-chair HMX are investigated by using the ONIOM2 (CAM-B3LYP/6-31++G(d,p):PM3) and ONIOM2 (M06-2X/6-31++G(d,p):PM3) methods. The solvent effect of FA or H 2 O on the cooperativity effect in HMX∙∙∙HMX∙∙∙HMX are evaluated by the integral equation formalism polarized continuum model. The results show that the cooperativity and anti-cooperativity effects are not notable in all the systems. Although the effect of solvation on the binding energy of ternary system HMX∙∙∙HMX∙∙∙HMX is not large, that on the cooperativity of H-bonds is notable, which leads to the mutually strengthened H-bonding interaction in solution. This is perhaps the reason for the formation of different conformation of HMX in different solvent. Surface electrostatic potential and reduced density gradient are used to reveal the nature of the solvent effect on cooperativity effect in HMX∙∙∙HMX∙∙∙HMX. Graphical abstract RDG isosurface and electrostatic potential surface of HMX∙∙∙HMX∙∙∙HMX.

  11. Electrostatics of aquaporin and aquaglyceroporin channels correlates with their transport selectivity

    Science.gov (United States)

    Oliva, Romina; Calamita, Giuseppe; Thornton, Janet M.; Pellegrini-Calace, Marialuisa

    2010-01-01

    Aquaporins are homotetrameric channel proteins, which allow the diffusion of water and small solutes across biological membranes. According to their transport function, aquaporins can be divided into “orthodox aquaporins”, which allow the flux of water molecules only, and “aquaglyceroporins”, which facilitate the diffusion of glycerol and other small solutes in addition to water. The contribution of individual residues in the pore to the selectivity of orthodox aquaporins and aquaglyceroporins is not yet fully understood. To gain insights into aquaporin selectivity, we focused on the sequence variation and electrostatics of their channels. The continuum Poisson-Boltzmann electrostatic potential along the channel was calculated and compared for ten three-dimensional-structures which are representatives of different aquaporin subfamilies, and a panel of functionally characterized mutants, for which high-accuracy three-dimensional-models could be derived. Interestingly, specific electrostatic profiles associated with the main selectivity to water or glycerol could be identified. In particular: (i) orthodox aquaporins showed a distinctive electrostatic potential maximum at the periplasmic side of the channel around the aromatic/Arg (ar/R) constriction site; (ii) aquaporin-0 (AQP0), a mammalian aquaporin with considerably low water permeability, had an additional deep minimum at the cytoplasmic side; (iii) aquaglyceroporins showed a rather flat potential all along the channel; and (iv) the bifunctional protozoan PfAQP had an unusual all negative profile. Evaluation of electrostatics of the mutants, along with a thorough sequence analysis of the aquaporin pore-lining residues, illuminated the contribution of specific residues to the electrostatics of the channels and possibly to their selectivity. PMID:20147624

  12. DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes

    Science.gov (United States)

    Sarkar, Subhra; Witham, Shawn; Zhang, Jie; Zhenirovskyy, Maxim; Rocchia, Walter; Alexov, Emil

    2011-01-01

    Here we report a web server, the DelPhi web server, which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions, and dielectric map. The server provides extra services to fix structural defects, as missing atoms in the structural file and allows for generation of missing hydrogen atoms. The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22, Amber98 or OPLS. Upon completion of the calculations, the user is given option to download fixed and protonated structural file, together with the parameter and Delphi output files for further analysis. Utilizing Jmol viewer, the user can see the corresponding structural file, to manipulate it and to change the presentation. In addition, if the potential map is requested to be calculated, the potential can be mapped onto the molecule surface. The DelPhi web server is available from http://compbio.clemson.edu/delphi_webserver. PMID:24683424

  13. Calculation of gas migration in fractured rock - a continuum approach

    International Nuclear Information System (INIS)

    Braester, C.

    1987-09-01

    A study of gas migration from low level radioactive repositories in which the fractured rock mass was conceptualized as a continuum, was carried out by the aid of a computer program based on a finite difference numerical method of solution to the equations of flow. The calculations are intended to correspond to the prevailing in the Forsmark low level repository area where radioactive waste repository caverns are planned to be located at a depth of about 50 metres below the sea level. Calculations were worked out for a constant gas flow rate equivalent to a gas production of 20 000 normal cubic metres per year. The investigated flow domain was a vertical cross-section passing through the repository. The results show that in the empty cavern the gas formed in the cavern moves almost instantaneously upward amd accumulates below the roof of the cavern. (orig./DG)

  14. Study of the solvent effects on the molecular structure and Cdbnd O stretching vibrations of flurbiprofen

    Science.gov (United States)

    Tekin, Nalan; Pir, Hacer; Sagdinc, Seda

    2012-12-01

    The effects of 15 solvents on the C=O stretching vibrational frequency of flurbiprofen (FBF) were determined to investigate solvent-solute interactions. Solvent effects on the geometry and C=O stretching vibrational frequency, ν(C=O), of FBF were studied theoretically at the DFT/B3LYP and HF level in combination with the polarizable continuum model and experimentally using attenuated total reflection infrared spectroscopy (ATR-IR). The calculated C=O stretching frequencies in the liquid phase are in agreement with experimental values. Moreover, the wavenumbers of ν(C=O) of FBF in different solvents have been obtained and correlated with the Kirkwood-Bauer-Magat equation (KBM), the solvent acceptor numbers (ANs), and the linear solvation energy relationships (LSERs). The solvent-induced stretching vibrational frequency shifts displayed a better correlation with the LSERs than with the ANs and KBM.

  15. On the theory of electric double layer with explicit account of a polarizable co-solvent

    Energy Technology Data Exchange (ETDEWEB)

    Budkov, Yu. A., E-mail: urabudkov@rambler.ru [Laboratory of NMR Spectroscopy and Numerical Investigations of Liquids, G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Ivanovo (Russian Federation); Department of Applied Mathematics, National Research University Higher School of Economics, Moscow (Russian Federation); Kolesnikov, A. L. [Institut für Nichtklassische Chemie e.V., Universität Leipzig, Leipzig (Germany); Kiselev, M. G. [Laboratory of NMR Spectroscopy and Numerical Investigations of Liquids, G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Ivanovo (Russian Federation)

    2016-05-14

    We present a continuation of our theoretical research into the influence of co-solvent polarizability on a differential capacitance of the electric double layer. We formulate a modified Poisson-Boltzmann theory, using the formalism of density functional approach on the level of local density approximation taking into account the electrostatic interactions of ions and co-solvent molecules as well as their excluded volume. We derive the modified Poisson-Boltzmann equation, considering the three-component symmetric lattice gas model as a reference system and minimizing the grand thermodynamic potential with respect to the electrostatic potential. We apply present modified Poisson-Boltzmann equation to the electric double layer theory, showing that accounting for the excluded volume of co-solvent molecules and ions slightly changes the main result of our previous simplified theory. Namely, in the case of small co-solvent polarizability with its increase under the enough small surface potentials of electrode, the differential capacitance undergoes the significant growth. Oppositely, when the surface potential exceeds some threshold value (which is slightly smaller than the saturation potential), the increase in the co-solvent polarizability results in a differential capacitance decrease. However, when the co-solvent polarizability exceeds some threshold value, its increase generates a considerable enhancement of the differential capacitance in a wide range of surface potentials. We demonstrate that two qualitatively different behaviors of the differential capacitance are related to the depletion and adsorption of co-solvent molecules at the charged electrode. We show that an additive of the strongly polarizable co-solvent to an electrolyte solution can shift significantly the saturation potential in two qualitatively different manners. Namely, a small additive of strongly polarizable co-solvent results in a shift of saturation potential to higher surface potentials. On

  16. On the theory of electric double layer with explicit account of a polarizable co-solvent

    International Nuclear Information System (INIS)

    Budkov, Yu. A.; Kolesnikov, A. L.; Kiselev, M. G.

    2016-01-01

    We present a continuation of our theoretical research into the influence of co-solvent polarizability on a differential capacitance of the electric double layer. We formulate a modified Poisson-Boltzmann theory, using the formalism of density functional approach on the level of local density approximation taking into account the electrostatic interactions of ions and co-solvent molecules as well as their excluded volume. We derive the modified Poisson-Boltzmann equation, considering the three-component symmetric lattice gas model as a reference system and minimizing the grand thermodynamic potential with respect to the electrostatic potential. We apply present modified Poisson-Boltzmann equation to the electric double layer theory, showing that accounting for the excluded volume of co-solvent molecules and ions slightly changes the main result of our previous simplified theory. Namely, in the case of small co-solvent polarizability with its increase under the enough small surface potentials of electrode, the differential capacitance undergoes the significant growth. Oppositely, when the surface potential exceeds some threshold value (which is slightly smaller than the saturation potential), the increase in the co-solvent polarizability results in a differential capacitance decrease. However, when the co-solvent polarizability exceeds some threshold value, its increase generates a considerable enhancement of the differential capacitance in a wide range of surface potentials. We demonstrate that two qualitatively different behaviors of the differential capacitance are related to the depletion and adsorption of co-solvent molecules at the charged electrode. We show that an additive of the strongly polarizable co-solvent to an electrolyte solution can shift significantly the saturation potential in two qualitatively different manners. Namely, a small additive of strongly polarizable co-solvent results in a shift of saturation potential to higher surface potentials. On

  17. Probing the electrostatics of active site microenvironments along the catalytic cycle for Escherichia coli dihydrofolate reductase.

    Science.gov (United States)

    Liu, C Tony; Layfield, Joshua P; Stewart, Robert J; French, Jarrod B; Hanoian, Philip; Asbury, John B; Hammes-Schiffer, Sharon; Benkovic, Stephen J

    2014-07-23

    Electrostatic interactions play an important role in enzyme catalysis by guiding ligand binding and facilitating chemical reactions. These electrostatic interactions are modulated by conformational changes occurring over the catalytic cycle. Herein, the changes in active site electrostatic microenvironments are examined for all enzyme complexes along the catalytic cycle of Escherichia coli dihydrofolate reductase (ecDHFR) by incorporation of thiocyanate probes at two site-specific locations in the active site. The electrostatics and degree of hydration of the microenvironments surrounding the probes are investigated with spectroscopic techniques and mixed quantum mechanical/molecular mechanical (QM/MM) calculations. Changes in the electrostatic microenvironments along the catalytic environment lead to different nitrile (CN) vibrational stretching frequencies and (13)C NMR chemical shifts. These environmental changes arise from protein conformational rearrangements during catalysis. The QM/MM calculations reproduce the experimentally measured vibrational frequency shifts of the thiocyanate probes across the catalyzed hydride transfer step, which spans the closed and occluded conformations of the enzyme. Analysis of the molecular dynamics trajectories provides insight into the conformational changes occurring between these two states and the resulting changes in classical electrostatics and specific hydrogen-bonding interactions. The electric fields along the CN axes of the probes are decomposed into contributions from specific residues, ligands, and solvent molecules that make up the microenvironments around the probes. Moreover, calculation of the electric field along the hydride donor-acceptor axis, along with decomposition of this field into specific contributions, indicates that the cofactor and substrate, as well as the enzyme, impose a substantial electric field that facilitates hydride transfer. Overall, experimental and theoretical data provide evidence for

  18. Mathematical analysis of the boundary-integral based electrostatics estimation approximation for molecular solvation: exact results for spherical inclusions.

    Science.gov (United States)

    Bardhan, Jaydeep P; Knepley, Matthew G

    2011-09-28

    We analyze the mathematically rigorous BIBEE (boundary-integral based electrostatics estimation) approximation of the mixed-dielectric continuum model of molecular electrostatics, using the analytically solvable case of a spherical solute containing an arbitrary charge distribution. Our analysis, which builds on Kirkwood's solution using spherical harmonics, clarifies important aspects of the approximation and its relationship to generalized Born models. First, our results suggest a new perspective for analyzing fast electrostatic models: the separation of variables between material properties (the dielectric constants) and geometry (the solute dielectric boundary and charge distribution). Second, we find that the eigenfunctions of the reaction-potential operator are exactly preserved in the BIBEE model for the sphere, which supports the use of this approximation for analyzing charge-charge interactions in molecular binding. Third, a comparison of BIBEE to the recent GBε theory suggests a modified BIBEE model capable of predicting electrostatic solvation free energies to within 4% of a full numerical Poisson calculation. This modified model leads to a projection-framework understanding of BIBEE and suggests opportunities for future improvements. © 2011 American Institute of Physics

  19. Electrostatic energy of KHF2

    NARCIS (Netherlands)

    Gool, W. van; Bruinink, J.; Bottelberghs, P.H.

    1972-01-01

    Electrostatic lattice energies are calculated in KHF2. Fractional charges occurring in the complex anions are treated with a general procedure and the results are compared to a specialized approach reported earlier. Interstitial potentials are calculated to obtain the electrostatic field through

  20. Embedding beyond electrostatics-The role of wave function confinement.

    Science.gov (United States)

    Nåbo, Lina J; Olsen, Jógvan Magnus Haugaard; Holmgaard List, Nanna; Solanko, Lukasz M; Wüstner, Daniel; Kongsted, Jacob

    2016-09-14

    We study excited states of cholesterol in solution and show that, in this specific case, solute wave-function confinement is the main effect of the solvent. This is rationalized on the basis of the polarizable density embedding scheme, which in addition to polarizable embedding includes non-electrostatic repulsion that effectively confines the solute wave function to its cavity. We illustrate how the inclusion of non-electrostatic repulsion results in a successful identification of the intense π → π(∗) transition, which was not possible using an embedding method that only includes electrostatics. This underlines the importance of non-electrostatic repulsion in quantum-mechanical embedding-based methods.

  1. Three-dimensional ray tracing of electrostatic cyclotron harmonic waves and Z mode electromagnetic waves in the magnetosphere

    International Nuclear Information System (INIS)

    Hashimoto, K.; Yamaashi, K.; Kimura, I.; Kyoto Univ., Japan)

    1987-01-01

    Three-dimensional ray tracing is performed for electrostatic electron cyclotron harmonic waves and Z mode electromagnetic waves in the earth's magnetosphere using the hot dispersion relation. Propagation characteristics of cyclotron harmonic waves under the electrostatic approximation are considered, and it is noted that waves starting near the equator can propagate over a long distance without damping. Ray tracing without the electrostatic approximation confirms mode conversion from cyclotron harmonic waves to Z mode electromagnetic waves, and the conditions for the conversion are clarified. It is suggested that further conversion to the L-O mode continuum radiation is possible under strict constraints. The present results are not inconsistent with the conversion mechanism for the generation of escaping continuum radiation in the magnetosphere. 20 references

  2. pKa values in proteins determined by electrostatics applied to molecular dynamics trajectories.

    Science.gov (United States)

    Meyer, Tim; Knapp, Ernst-Walter

    2015-06-09

    For a benchmark set of 194 measured pKa values in 13 proteins, electrostatic energy computations are performed in which pKa values are computed by solving the Poisson-Boltzmann equation. In contrast to the previous approach of Karlsberg(+) (KB(+)) that essentially used protein crystal structures with variations in their side chain conformations, the present approach (KB2(+)MD) uses protein conformations from four molecular dynamics (MD) simulations of 10 ns each. These MD simulations are performed with different specific but fixed protonation patterns, selected to sample the conformational space for the different protonation patterns faithfully. The root-mean-square deviation between computed and measured pKa values (pKa RMSD) is shown to be reduced from 1.17 pH units using KB(+) to 0.96 pH units using KB2(+)MD. The pKa RMSD can be further reduced to 0.79 pH units, if each conformation is energy-minimized with a dielectric constant of εmin = 4 prior to calculating the electrostatic energy. The electrostatic energy expressions upon which the computations are based have been reformulated such that they do not involve terms that mix protein and solvent environment contributions and no thermodynamic cycle is needed. As a consequence, conformations of the titratable residues can be treated independently in the protein and solvent environments. In addition, the energy terms used here avoid the so-called intrinsic pKa and can therefore be interpreted without reference to arbitrary protonation states and conformations.

  3. Solvent effect on the intermolecular proton transfer of the Watson and Crick guanine-cytosine and adenine-thymine base pairs: a polarizable continuum model study.

    Science.gov (United States)

    Romero, Eduardo E; Hernandez, Florencio E

    2018-01-03

    Herein we present our results on the study of the double proton transfer (DPT) mechanism in the adenine-thymine (AT) and guanine-cytosine (GC) base pairs, both in gas phase and in solution. The latter was modeled using the polarizable continuum method (PCM) in different solvents. According to our DFT calculations, the DPT may occur for both complexes in a stepwise mechanism in condensate phase. In gas phase only the GC base pair exhibits a concerted DPT mechanism. Using the Wigner's tunneling corrections to the transition state theory we demonstrate that such corrections are important for the prediction of the rate constants of both systems in gas and in condensate phase. We also show that (i) as the polarity of the medium decreases the equilibrium constant of the DPT reaction increases in both complexes, and (ii) that the equilibrium constant in the GC complex is four orders of magnitude larger than in AT. This observation suggests that the spontaneous mutations in DNA base pairs are more probable in GC than in AT.

  4. Analytical Calculation of Stored Electrostatic Energy per Unit Length for an Infinite Charged Line and an Infinitely Long Cylinder in the Framework of Born-Infeld Electrostatics

    International Nuclear Information System (INIS)

    Fathi, F.; Moayedi, S. K.; Shafabakhsh, M.

    2015-01-01

    More than 80 years ago, Born-Infeld electrodynamics was proposed in order to remove the point charge singularity in Maxwell electrodynamics. In this work, after a brief introduction to Lagrangian formulation of Abelian Born-Infeld model in the presence of an external source, we obtain the explicit forms of Gauss’s law and the energy density of an electrostatic field for Born-Infeld electrostatics. The electric field and the stored electrostatic energy per unit length for an infinite charged line and an infinitely long cylinder in Born-Infeld electrostatics are calculated. Numerical estimations in this paper show that the nonlinear corrections to Maxwell electrodynamics are considerable only for strong electric fields. We present an action functional for Abelian Born-Infeld model with an auxiliary scalar field in the presence of an external source. This action functional is a generalization of the action functional which was presented by Tseytlin in his studies on low energy dynamics of D-branes (Nucl. Phys. B469, 51 (1996); Int. J. Mod. Phys. A 19, 3427 (2004)). Finally, we derive the symmetric energy-momentum tensor for Abelian Born-Infeld model with an auxiliary scalar field

  5. The pKa Cooperative: a collaborative effort to advance structure-based calculations of pKa values and electrostatic effects in proteins.

    Science.gov (United States)

    Nielsen, Jens E; Gunner, M R; García-Moreno, Bertrand E

    2011-12-01

    The pK(a) Cooperative (http://www.pkacoop.org) was organized to advance development of accurate and useful computational methods for structure-based calculation of pK(a) values and electrostatic energies in proteins. The Cooperative brings together laboratories with expertise and interest in theoretical, computational, and experimental studies of protein electrostatics. To improve structure-based energy calculations, it is necessary to better understand the physical character and molecular determinants of electrostatic effects. Thus, the Cooperative intends to foment experimental research into fundamental aspects of proteins that depend on electrostatic interactions. It will maintain a depository for experimental data useful for critical assessment of methods for structure-based electrostatics calculations. To help guide the development of computational methods, the Cooperative will organize blind prediction exercises. As a first step, computational laboratories were invited to reproduce an unpublished set of experimental pK(a) values of acidic and basic residues introduced in the interior of staphylococcal nuclease by site-directed mutagenesis. The pK(a) values of these groups are unique and challenging to simulate owing to the large magnitude of their shifts relative to normal pK(a) values in water. Many computational methods were tested in this first Blind Prediction Challenge and critical assessment exercise. A workshop was organized in the Telluride Science Research Center to objectively assess the performance of many computational methods tested on this one extensive data set. This volume of Proteins: Structure, Function, and Bioinformatics introduces the pK(a) Cooperative, presents reports submitted by participants in the Blind Prediction Challenge, and highlights some of the problems in structure-based calculations identified during this exercise. Copyright © 2011 Wiley-Liss, Inc.

  6. Unexpected solvent effects on the UV/Vis absorption spectra of o-cresol in toluene and benzene: in contrast with non-aromatic solvents.

    Science.gov (United States)

    Zheng, Dong; Yuan, Xiang-Ai; Ma, Haibo; Li, Xiaoxiong; Wang, Xizhang; Liu, Ziteng; Ma, Jing

    2018-03-01

    Cresol is a prototype molecule in understanding intermolecular interactions in material and biological systems, because it offers different binding sites with various solvents and protonation states under different pH values. It is found that the UV/Vis absorption spectra of o -cresol in aromatic solvents (benzene, toluene) are characterized by a sharp peak, unlike the broad double-peaks in 11 non-aromatic solvents. Both molecular dynamics simulations and electronic structure calculations revealed the formation of intermolecular π-complexation between o -cresol and aromatic solvents. The thermal movements of solvent and solute molecules render the conformations of o -cresol changing between trans and cis isomers. The π-interaction makes the cis configuration a dominant isomer, hence leading to the single keen-edged UV/Vis absorption peak at approximately 283 nm. The free conformation changes between trans and cis in aqueous solution rationalize the broader absorption peaks in the range of 260-280 nm. The pH dependence of the UV/Vis absorption spectra in aqueous solutions is also rationalized by different protonation states of o -cresol. The explicit solvent model with long-ranged interactions is vital to describe the effects of π-complexation and electrostatic interaction on the UV/Vis absorption spectra of o -cresol in toluene and alkaline aqueous (pH > 10.3) solutions, respectively.

  7. Electrostatic dry powder prepregging of carbon fiber

    Science.gov (United States)

    Throne, James L.; Sohn, Min-Seok

    1990-01-01

    Ultrafine, 5-10 micron polymer-matrix resin powders are directly applied to carbon fiber tows by passing then in an air or nitrogen stream through an electrostatic potential; the particles thus charged will strongly adhere to grounded carbon fibers, and can be subsequently fused to the fiber in a continuously-fed radiant oven. This electrostatic technique derived significant end-use mechanical property advantages from the obviation of solvents, binders, and other adulterants. Additional matrix resins used to produce prepregs to date have been PMR-15, Torlon 40000, and LaRC TPI.

  8. THE DEVELOPMENT OF THE CALCULATION MODEL FOR THE ESTIMATION OF THE BOILING POINT OF THE ­POLYMER-SOLVENT MIXTURES

    Directory of Open Access Journals (Sweden)

    Matseevich Andrey Vyacheslavovich

    2018-03-01

    Full Text Available Subject of the study: one of the most promising areas in the field of polymer physics is the development of the calculation models allowing to quantify the properties of polymers. This work provides the calculation model for the quantitative assessment of the boiling point of solutions of polymer in the organic solvent. The model is based on the chemical structure of polymer and solvent. For the components the Hildebrand solubility parameter, the latent heat of vaporization and the boiling point of the solvent are calculated. Objectives: to generate the equation connecting the boiling point of polymer solution in the chosen solvent with the boiling point of the pure solvent, the molecular weights of the repeating unit of polymer and the molecule of solvent, the weight fraction of polymer in solution, the Hildebrand solubility parameter and the molar volume of the repeating unit of polymer. Materials and methods: the Hildebrand solubility parameter of solutions and polymers and also the van der Waals volume were calculated using the method of A.A. Askadsky; the enthalpy of vaporization of the solvent at the boiling point was expressed through the Hildebrand solubility parameter. The dependence of the enthalpy of vaporization from the temperature was taken into consideration. The computerization of the method was implemented, according to which all calculations are performed automatically after entering the information on the chemical structure of polymer and solvent into the computer. Results: the equation connecting the ebulliometric constant of the low concentration polymer solution with the boiling point of the solvent, the molar volume of the solvent and the Hildebrand parameter was generated. The results of the analysis were checked with regard to the system of polystyrene/toluene; the possibility of practical application of the offered method was shown. Conclusions: the method presented in this article allows to predict the ebulliometric

  9. Crack Propagation Calculations for Optical Fibers under Static Bending and Tensile Loads Using Continuum Damage Mechanics

    Science.gov (United States)

    Chen, Yunxia; Cui, Yuxuan; Gong, Wenjun

    2017-01-01

    Static fatigue behavior is the main failure mode of optical fibers applied in sensors. In this paper, a computational framework based on continuum damage mechanics (CDM) is presented to calculate the crack propagation process and failure time of optical fibers subjected to static bending and tensile loads. For this purpose, the static fatigue crack propagation in the glass core of the optical fiber is studied. Combining a finite element method (FEM), we use the continuum damage mechanics for the glass core to calculate the crack propagation path and corresponding failure time. In addition, three factors including bending radius, tensile force and optical fiber diameter are investigated to find their impacts on the crack propagation process and failure time of the optical fiber under concerned situations. Finally, experiments are conducted and the results verify the correctness of the simulation calculation. It is believed that the proposed method could give a straightforward description of the crack propagation path in the inner glass core. Additionally, the predicted crack propagation time of the optical fiber with different factors can provide effective suggestions for improving the long-term usage of optical fibers. PMID:29140284

  10. Calculations of the electrostatic potential adjacent to model phospholipid bilayers.

    Science.gov (United States)

    Peitzsch, R M; Eisenberg, M; Sharp, K A; McLaughlin, S

    1995-03-01

    We used the nonlinear Poisson-Boltzmann equation to calculate electrostatic potentials in the aqueous phase adjacent to model phospholipid bilayers containing mixtures of zwitterionic lipids (phosphatidylcholine) and acidic lipids (phosphatidylserine or phosphatidylglycerol). The aqueous phase (relative permittivity, epsilon r = 80) contains 0.1 M monovalent salt. When the bilayers contain equipotential surfaces are discrete domes centered over the negatively charged lipids and are approximately twice the value calculated using Debye-Hückel theory. When the bilayers contain > 25% acidic lipid, the -25 mV equipotential profiles are essentially flat and agree well with the values calculated using Gouy-Chapman theory. When the bilayers contain 100% acidic lipid, all of the equipotential surfaces are flat and agree with Gouy-Chapman predictions (including the -100 mV surface, which is located only 1 A from the outermost atoms). Even our model bilayers are not simple systems: the charge on each lipid is distributed over several atoms, these partial charges are non-coplanar, there is a 2 A ion-exclusion region (epsilon r = 80) adjacent to the polar headgroups, and the molecular surface is rough. We investigated the effect of these four factors using smooth (or bumpy) epsilon r = 2 slabs with embedded point charges: these factors had only minor effects on the potential in the aqueous phase.

  11. Continuum theory for nanotube piezoelectricity.

    Science.gov (United States)

    Michalski, P J; Sai, Na; Mele, E J

    2005-09-09

    We develop and solve a continuum theory for the piezoelectric response of one-dimensional nanotubes and nanowires, and apply the theory to study electromechanical effects in boron-nitride nanotubes. We find that the polarization of a nanotube depends on its aspect ratio, and a dimensionless constant specifying the ratio of the strengths of the elastic and electrostatic interactions. The solutions of the model as these two parameters are varied are discussed. The theory is applied to estimate the electric potential induced along the length of a boron-nitride nanotube in response to a uniaxial stress.

  12. Analysis of fast boundary-integral approximations for modeling electrostatic contributions of molecular binding

    Science.gov (United States)

    Kreienkamp, Amelia B.; Liu, Lucy Y.; Minkara, Mona S.; Knepley, Matthew G.; Bardhan, Jaydeep P.; Radhakrishnan, Mala L.

    2013-01-01

    We analyze and suggest improvements to a recently developed approximate continuum-electrostatic model for proteins. The model, called BIBEE/I (boundary-integral based electrostatics estimation with interpolation), was able to estimate electrostatic solvation free energies to within a mean unsigned error of 4% on a test set of more than 600 proteins—a significant improvement over previous BIBEE models. In this work, we tested the BIBEE/I model for its capability to predict residue-by-residue interactions in protein–protein binding, using the widely studied model system of trypsin and bovine pancreatic trypsin inhibitor (BPTI). Finding that the BIBEE/I model performs surprisingly less well in this task than simpler BIBEE models, we seek to explain this behavior in terms of the models’ differing spectral approximations of the exact boundary-integral operator. Calculations of analytically solvable systems (spheres and tri-axial ellipsoids) suggest two possibilities for improvement. The first is a modified BIBEE/I approach that captures the asymptotic eigenvalue limit correctly, and the second involves the dipole and quadrupole modes for ellipsoidal approximations of protein geometries. Our analysis suggests that fast, rigorous approximate models derived from reduced-basis approximation of boundary-integral equations might reach unprecedented accuracy, if the dipole and quadrupole modes can be captured quickly for general shapes. PMID:24466561

  13. Efficient optimization of electrostatic interactions between biomolecules.

    Energy Technology Data Exchange (ETDEWEB)

    Bardhan, J. P.; Altman, M. D.; White, J. K.; Tidor, B.; Mathematics and Computer Science; MIT

    2007-01-01

    We present a PDE-constrained approach to optimizing the electrostatic interactions between two biomolecules. These interactions play important roles in the determination of binding affinity and specificity, and are therefore of significant interest when designing a ligand molecule to bind tightly to a receptor. Using a popular continuum model and physically reasonable assumptions, the electrostatic component of the binding free energy is a convex, quadratic function of the ligand charge distribution. Traditional optimization methods require exhaustive pre-computation, and the expense has precluded a full exploration of the promise of electrostatic optimization in biomolecule analysis and design. In this paper we describe an approach in which the electrostatic simulations and optimization problem are solved simultaneously; unlike many PDE- constrained optimization frameworks, the proposed method does not incorporate the PDE as a set of equality constraints. This co-optimization approach can be used by itself to solve unconstrained problems or those with linear equality constraints, or in conjunction with primal-dual interior point methods to solve problems with inequality constraints. Model problems demonstrate that the co-optimization method is computationally efficient and can be used to solve realistic problems.

  14. Model for calculation of electrostatic contribution into protein stability

    Science.gov (United States)

    Kundrotas, Petras; Karshikoff, Andrey

    2003-03-01

    Existing models of the denatured state of proteins consider only one possible spatial distribution of protein charges and therefore are applicable to a limited number of cases. In this presentation a more general framework for the modeling of the denatured state is proposed. It is based on the assumption that the titratable groups of an unfolded protein can adopt a quasi-random distribution, restricted by the protein sequence. The model was tested on two proteins, barnase and N-terminal domain of the ribosomal protein L9. The calculated free energy of denaturation, Δ G( pH), reproduces the experimental data essentially better than the commonly used null approximation (NA). It was demonstrated that the seemingly good agreement with experimental data obtained by NA originates from the compensatory effect between the pair-wise electrostatic interactions and the desolvation energy of the individual sites. It was also found that the ionization properties of denatured proteins are influenced by the protein sequence.

  15. Continuum Level Density in Complex Scaling Method

    International Nuclear Information System (INIS)

    Suzuki, R.; Myo, T.; Kato, K.

    2005-01-01

    A new calculational method of continuum level density (CLD) at unbound energies is studied in the complex scaling method (CSM). It is shown that the CLD can be calculated by employing the discretization of continuum states in the CSM without any smoothing technique

  16. Nonadiabatic dynamics of electron transfer in solution: Explicit and implicit solvent treatments that include multiple relaxation time scales

    International Nuclear Information System (INIS)

    Schwerdtfeger, Christine A.; Soudackov, Alexander V.; Hammes-Schiffer, Sharon

    2014-01-01

    The development of efficient theoretical methods for describing electron transfer (ET) reactions in condensed phases is important for a variety of chemical and biological applications. Previously, dynamical dielectric continuum theory was used to derive Langevin equations for a single collective solvent coordinate describing ET in a polar solvent. In this theory, the parameters are directly related to the physical properties of the system and can be determined from experimental data or explicit molecular dynamics simulations. Herein, we combine these Langevin equations with surface hopping nonadiabatic dynamics methods to calculate the rate constants for thermal ET reactions in polar solvents for a wide range of electronic couplings and reaction free energies. Comparison of explicit and implicit solvent calculations illustrates that the mapping from explicit to implicit solvent models is valid even for solvents exhibiting complex relaxation behavior with multiple relaxation time scales and a short-time inertial response. The rate constants calculated for implicit solvent models with a single solvent relaxation time scale corresponding to water, acetonitrile, and methanol agree well with analytical theories in the Golden rule and solvent-controlled regimes, as well as in the intermediate regime. The implicit solvent models with two relaxation time scales are in qualitative agreement with the analytical theories but quantitatively overestimate the rate constants compared to these theories. Analysis of these simulations elucidates the importance of multiple relaxation time scales and the inertial component of the solvent response, as well as potential shortcomings of the analytical theories based on single time scale solvent relaxation models. This implicit solvent approach will enable the simulation of a wide range of ET reactions via the stochastic dynamics of a single collective solvent coordinate with parameters that are relevant to experimentally accessible

  17. A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson–Boltzmann electrostatics

    Science.gov (United States)

    Sun, Hui; Wen, Jiayi; Zhao, Yanxiang; Li, Bo; McCammon, J. Andrew

    2015-01-01

    Dielectric boundary based implicit-solvent models provide efficient descriptions of coarse-grained effects, particularly the electrostatic effect, of aqueous solvent. Recent years have seen the initial success of a new such model, variational implicit-solvent model (VISM) [Dzubiella, Swanson, and McCammon Phys. Rev. Lett. 96, 087802 (2006) and J. Chem. Phys. 124, 084905 (2006)], in capturing multiple dry and wet hydration states, describing the subtle electrostatic effect in hydrophobic interactions, and providing qualitatively good estimates of solvation free energies. Here, we develop a phase-field VISM to the solvation of charged molecules in aqueous solvent to include more flexibility. In this approach, a stable equilibrium molecular system is described by a phase field that takes one constant value in the solute region and a different constant value in the solvent region, and smoothly changes its value on a thin transition layer representing a smeared solute-solvent interface or dielectric boundary. Such a phase field minimizes an effective solvation free-energy functional that consists of the solute-solvent interfacial energy, solute-solvent van der Waals interaction energy, and electrostatic free energy described by the Poisson–Boltzmann theory. We apply our model and methods to the solvation of single ions, two parallel plates, and protein complexes BphC and p53/MDM2 to demonstrate the capability and efficiency of our approach at different levels. With a diffuse dielectric boundary, our new approach can describe the dielectric asymmetry in the solute-solvent interfacial region. Our theory is developed based on rigorous mathematical studies and is also connected to the Lum–Chandler–Weeks theory (1999). We discuss these connections and possible extensions of our theory and methods. PMID:26723595

  18. A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson-Boltzmann electrostatics.

    Science.gov (United States)

    Sun, Hui; Wen, Jiayi; Zhao, Yanxiang; Li, Bo; McCammon, J Andrew

    2015-12-28

    Dielectric boundary based implicit-solvent models provide efficient descriptions of coarse-grained effects, particularly the electrostatic effect, of aqueous solvent. Recent years have seen the initial success of a new such model, variational implicit-solvent model (VISM) [Dzubiella, Swanson, and McCammon Phys. Rev. Lett. 96, 087802 (2006) and J. Chem. Phys. 124, 084905 (2006)], in capturing multiple dry and wet hydration states, describing the subtle electrostatic effect in hydrophobic interactions, and providing qualitatively good estimates of solvation free energies. Here, we develop a phase-field VISM to the solvation of charged molecules in aqueous solvent to include more flexibility. In this approach, a stable equilibrium molecular system is described by a phase field that takes one constant value in the solute region and a different constant value in the solvent region, and smoothly changes its value on a thin transition layer representing a smeared solute-solvent interface or dielectric boundary. Such a phase field minimizes an effective solvation free-energy functional that consists of the solute-solvent interfacial energy, solute-solvent van der Waals interaction energy, and electrostatic free energy described by the Poisson-Boltzmann theory. We apply our model and methods to the solvation of single ions, two parallel plates, and protein complexes BphC and p53/MDM2 to demonstrate the capability and efficiency of our approach at different levels. With a diffuse dielectric boundary, our new approach can describe the dielectric asymmetry in the solute-solvent interfacial region. Our theory is developed based on rigorous mathematical studies and is also connected to the Lum-Chandler-Weeks theory (1999). We discuss these connections and possible extensions of our theory and methods.

  19. The optimization of the electrostatic field inside the ZEUS forward drift chambers: Calculations and measurements

    International Nuclear Information System (INIS)

    Dobberstein, M.P.; Krawczyk, F.; Schaefer-Jotter, M.

    1990-11-01

    The electrostatic field inside small drift cells shows in general edge effects which are not negligible. These are usually corrected by field shaping wires or strips. The operating voltages of the field shaping electrodes have to be adjusted to maximize the field homogeneity. We present the underlying ideas of such an optimization procedure for the cells of the ZEUS forward drift chambers. Using the finite difference code PROFI, the optimization can be performed automatically by a multiple solution of the Poisson equation. An experimental verification of the optimal voltages was carried out measuring the gas amplifications at the six sense wires. Modifications of the drift cell geometry were necessary for calibration measurements with a laser beam. This caused additional distortions of the electrostatic field. Their influence was calculated using the MAFIA code, which allows to include open boundary conditions. (orig.)

  20. Physics of the continuum of borromean nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Vaagen, J S; Rogde, T [Dept. of Physics, Univ. of Bergen (Norway); Danilin, B V [RRC The Kurchatov Inst., Kurchatov, Moscow (Russian Federation); Ershov, S N [JINR, Dubna, Moscow (Russian Federation); Thompson, I J [Dept. of Physics, Univ. of Surrey, Guildford (United Kingdom); Zhukov, M V [Chalmers Univ. of Technology and Goeteborg Univ., Goeteborg (Sweden); RNBT Collaboration

    1998-06-01

    The continuum states of two-neutron halo nuclei are calculated in the method of hyperspherical harmonics. Using DWIA theory appropriate for dilute halo matter we have probed the structure of the low-lying {sup 6}He continuum via calculations of charge-exchange and inelastic scattering. (orig.)

  1. Theoretical Study on the Extraction of Alkaline Earth Salts by 18-Crown-6: Roles of Counterions, Solvent Types and Extraction Temperatures

    Directory of Open Access Journals (Sweden)

    Saprizal Hadisaputra

    2014-07-01

    Full Text Available The roles of counterions, solvent types and extraction temperatures on the selectivity of 18-crown-6 (L toward alkaline earth salts MX2 (M = Ca, Sr, Ba; X = Cl-, NO3- have been studied by density functional method at B3LYP level of theory in gas and solvent phase. In gas phase, the chloride anion Cl- is the preference counterion than nitrate anion NO3-. This result is confirmed by the interaction energies, the second order interaction energies, charge transfers, energy difference between HOMO-LUMO and electrostatic potential maps. The presence of solvent reversed the gas phase trend. It is found that NO3- is the preference counterion in solvent phase. The calculated free energies demonstrate that the solvent types strongly change the strength of the complex formation. The free energies are exothermic in polar solvent while for the non polar solvent the free energies are endothermic. As the temperature changes the free energies also vary where the higher the temperatures the lower the free energy values. The calculated free energies are correlated well with the experimental stability constants. This theoretical study would have a strong contribution in planning the experimental conditions in terms of the preference counterions, solvent types and optimum extraction temperatures.

  2. Including diverging electrostatic potential in 3D-RISM theory: The charged wall case

    Science.gov (United States)

    Vyalov, Ivan; Rocchia, Walter

    2018-03-01

    Although three-dimensional site-site molecular integral equations of liquids are a powerful tool of the modern theoretical chemistry, their applications to the problem of characterizing the electrical double layer originating at the solid-liquid interface with a macroscopic substrate are severely limited by the fact that an infinitely extended charged plane generates a divergent electrostatic potential. Such potentials cannot be treated within the standard 3D-Reference Interaction Site Model equation solution framework since it leads to functions that are not Fourier transformable. In this paper, we apply a renormalization procedure to overcome this obstacle. We then check the validity and numerical accuracy of the proposed computational scheme on the prototypical gold (111) surface in contact with water/alkali chloride solution. We observe that despite the proposed method requires, to achieve converged charge densities, a higher spatial resolution than that suited to the estimation of biomolecular solvation with either 3D-RISM or continuum electrostatics approaches, it still is computationally efficient. Introducing the electrostatic potential of an infinite wall, which is periodic in 2 dimensions, we avoid edge effects, permit a robust integration of Poisson's equation, and obtain the 3D electrostatic potential profile for the first time in such calculations. We show that the potential within the electrical double layer presents oscillations which are not grasped by the Debye-Hückel and Gouy-Chapman theories. This electrostatic potential deviates from its average of up to 1-2 V at small distances from the substrate along the lateral directions. Applications of this theoretical development are relevant, for example, for liquid scanning tunneling microscopy imaging.

  3. Effect of a pH Gradient on the Protonation States of Cytochrome c Oxidase: A Continuum Electrostatics Study.

    Science.gov (United States)

    Magalhães, Pedro R; Oliveira, A Sofia F; Campos, Sara R R; Soares, Cláudio M; Baptista, António M

    2017-02-27

    Cytochrome c oxidase (CcO) couples the reduction of dioxygen to water with transmembrane proton pumping, which leads to the generation of an electrochemical gradient. In this study we analyze how one of the components of the electrochemical gradient, the difference in pH across the membrane, or ΔpH, influences the protonation states of residues in CcO. We modified our continuum electrostatics/Monte Carlo (CE/MC) method in order to include the ΔpH and applied it to the study of CcO, in what is, to our best knowledge, the first CE/MC study of CcO in the presence of a pH gradient. The inclusion of a transmembrane pH gradient allows for the identification of residues whose titration behavior depends on the pH on both sides of the membrane. Among the several residues with unusual titration profiles, three are well-known key residues in the proton transfer process of CcO: E286 I , Y288 I , and K362 I . All three residues have been previously identified as being critical for the catalytic or proton pumping functions of CcO. Our results suggest that when the pH gradient increases, these residues may be part of a regulatory mechanism to stem the proton flow.

  4. Calculations of optical rotation: Influence of molecular structure

    Directory of Open Access Journals (Sweden)

    Yu Jia

    2012-01-01

    Full Text Available Ab initio Hartree-Fock (HF method and Density Functional Theory (DFT were used to calculate the optical rotation of 26 chiral compounds. The effects of theory and basis sets used for calculation, solvents influence on the geometry and values of calculated optical rotation were all discussed. The polarizable continuum model, included in the calculation, did not improve the accuracy effectively, but it was superior to γs. Optical rotation of five or sixmembered of cyclic compound has been calculated and 17 pyrrolidine or piperidine derivatives which were calculated by HF and DFT methods gave acceptable predictions. The nitrogen atom affects the calculation results dramatically, and it is necessary in the molecular structure in order to get an accurate computation result. Namely, when the nitrogen atom was substituted by oxygen atom in the ring, the calculation result deteriorated.

  5. Extracting continuum information from Ψ(t) in time-dependent wave-packet calculations

    International Nuclear Information System (INIS)

    Madsen, L. B.; Nikolopoulos, L. A. A.; Kjeldsen, T. K.; Fernandez, J.

    2007-01-01

    The theory of measurement projection operators in grid-based time-dependent wave-packet calculations involving electronic continua in atoms and molecules is discussed. A hierarchy of projection operators relevant in their individual restricted configuration spaces is presented. At asymptotically large distances from the scattering or interaction center the projection operators involve plane waves only. To reach this asymptotic regime, however, large propagation times and large boxes may be required. At somewhat smaller distances from the scattering center, the projection operators are expressed in terms of analytical single-center Coulomb scattering waves with incoming wave boundary conditions. If propagation of the wave packet to these asymptotic regimes is impeded, the projection operators involve the exact scattering states which are not readily available in the wave-packet calculation and hence must be supplied by an additional, typically very demanding, calculation. The present approach suggests an exact way of analyzing the timely problem of the one-electron continuum in nonperturbative calculations. A key feature is that the propagated wave packet includes every interaction of the full Hamiltonian. The practicality of the proposed method is illustrated by the nontrivial example of strong-field ionization of the molecular hydrogen ion. Finally, the extension of the presented ideas to single and double ionization of two-electron systems is discussed

  6. Accurate pKa Calculation of the Conjugate Acids of Alkanolamines, Alkaloids and Nucleotide Bases by Quantum Chemical Methods

    NARCIS (Netherlands)

    Gangarapu, S.; Marcelis, A.T.M.; Zuilhof, H.

    2013-01-01

    The pKa of the conjugate acids of alkanolamines, neurotransmitters, alkaloid drugs and nucleotide bases are calculated with density functional methods (B3LYP, M08-HX and M11-L) and ab initio methods (SCS-MP2, G3). Implicit solvent effects are included with a conductor-like polarizable continuum

  7. Yukawa multipole electrostatics and nontrivial coupling between electrostatic and dispersion interactions in electrolytes

    International Nuclear Information System (INIS)

    Kjellander, Roland; Ramirez, Rosa

    2008-01-01

    An exact treatment of screened electrostatics in electrolyte solutions is presented. In electrolytes the anisotropy of the exponentially decaying electrostatic potential from a molecule extends to the far field region. The full directional dependence of the electrostatic potential from a charged or uncharged molecule remains in the longest range tail (i.e. from all multipole moments). In particular, the range of the potential from an ion and that from an electroneutral polar particle is generally exactly the same. This is in contrast to the case in vacuum or pure polar liquids, where the potential from a single charge is longer ranged than that from a dipole, which is, itself, longer ranged than the one from a quadrupole etc. The orientational dependence of the exponentially screened electrostatic interaction between two molecules in electrolytes is therefore rather complex even at long distances. These facts are formalized in Yukawa multipole expansions of the electrostatic potential and the pair interaction free energy based on the Yukawa function family exp(-κr)/r m , where r is the distance, κ is a decay parameter and m is a positive integer. The expansion is formally exact for electrolytes with molecular solvent and in the primitive model, provided the non-Coulombic interactions between the particles are sufficiently short ranged. The results can also be applied in the Poisson-Boltzmann approximation. Differences and similarities to the ordinary multipole expansion of electrostatics are pointed out. On the other hand, when the non-Coulombic interactions between the constituent particles of the electrolyte solution contain a dispersion 1/r 6 potential, the electrostatic potential from a molecule decays like a power law for long distances rather than as a Yukawa function. This is due to nontrivial coupling between the electrostatic and dispersion interactions. There remains an exponentially decaying component in the electrostatic potential, but it becomes

  8. Dependence of Interaction Free Energy between Solutes on an External Electrostatic Field

    Directory of Open Access Journals (Sweden)

    Pei-Kun Yang

    2013-07-01

    Full Text Available To explore the athermal effect of an external electrostatic field on the stabilities of protein conformations and the binding affinities of protein-protein/ligand interactions, the dependences of the polar and hydrophobic interactions on the external electrostatic field, −Eext, were studied using molecular dynamics (MD simulations. By decomposing Eext into, along, and perpendicular to the direction formed by the two solutes, the effect of Eext on the interactions between these two solutes can be estimated based on the effects from these two components. Eext was applied along the direction of the electric dipole formed by two solutes with opposite charges. The attractive interaction free energy between these two solutes decreased for solutes treated as point charges. In contrast, the attractive interaction free energy between these two solutes increased, as observed by MD simulations, for Eext = 40 or 60 MV/cm. Eext was applied perpendicular to the direction of the electric dipole formed by these two solutes. The attractive interaction free energy was increased for Eext = 100 MV/cm as a result of dielectric saturation. The force on the solutes along the direction of Eext computed from MD simulations was greater than that estimated from a continuum solvent in which the solutes were treated as point charges. To explore the hydrophobic interactions, Eext was applied to a water cluster containing two neutral solutes. The repulsive force between these solutes was decreased/increased for Eext along/perpendicular to the direction of the electric dipole formed by these two solutes.

  9. Calculation of surface potentials at the silica–water interface using molecular dynamics: Challenges and opportunities

    Science.gov (United States)

    Lowe, Benjamin M.; Skylaris, Chris-Kriton; Green, Nicolas G.; Shibuta, Yasushi; Sakata, Toshiya

    2018-04-01

    Continuum-based methods are important in calculating electrostatic properties of interfacial systems such as the electric field and surface potential but are incapable of providing sufficient insight into a range of fundamentally and technologically important phenomena which occur at atomistic length-scales. In this work a molecular dynamics methodology is presented for interfacial electric field and potential calculations. The silica–water interface was chosen as an example system, which is highly relevant for understanding the response of field-effect transistors sensors (FET sensors). Detailed validation work is presented, followed by the simulated surface charge/surface potential relationship. This showed good agreement with experiment at low surface charge density but at high surface charge density the results highlighted challenges presented by an atomistic definition of the surface potential. This methodology will be used to investigate the effect of surface morphology and biomolecule addition; both factors which are challenging using conventional continuum models.

  10. Direct Analysis of Large Living Organism by Megavolt Electrostatic Ionization Mass Spectrometry

    Science.gov (United States)

    Ng, Kwan-Ming; Tang, Ho-Wai; Man, Sin-Heng; Mak, Pui-Yuk; Choi, Yi-Ching; Wong, Melody Yee-Man

    2014-09-01

    A new ambient ionization method allowing the direct chemical analysis of living human body by mass spectrometry (MS) was developed. This MS method, namely Megavolt Electrostatic Ionization Mass Spectrometry, is based on electrostatic charging of a living individual to megavolt (MV) potential, illicit drugs, and explosives on skin/glove, flammable solvent on cloth/tissue paper, and volatile food substances in breath were readily ionized and detected by a mass spectrometer.

  11. On the role of electrostatics on protein-protein interactions

    Science.gov (United States)

    Zhang, Zhe; Witham, Shawn; Alexov, Emil

    2011-01-01

    The role of electrostatics on protein-protein interactions and binding is reviewed in this article. A brief outline of the computational modeling, in the framework of continuum electrostatics, is presented and basic electrostatic effects occurring upon the formation of the complex are discussed. The role of the salt concentration and pH of the water phase on protein-protein binding free energy is demonstrated and indicates that the increase of the salt concentration tends to weaken the binding, an observation that is attributed to the optimization of the charge-charge interactions across the interface. It is pointed out that the pH-optimum (pH of optimal binding affinity) varies among the protein-protein complexes, and perhaps is a result of their adaptation to particular subcellular compartment. At the end, the similarities and differences between hetero- and homo-complexes are outlined and discussed with respect to the binding mode and charge complementarity. PMID:21572182

  12. Magnetic effects on the solvent properties investigated by molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Moosavi, Fatemeh, E-mail: moosavibaigi@um.ac.ir; Gholizadeh, Mostafa

    2014-03-15

    This paper investigates how an external constant magnetic field in the Z-direction affects the performance of a solvent. The molecular dynamics simulation comprised common inorganic and organic solvents including water, acetone, acetonitrile, toluene, and n-hexane at the ambient temperature and pressure. A static magnetic field applied in the simulation process is able to reduce the solvent mobility in the solution in order to enhance the solvent–solute reaction. Simulation results show that the diffusivity decreases because of increasing the effective interactions. Besides, magnetic field reduces the volume of the solvent and increases the strength of the hydrogen bonds by maximizing attractive electrostatic and vdW interactions caused by changes in the radial distribution function of the solvents. Hydrogen-bonding characteristics of solvents investigated by molecular dynamics simulations were evidence for the hydrogen bonding strength of O···H that is a more efficient intermolecular hydrogen-bonding in comparison with N···H. - Highlights: • Molecular dynamics simulation technique investigates the effect of magnetic field on transport dynamics inside the solvent bulk. • External constant magnetic field influences on intermolecular interactions, thermophysics, and transport properties of the solvents. • Applying magnetic field strengthened hydrogen bond maximizes attractive electrostatic interactions, charge distribution becomes stronger, and the molecule mobility is demoted. • The low diffusivity of the solvents in the solutions increases the performance of the interactions and promotes the interactions. • On introducing a magnetic field of flux density parallel to the Z-direction, solvent acts as an obstacle to diffusion of solutes.

  13. Antagonistic properties of a natural product-Bicuculline with the gamma-aminobutyric acid receptor: studied through electrostatic potential mapping, electronic and vibrational spectra using ab initio and density functional theory.

    Science.gov (United States)

    Srivastava, Anubha; Tandon, Poonam; Jain, Sudha; Asthana, B P

    2011-12-15

    (+)-Bicuculline (hereinafter referred to as bicuculline), a phthalide isoquinoline alkaloid is of current interest as an antagonist of gamma-aminobutyric acid (GABA). Its inhibitor properties have been studied through molecular electrostatic potential (MEP) mapping of this molecule and GABA receptor. The hot site on the potential surface of bicuculline, which is also isosteric with GABA receptor, has been used to interpret the inhibitor property. A systematic quantum chemical study of the possible conformations, their relative stabilities, FT-Raman, FT-IR and UV-vis spectroscopic analysis of bicuculline has been reported. The optimized geometries, wavenumber and intensity of the vibrational bands of all the conformers of bicuculline have been calculated using ab initio Hartree-Fock (HF) and density functional theory (DFT) employing B3LYP functional and 6-311G(d,p) basis set. Mulliken atomic charges, HOMO-LUMO gap ΔE, ionization potential, dipole moments and total energy have also been obtained for the optimized geometries of both the molecules. TD-DFT method is used to calculate the electronic absorption parameters in gas phase as well as in solvent environment using integral equation formalism-polarizable continuum model (IEF-PCM) employing 6-31G basis set and the results thus obtained are compared with the UV absorption spectra. The combination of experimental and calculated results provides an insight into the structural and vibrational spectroscopic properties of bicuculline. Copyright © 2011 Elsevier B.V. All rights reserved.

  14. Effects of electrostatic interactions on electron transfer reactions

    International Nuclear Information System (INIS)

    Hickel, B.

    1987-01-01

    The fast reactions of electron transfer are studied by pulse radiolysis. This technique allows the creation in about 10 -8 second radicals and radical ions with high redox potentials. For solvated electrons electrostatic interaction on the kinetics of reactions limited by diffusion is described by Debye's equation when ion mobility is known. Deviation from theory can occur in ion pairs formation. This is evidenced experimentally for anions by cation complexation with a cryptate. Relatively slow reactions are more sensitive to electrostatic interactions than limited by diffusion. If ion pairs are not formed kinetics constant depends on dielectric constant of solvent and reaction radius. Experimentally is studied the effect of electrostatic interaction on the rate constants of solvated electrons with anions and cations in water-ethanol mixtures where the dielectric constant change from 80 to 25 at room temperature. 17 refs

  15. Biomolecular electrostatics and solvation: a computational perspective.

    Science.gov (United States)

    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.

  16. Solvent Effects on Nuclear Magnetic Resonance 2J(C,Hf and 1J(C,Hf Spin–Spin Coupling Constants in Acetaldehyde

    Directory of Open Access Journals (Sweden)

    Angel Esteban

    2003-02-01

    Full Text Available Abstract: The known solvent dependence of 1J(Cc,Hf and 2J(C1,Hf couplings in acetaldehyde is studied from a theoretical viewpoint based on the density functional theory approach where the dielectric solvent effect is taken into account with the polarizable continuum model. The four terms of scalar couplings, Fermi contact, paramagnetic spin orbital, diamagnetic spin orbital and spin dipolar, are calculated but the solvent effect analysis is restricted to the first term since for both couplings it is by far the dominant contribution. Experimental trends of Δ1J(Cc,Hf and Δ2J(C1,Hf Vs ε (the solvent dielectric constant are correctly reproduced although they are somewhat underestimated. Specific interactions between solute and solvent molecules are studied for dimethylsulfoxide, DMSO, solutions considering two different one-to-one molecular complexes between acetaldehyde and DMSO. They are determined by interactions of type C=O---H---C and S=O---H---C, and the effects of such interactions on 1J(Cc,Hf and 2J(C1,Hf couplings are analyzed. Even though only in a semiquantitative way, it is shown that the effect of such interactions on the solvent effects, of Δ1J(Cc,Hf and Δ2J(C1,Hf, tend to improve the agreement between calculated and experimental values. These results seem to indicate that a continuum dielectric model has not enough flexibility for describing quantitatively solvent effects on spin-spin couplings. Apparently, even for relatively weak hydrogen bonding, the contribution from “direct” interactions is of the same order of magnitude as the “dielectric” effect.

  17. Advanced dielectric continuum model of preferential solvation

    Science.gov (United States)

    Basilevsky, Mikhail; Odinokov, Alexey; Nikitina, Ekaterina; Grigoriev, Fedor; Petrov, Nikolai; Alfimov, Mikhail

    2009-01-01

    A continuum model for solvation effects in binary solvent mixtures is formulated in terms of the density functional theory. The presence of two variables, namely, the dimensionless solvent composition y and the dimensionless total solvent density z, is an essential feature of binary systems. Their coupling, hidden in the structure of the local dielectric permittivity function, is postulated at the phenomenological level. Local equilibrium conditions are derived by a variation in the free energy functional expressed in terms of the composition and density variables. They appear as a pair of coupled equations defining y and z as spatial distributions. We consider the simplest spherically symmetric case of the Born-type ion immersed in the benzene/dimethylsulfoxide (DMSO) solvent mixture. The profiles of y(R ) and z(R ) along the radius R, which measures the distance from the ion center, are found in molecular dynamics (MD) simulations. It is shown that for a given solute ion z(R ) does not depend significantly on the composition variable y. A simplified solution is then obtained by inserting z(R ), found in the MD simulation for the pure DMSO, in the single equation which defines y(R ). In this way composition dependences of the main solvation effects are investigated. The local density augmentation appears as a peak of z(R ) at the ion boundary. It is responsible for the fine solvation effects missing when the ordinary solvation theories, in which z =1, are applied. These phenomena, studied for negative ions, reproduce consistently the simulation results. For positive ions the simulation shows that z ≫1 (z =5-6 at the maximum of the z peak), which means that an extremely dense solvation shell is formed. In such a situation the continuum description fails to be valid within a consistent parametrization.

  18. Electrostatic potential map modelling with COSY Infinity

    International Nuclear Information System (INIS)

    Maloney, J.A.; Baartman, R.; Planche, T.; Saminathan, S.

    2016-01-01

    COSY Infinity (Makino and Berz, 2005) is a differential-algebra based simulation code which allows accurate calculation of transfer maps to arbitrary order. COSY’s existing internal procedures were modified to allow electrostatic elements to be specified using an array of field potential data from the midplane. Additionally, a new procedure was created allowing electrostatic elements and their fringe fields to be specified by an analytic function. This allows greater flexibility in accurately modelling electrostatic elements and their fringe fields. Applied examples of these new procedures are presented including the modelling of a shunted electrostatic multipole designed with OPERA, a spherical electrostatic bender, and the effects of different shaped apertures in an electrostatic beam line.

  19. Calculation of the electrostatic potential of lipid bilayers from molecular dynamics simulations: methodological issues

    DEFF Research Database (Denmark)

    Gurtovenko, Andrey A; Vattulainen, Ilpo

    2009-01-01

    of the electrostatic potential from atomic-scale molecular dynamics simulations of lipid bilayers. We discuss two slightly different forms of Poisson equation that are normally used to calculate the membrane potential: (i) a classical form when the potential and the electric field are chosen to be zero on one...... systems). For symmetric bilayers we demonstrate that both approaches give essentially the same potential profiles, provided that simulations are long enough (a production run of at least 100 ns is required) and that fluctuations of the center of mass of a bilayer are properly accounted for. In contrast...

  20. The impact of electrostatic correlations on Dielectrophoresis of Non-conducting Particles

    Science.gov (United States)

    Alidoosti, Elaheh; Zhao, Hui

    2017-11-01

    The dipole moment of a charged, dielectric, spherical particle under the influence of a uniform alternating electric field is computed theoretically and numerically by solving the modified continuum Poisson-Nernst-Planck (PNP) equations accounting for ion-ion electrostatic correlations that is important at concentrated electrolytes (Phys. Rev. Lett. 106, 2011). The dependence on the frequency, zeta potential, electrostatic correlation lengths, and double layer thickness is thoroughly investigated. In the limit of thin double layers, we carry out asymptotic analysis to develop simple models which are in good agreement with the modified PNP model. Our results suggest that the electrostatic correlations have a complicated impact on the dipole moment. As the electrostatic correlations length increases, the dipole moment decreases, initially, reach a minimum, and then increases since the surface conduction first decreases and then increases due to the ion-ion correlations. The modified PNP model can improve the theoretical predictions particularly at low frequencies where the simple model can't qualitatively predict the dipole moment. This work was supported, in part, by NIH R15GM116039.

  1. Third-order transfer matrices calculated for an electrostatic toroidal sector condenser including fringing-field effects

    CERN Document Server

    Mordik, S N

    2002-01-01

    The third-order transfer matrices are calculated for an electrostatic toroidal sector condenser using a rigorously conserved matrix method that implies the conservation of the beam phase volume at each step in the calculations. The transfer matrices (matrizants) obtained, include the fringing-field effect due to the stray fields. In the case of a rectangular distribution of the field components along the optical axis, the analytical expressions for all aberration coefficients, including the dispersion ones, are derived accurate to the third-order terms. In simulations of real fields with the stray field width other than zero, a smooth distribution of the field components is used for which similar aberration coefficients were calculated by means of the conserved numerical method . It has been found that for a smooth model, as the stray field width tends to zero, the aberration coefficients approach the corresponding aberration values in the rectangular model.

  2. Third-order transfer matrices calculated for an electrostatic toroidal sector condenser including fringing-field effects

    International Nuclear Information System (INIS)

    Mordik, S.N.; Ponomarev, A.G.

    2002-01-01

    The third-order transfer matrices are calculated for an electrostatic toroidal sector condenser using a rigorously conserved matrix method that implies the conservation of the beam phase volume at each step in the calculations. The transfer matrices (matrizants) obtained, include the fringing-field effect due to the stray fields. In the case of a rectangular distribution of the field components along the optical axis, the analytical expressions for all aberration coefficients, including the dispersion ones, are derived accurate to the third-order terms. In simulations of real fields with the stray field width other than zero, a smooth distribution of the field components is used for which similar aberration coefficients were calculated by means of the conserved numerical method . It has been found that for a smooth model, as the stray field width tends to zero, the aberration coefficients approach the corresponding aberration values in the rectangular model

  3. 40 CFR 63.5749 - How do I calculate the organic HAP content of aluminum wipedown solvents?

    Science.gov (United States)

    2010-07-01

    ... Manufacturing Standards for Aluminum Recreational Boat Surface Coating Operations § 63.5749 How do I calculate... fraction of organic HAP in aluminum wipedown solvent j. m = number of different aluminum surface coatings...

  4. Comparison of the Marcus and Pekar partitions in the context of non-equilibrium, polarizable-continuum solvation models

    International Nuclear Information System (INIS)

    You, Zhi-Qiang; Herbert, John M.; Mewes, Jan-Michael; Dreuw, Andreas

    2015-01-01

    The Marcus and Pekar partitions are common, alternative models to describe the non-equilibrium dielectric polarization response that accompanies instantaneous perturbation of a solute embedded in a dielectric continuum. Examples of such a perturbation include vertical electronic excitation and vertical ionization of a solution-phase molecule. Here, we provide a general derivation of the accompanying polarization response, for a quantum-mechanical solute described within the framework of a polarizable continuum model (PCM) of electrostatic solvation. Although the non-equilibrium free energy is formally equivalent within the two partitions, albeit partitioned differently into “fast” versus “slow” polarization contributions, discretization of the PCM integral equations fails to preserve certain symmetries contained in these equations (except in the case of the conductor-like models or when the solute cavity is spherical), leading to alternative, non-equivalent matrix equations. Unlike the total equilibrium solvation energy, however, which can differ dramatically between different formulations, we demonstrate that the equivalence of the Marcus and Pekar partitions for the non-equilibrium solvation correction is preserved to high accuracy. Differences in vertical excitation and ionization energies are <0.2 eV (and often <0.01 eV), even for systems specifically selected to afford a large polarization response. Numerical results therefore support the interchangeability of the Marcus and Pekar partitions, but also caution against relying too much on the fast PCM charges for interpretive value, as these charges differ greatly between the two partitions, especially in polar solvents

  5. Comparison of the Marcus and Pekar partitions in the context of non-equilibrium, polarizable-continuum solvation models

    Energy Technology Data Exchange (ETDEWEB)

    You, Zhi-Qiang; Herbert, John M., E-mail: herbert@chemistry.ohio-state.edu [Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210 (United States); Mewes, Jan-Michael; Dreuw, Andreas [Interdisciplinary Center for Scientific Computing, Ruprechts-Karls University, Im Neuenheimer Feld 368, 69120 Heidelberg (Germany)

    2015-11-28

    The Marcus and Pekar partitions are common, alternative models to describe the non-equilibrium dielectric polarization response that accompanies instantaneous perturbation of a solute embedded in a dielectric continuum. Examples of such a perturbation include vertical electronic excitation and vertical ionization of a solution-phase molecule. Here, we provide a general derivation of the accompanying polarization response, for a quantum-mechanical solute described within the framework of a polarizable continuum model (PCM) of electrostatic solvation. Although the non-equilibrium free energy is formally equivalent within the two partitions, albeit partitioned differently into “fast” versus “slow” polarization contributions, discretization of the PCM integral equations fails to preserve certain symmetries contained in these equations (except in the case of the conductor-like models or when the solute cavity is spherical), leading to alternative, non-equivalent matrix equations. Unlike the total equilibrium solvation energy, however, which can differ dramatically between different formulations, we demonstrate that the equivalence of the Marcus and Pekar partitions for the non-equilibrium solvation correction is preserved to high accuracy. Differences in vertical excitation and ionization energies are <0.2 eV (and often <0.01 eV), even for systems specifically selected to afford a large polarization response. Numerical results therefore support the interchangeability of the Marcus and Pekar partitions, but also caution against relying too much on the fast PCM charges for interpretive value, as these charges differ greatly between the two partitions, especially in polar solvents.

  6. Multipolar electrostatics for proteins: atom-atom electrostatic energies in crambin.

    Science.gov (United States)

    Yuan, Yongna; Mills, Matthew J L; Popelier, Paul L A

    2014-02-15

    Accurate electrostatics necessitates the use of multipole moments centered on nuclei or extra point charges centered away from the nuclei. Here, we follow the former alternative and investigate the convergence behavior of atom-atom electrostatic interactions in the pilot protein crambin. Amino acids are cut out from a Protein Data Bank structure of crambin, as single amino acids, di, or tripeptides, and are then capped with a peptide bond at each side. The atoms in the amino acids are defined through Quantum Chemical Topology (QCT) as finite volume electron density fragments. Atom-atom electrostatic energies are computed by means of a multipole expansion with regular spherical harmonics, up to a total interaction rank of L = ℓA+ ℓB + 1 = 10. The minimum internuclear distance in the convergent region of all the 15 possible types of atom-atom interactions in crambin that were calculated based on single amino acids are close to the values calculated from di and tripeptides. Values obtained at B3LYP/aug-cc-pVTZ and MP2/aug-cc-pVTZ levels are only slightly larger than those calculated at HF/6-31G(d,p) level. This convergence behavior is transferable to the well-known amyloid beta polypeptide Aβ1-42. Moreover, for a selected central atom, the influence of its neighbors on its multipole moments is investigated, and how far away this influence can be ignored is also determined. Finally, the convergence behavior of AMBER becomes closer to that of QCT with increasing internuclear distance. Copyright © 2013 Wiley Periodicals, Inc.

  7. Calculation of field configurations of the electrostatic septum and massless septum magnet for the slow extraction system of the JHF main ring

    International Nuclear Information System (INIS)

    Watanabe, Tamaki; Tokuda, Noboru; Tomizawa, Masahito; Arakaki, Yoshitsugu; Machida, Shinji; Mori, Yoshiharu; Shibuya, Shinji

    1997-01-01

    Since accelerating beam intensity is enormous in the JHF synchrotron, even small beam losses during the slow extraction leads to unacceptable level of radiation. We set a criterion such that tolerable beam loss in the slow extraction process should be less than 1% of the averaged beam current of 10 μA. We have examined the field configurations of the electrostatic septum and the massless septum magnet, respectively. The calculations of electrostatic and magnetic fields were carried out by the computer code POISSON. (author)

  8. 2D director calculation for liquid crystal optical phased array

    International Nuclear Information System (INIS)

    Xu, L; Zhang, J; Wu, L Y

    2005-01-01

    A practical numerical model for a liquid crystal cell is set up based on the geometrical structure of liquid crystal optical phased arrays. Model parameters include width and space of electrodes, thickness of liquid crystal layer, alignment layers and glass substrates, pre-tilted angles, dielectric constants, elastic constants and so on. According to electrostatic field theory and Frank-Oseen elastic continuum theory, 2D electric potential distribution and 2D director distribution are calculated by means of the finite difference method on non-uniform grids. The influence of cell sizes on director distribution is analyzed. The fringe field effect between electrodes is also discussed

  9. Accelerating Electrostatic Surface Potential Calculation with Multiscale Approximation on Graphics Processing Units

    Science.gov (United States)

    Anandakrishnan, Ramu; Scogland, Tom R. W.; Fenley, Andrew T.; Gordon, John C.; Feng, Wu-chun; Onufriev, Alexey V.

    2010-01-01

    Tools that compute and visualize biomolecular electrostatic surface potential have been used extensively for studying biomolecular function. However, determining the surface potential for large biomolecules on a typical desktop computer can take days or longer using currently available tools and methods. Two commonly used techniques to speed up these types of electrostatic computations are approximations based on multi-scale coarse-graining and parallelization across multiple processors. This paper demonstrates that for the computation of electrostatic surface potential, these two techniques can be combined to deliver significantly greater speed-up than either one separately, something that is in general not always possible. Specifically, the electrostatic potential computation, using an analytical linearized Poisson Boltzmann (ALPB) method, is approximated using the hierarchical charge partitioning (HCP) multiscale method, and parallelized on an ATI Radeon 4870 graphical processing unit (GPU). The implementation delivers a combined 934-fold speed-up for a 476,040 atom viral capsid, compared to an equivalent non-parallel implementation on an Intel E6550 CPU without the approximation. This speed-up is significantly greater than the 42-fold speed-up for the HCP approximation alone or the 182-fold speed-up for the GPU alone. PMID:20452792

  10. High precision electrostatic potential calculations for cylindrically symmetric lenses

    International Nuclear Information System (INIS)

    Edwards, David Jr.

    2007-01-01

    A method is developed for a potential calculation within cylindrically symmetric electrostatic lenses using mesh relaxation techniques, and it is capable of considerably higher accuracies than currently available. The method involves (i) creating very high order algorithms (orders of 6, 8, and 10) for determining the potentials at points in the net using surrounding point values, (ii) eliminating the effect of the large errors caused by singular points, and (iii) reducing gradients in the high gradient regions of the geometry, thereby allowing the algorithms used in these regions to achieve greater precisions--(ii) and (iii) achieved by the use of telescopic multiregions. In addition, an algorithm for points one unit from a metal surface is developed, allowing general mesh point algorithms to be used in these situations, thereby taking advantage of the enhanced precision of the latter. A maximum error function dependent on a sixth order gradient of the potential is defined. With this the single point algorithmic errors are able to be viewed over the entire net. Finally, it is demonstrated that by utilizing the above concepts and procedures, the potential of a point in a reasonably high gradient region of a test geometry can realize a precision of less than 10 -10

  11. MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations

    OpenAIRE

    Vergara-Perez, Sandra; Marucho, Marcelo

    2015-01-01

    One of the most used and efficient approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation. There are several software packages available that solve the PB equation for molecules in aqueous electrolyte solutions. Most of these software packages are useful for scientists with specialized training and expertise in computational biophysics. However, the user is usually required to manually take several important choices, de...

  12. Aqueous solvation of polyalanine α-helices with specific water molecules and with the CPCM and SM5.2 aqueous continuum models using density functional theory.

    Science.gov (United States)

    Marianski, Mateusz; Dannenberg, J J

    2012-02-02

    We present density functional theory (DFT) calculations at the X3LYP/D95(d,p) level on the solvation of polyalanine α-helices in water. The study includes the effects of discrete water molecules and the CPCM and AMSOL SM5.2 solvent continuum model both separately and in combination. We find that individual water molecules cooperatively hydrogen-bond to both the C- and N-termini of the helix, which results in increases in the dipole moment of the helix/water complex to more than the vector sum of their individual dipole moments. These waters are found to be more stable than in bulk solvent. On the other hand, individual water molecules that interact with the backbone lower the dipole moment of the helix/water complex to below that of the helix itself. Small clusters of waters at the termini increase the dipole moments of the helix/water aggregates, but the effect diminishes as more waters are added. We discuss the somewhat complex behavior of the helix with the discrete waters in the continuum models.

  13. Insights into the effects of solvent properties in graphene based electric double-layer capacitors with organic electrolytes

    Science.gov (United States)

    Zhang, Shuo; Bo, Zheng; Yang, Huachao; Yang, Jinyuan; Duan, Liangping; Yan, Jianhua; Cen, Kefa

    2016-12-01

    Organic electrolytes are widely used in electric double-layer capacitors (EDLCs). In this work, the microstructure of planar graphene-based EDLCs with different organic solvents are investigated with molecular dynamics simulations. Results show that an increase of solvent polarity could weaken the accumulation of counter-ions nearby the electrode surface, due to the screen of electrode charges and relatively lower ionic desolvation. It thus suggests that solvents with low polarity could be preferable to yield high EDL capacitance. Meanwhile, the significant effects of the size and structure of solvent molecules are reflected by non-electrostatic molecule-electrode interactions, further influencing the adsorption of solvent molecules on electrode surface. Compared with dimethyl carbonate, γ-butyrolactone, and propylene carbonate, acetonitrile with relatively small-size and linear structure owns weak non-electrostatic interactions, which favors the easy re-orientation of solvent molecules. Moreover, the shift of solvent orientation in surface layer, from parallel orientation to perpendicular orientation relative to the electrode surface, deciphers the solvent twin-peak behavior near negative electrode. The as-obtained insights into the roles of solvent properties on the interplays among particles and electrodes elucidate the solvent influences on the microstructure and capacitive behavior of EDLCs using organic electrolytes.

  14. Theory of polyelectrolytes in solvents.

    Science.gov (United States)

    Chitanvis, Shirish M

    2003-12-01

    Using a continuum description, we account for fluctuations in the ionic solvent surrounding a Gaussian, charged chain and derive an effective short-ranged potential between the charges on the chain. This potential is repulsive at short separations and attractive at longer distances. The chemical potential can be derived from this potential. When the chemical potential is positive, it leads to a meltlike state. For a vanishingly low concentration of segments, this state exhibits scaling behavior for long chains. The Flory exponent characterizing the radius of gyration for long chains is calculated to be approximately 0.63, close to the classical value obtained for second order phase transitions. For short chains, the radius of gyration varies linearly with N, the chain length, and is sensitive to the parameters in the interaction potential. The linear dependence on the chain length N indicates a stiff behavior. The chemical potential associated with this interaction changes sign, when the screening length in the ionic solvent exceeds a critical value. This leads to condensation when the chemical potential is negative. In this state, it is shown using the mean-field approximation that spherical and toroidal condensed shapes can be obtained. The thickness of the toroidal polyelectrolyte is studied as a function of the parameters of the model, such as the ionic screening length. The predictions of this theory should be amenable to experimental verification.

  15. Solvent Boundary Potentials for Hybrid QM/MM Computations Using Classical Drude Oscillators: A Fully Polarizable Model.

    Science.gov (United States)

    Boulanger, Eliot; Thiel, Walter

    2012-11-13

    Accurate quantum mechanical/molecular mechanical (QM/MM) treatments should account for MM polarization and properly include long-range electrostatic interactions. We report on a development that covers both these aspects. Our approach combines the classical Drude oscillator (DO) model for the electronic polarizability of the MM atoms with the generalized solvent boundary Potential (GSBP) and the solvated macromolecule boundary potential (SMBP). These boundary potentials (BP) are designed to capture the long-range effects of the outer region of a large system on its interior. They employ a finite difference approximation to the Poisson-Boltzmann equation for computing electrostatic interactions and take into account outer-region bulk solvent through a polarizable dielectric continuum (PDC). This approach thus leads to fully polarizable three-layer QM/MM-DO/BP methods. As the mutual responses of each of the subsystems have to be taken into account, we propose efficient schemes to converge the polarization of each layer simultaneously. For molecular dynamics (MD) simulations using GSBP, this is achieved by considering the MM polarizable model as a dynamical degree of freedom, and hence contributions from the boundary potential can be evaluated for a frozen state of polarization at every time step. For geometry optimizations using SMBP, we propose a dual self-consistent field approach for relaxing the Drude oscillators to their ideal positions and converging the QM wave function with the proper boundary potential. The chosen coupling schemes are evaluated with a test system consisting of a glycine molecule in a water ball. Both boundary potentials are capable of properly reproducing the gradients at the inner-region atoms and the Drude oscillators. We show that the effect of the Drude oscillators must be included in all terms of the boundary potentials to obtain accurate results and that the use of a high dielectric constant for the PDC does not lead to a polarization

  16. FreeSASA: An open source C library for solvent accessible surface area calculations.

    Science.gov (United States)

    Mitternacht, Simon

    2016-01-01

    Calculating solvent accessible surface areas (SASA) is a run-of-the-mill calculation in structural biology. Although there are many programs available for this calculation, there are no free-standing, open-source tools designed for easy tool-chain integration. FreeSASA is an open source C library for SASA calculations that provides both command-line and Python interfaces in addition to its C API. The library implements both Lee and Richards' and Shrake and Rupley's approximations, and is highly configurable to allow the user to control molecular parameters, accuracy and output granularity. It only depends on standard C libraries and should therefore be easy to compile and install on any platform. The library is well-documented, stable and efficient. The command-line interface can easily replace closed source legacy programs, with comparable or better accuracy and speed, and with some added functionality.

  17. Effect of electrostatic interactions on electron-transfer reactions

    International Nuclear Information System (INIS)

    Hickel, B.

    1987-01-01

    Fast reactions of electron transfer are studied by pulsed radiolysis. By this technique radicals and ionic radicals with high redox potentials are created homogeneously in the solution in about 10 -8 second. For solvated electron effect of electrostatic interaction on kinetics of reactions limited by diffusion is obtained with a good approximation by the Debye equation when ion mobility is known. Deviation from the theory occurs in ion pair formation, which is evidenced experimentally in reactions between anions when cations are complexed by a cryptate. Slow reactions k 8 M -1 s -1 are more sensitive to electrostatic interactions than reactions limited by diffusion. When there is no ion pair formation the velocity constant depends upon dielectric constant of the solvent and reaction distance. 17 refs

  18. Solvent Effect on Redox Properties of Hexanethiolate Monolayer-Protected Gold Nanoclusters

    OpenAIRE

    Su, B; Zhang, M; Shao, Y; Girault, HH

    2006-01-01

    The capacitance of monolayer-protected gold nanoclusters (MPCs), CMPC, in solution has been theoretically reconsidered from an electrostatic viewpoint, in which an MPC is considered as an isolated charged sphere within two dielectric layers, the intrinsic coating monolayer, and the bulk solvent. The model predicts that the bulk solvent provides an important contribution to CMPC and influences the redox properties of MPCs. This theoretical prediction is then examined experimentally by comparin...

  19. Variation and decomposition of the partial molar volume of small gas molecules in different organic solvents derived from molecular dynamics simulations.

    Science.gov (United States)

    Klähn, Marco; Martin, Alistair; Cheong, Daniel W; Garland, Marc V

    2013-12-28

    The partial molar volumes, V(i), of the gas solutes H2, CO, and CO2, solvated in acetone, methanol, heptane, and diethylether are determined computationally in the limit of infinite dilution and standard conditions. Solutions are described with molecular dynamics simulations in combination with the OPLS-aa force field for solvents and customized force field for solutes. V(i) is determined with the direct method, while the composition of V(i) is studied with Kirkwood-Buff integrals (KBIs). Subsequently, the amount of unoccupied space and size of pre-formed cavities in pure solvents is determined. Additionally, the shape of individual solvent cages is analyzed. Calculated V(i) deviate only 3.4 cm(3) mol(-1) (7.1%) from experimental literature values. Experimental V(i) variations across solutions are reproduced qualitatively and also quantitatively in most cases. The KBI analysis identifies differences in solute induced solvent reorganization in the immediate vicinity of H2 (<0.7 nm) and solvent reorganization up to the third solvation shell of CO and CO2 (<1.6 nm) as the origin of V(i) variations. In all solutions, larger V(i) are found in solvents that exhibit weak internal interactions, low cohesive energy density and large compressibility. Weak internal interactions facilitate solvent displacement by thermal solute movement, which enhances the size of solvent cages and thus V(i). Additionally, attractive electrostatic interactions of CO2 and the solvents, which do not depend on internal solvent interactions only, partially reversed the V(i) trends observed in H2 and CO solutions where electrostatic interactions with the solvents are absent. More empty space and larger pre-formed cavities are found in solvents with weak internal interactions, however, no evidence is found that solutes in any considered solvent are accommodated in pre-formed cavities. Individual solvent cages are found to be elongated in the negative direction of solute movement. This wake behind

  20. Variation and decomposition of the partial molar volume of small gas molecules in different organic solvents derived from molecular dynamics simulations

    Science.gov (United States)

    Klähn, Marco; Martin, Alistair; Cheong, Daniel W.; Garland, Marc V.

    2013-12-01

    The partial molar volumes, bar V_i, of the gas solutes H2, CO, and CO2, solvated in acetone, methanol, heptane, and diethylether are determined computationally in the limit of infinite dilution and standard conditions. Solutions are described with molecular dynamics simulations in combination with the OPLS-aa force field for solvents and customized force field for solutes. bar V_i is determined with the direct method, while the composition of bar V_i is studied with Kirkwood-Buff integrals (KBIs). Subsequently, the amount of unoccupied space and size of pre-formed cavities in pure solvents is determined. Additionally, the shape of individual solvent cages is analyzed. Calculated bar V_i deviate only 3.4 cm3 mol-1 (7.1%) from experimental literature values. Experimental bar V_i variations across solutions are reproduced qualitatively and also quantitatively in most cases. The KBI analysis identifies differences in solute induced solvent reorganization in the immediate vicinity of H2 (<0.7 nm) and solvent reorganization up to the third solvation shell of CO and CO2 (<1.6 nm) as the origin of bar V_i variations. In all solutions, larger bar V_i are found in solvents that exhibit weak internal interactions, low cohesive energy density and large compressibility. Weak internal interactions facilitate solvent displacement by thermal solute movement, which enhances the size of solvent cages and thus bar V_i. Additionally, attractive electrostatic interactions of CO2 and the solvents, which do not depend on internal solvent interactions only, partially reversed the bar V_i trends observed in H2 and CO solutions where electrostatic interactions with the solvents are absent. More empty space and larger pre-formed cavities are found in solvents with weak internal interactions, however, no evidence is found that solutes in any considered solvent are accommodated in pre-formed cavities. Individual solvent cages are found to be elongated in the negative direction of solute

  1. Wall Climbing Robot Using Electrostatic Adhesion Force Generated by Flexible Interdigital Electrodes

    Directory of Open Access Journals (Sweden)

    Rong Liu

    2013-01-01

    Full Text Available Electrostatic adhesion technology has broad application prospects on wall climbing robots because of its unique characteristics compared with other types of adhesion technologies. A double tracked wall climbing robot based on electrostatic adhesion technology is presented including electrode panel design, mechanical structure design, power supply system design and control system design. A theoretical adhesion model was established and the electrostatic potential and field were expressed by series expansions in terms of solutions of the Laplace function. Based on this model, the electrostatic adhesion force was calculated using the Maxwell stress tensor formulation. Several important factors which may influence the electrostatic adhesion force were analysed and discussed by both FEM simulation and theoretical calculation. In addition, experiments on the adhesion performance of the electrode panel and the climbing performance of the robot on various wall materials were carried out. Both the simulation and experiment results verify the feasibility of electrostatic adhesion technology being applied on wall climbing robots. The theoretical model and calculation method for the electrostatic adhesion force proposed in this paper are also justified.

  2. Effects of neglecting carrier tunneling on electrostatic potential in calculating direct tunneling gate current in deep submicron MOSFETs

    OpenAIRE

    Hakim, MMA; Haque, A

    2002-01-01

    We investigate the validity of the assumption of neglecting carrier tunneling effects on self-consistent electrostatic potential in calculating direct tunneling gate current in deep submicron MOSFETs. Comparison between simulated and experimental results shows that for accurate modeling of direct tunneling current, tunneling effects on potential profile need to be considered. The relative error in gate current due to neglecting carrier tunneling is higher at higher gate voltages and increases...

  3. Calculation of electrostatic multipoles of electron localized in narrow-band InSb spherical nanolayer

    International Nuclear Information System (INIS)

    Amirkhanyan, S.M.; Kazaryan, E.M.; Sarkisyan, H.A.

    2015-01-01

    Behavior of electron in narrow-gap spherical nanolayer of InSb is considered. Dispersion law of electron is described within the double-gap Kane model, when arises a necessity for considering of Klein-Gordon equation for description of behavior of electrons and light holes. Dipole and quadrupole momentums of electron in specified systems are defined on the base of the obtained expressions. It is shown, that average value of dipole momentum equals to zero and that for definition of average value of tensor of quadrupole momentum it is enough to calculate the average value of diagonal z-component of this tensor. Electrostatic potentials and tensions of fields created by electron located in different quantum states are defined

  4. Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH.

    Science.gov (United States)

    Wallace, Jason A; Shen, Jana K

    2012-11-14

    Recent development of constant pH molecular dynamics (CpHMD) methods has offered promise for adding pH-stat in molecular dynamics simulations. However, until now the working pH molecular dynamics (pHMD) implementations are dependent in part or whole on implicit-solvent models. Here we show that proper treatment of long-range electrostatics and maintaining charge neutrality of the system are critical for extending the continuous pHMD framework to the all-atom representation. The former is achieved here by adding forces to titration coordinates due to long-range electrostatics based on the generalized reaction field method, while the latter is made possible by a charge-leveling technique that couples proton titration with simultaneous ionization or neutralization of a co-ion in solution. We test the new method using the pH-replica-exchange CpHMD simulations of a series of aliphatic dicarboxylic acids with varying carbon chain length. The average absolute deviation from the experimental pK(a) values is merely 0.18 units. The results show that accounting for the forces due to extended electrostatics removes the large random noise in propagating titration coordinates, while maintaining charge neutrality of the system improves the accuracy in the calculated electrostatic interaction between ionizable sites. Thus, we believe that the way is paved for realizing pH-controlled all-atom molecular dynamics in the near future.

  5. Realistic electrostatic potentials in a neutron star crust

    International Nuclear Information System (INIS)

    Ebel, Claudio; Mishustin, Igor; Greiner, Walter

    2015-01-01

    We study the electrostatic properties of inhomogeneous nuclear matter which can be formed in the crusts of neutron stars or in supernova explosions. Such matter is represented by Wigner–Seitz cells of different geometries (spherical, cylindrical, cartesian), which contain nuclei, free neutrons and electrons under the conditions of electrical neutrality. Using the Thomas–Fermi approximation, we have solved the Poisson equation for the electrostatic potential and calculated the corresponding electron density distributions in individual cells. The calculations are done for different shapes and sizes of the cells and different average baryon densities. The electron-to-baryon fraction was fixed at 0.3. Using realistic electron distributions leads to a significant reduction in electrostatic energy and electron chemical potential. (paper)

  6. Processive pectin methylesterases: the role of electrostatic potential, breathing motions and bond cleavage in the rectification of Brownian motions.

    Directory of Open Access Journals (Sweden)

    Davide Mercadante

    Full Text Available Pectin methylesterases (PMEs hydrolyze the methylester groups that are found on the homogalacturonan (HG chains of pectic polysaccharides in the plant cell wall. Plant and bacterial PMEs are especially interesting as the resulting de-methylesterified (carboxylated sugar residues are found to be arranged contiguously, indicating a so-called processive nature of these enzymes. Here we report the results of continuum electrostatics calculations performed along the molecular dynamics trajectory of a PME-HG-decasaccharide complex. In particular it was observed that, when the methylester groups of the decasaccharide were arranged in order to mimic the just-formed carboxylate product of de-methylesterification, a net unidirectional sliding of the model decasaccharide was subsequently observed along the enzyme's binding groove. The changes that occurred in the electrostatic binding energy and protein dynamics during this translocation provide insights into the mechanism by which the enzyme rectifies Brownian motions to achieve processivity. The free energy that drives these molecular motors is thus demonstrated to be incorporated endogenously in the methylesterified groups of the HG chains and is not supplied exogenously.

  7. CPdock: the complementarity plot for docking of proteins: implementing multi-dielectric continuum electrostatics.

    Science.gov (United States)

    Basu, Sankar

    2017-12-07

    The complementarity plot (CP) is an established validation tool for protein structures, applicable to both globular proteins (folding) as well as protein-protein complexes (binding). It computes the shape and electrostatic complementarities (S m , E m ) for amino acid side-chains buried within the protein interior or interface and plots them in a two-dimensional plot having knowledge-based probabilistic quality estimates for the residues as well as for the whole structure. The current report essentially presents an upgraded version of the plot with the implementation of the advanced multi-dielectric functionality (as in Delphi version 6.2 or higher) in the computation of electrostatic complementarity to make the validation tool physico-chemically more realistic. The two methods (single- and multi-dielectric) agree decently in their resultant E m values, and hence, provisions for both methods have been kept in the software suite. So to speak, the global electrostatic balance within a well-folded protein and/or a well-packed interface seems only marginally perturbed by the choice of different internal dielectric values. However, both from theoretical as well as practical grounds, the more advanced multi-dielectric version of the plot is certainly recommended for potentially producing more reliable results. The report also presents a new methodology and a variant plot, namely CP dock , based on the same principles of complementarity specifically designed to be used in the docking of proteins. The efficacy of the method to discriminate between good and bad docked protein complexes has been tested on a recent state-of-the-art docking benchmark. The results unambiguously indicate that CP dock can indeed be effective in the initial screening phase of a docking scoring pipeline before going into more sophisticated and computationally expensive scoring functions. CP dock has been made available at https://github.com/nemo8130/CPdock . Graphical Abstract An example showing

  8. Probing lipid membrane electrostatics

    Science.gov (United States)

    Yang, Yi

    The electrostatic properties of lipid bilayer membranes play a significant role in many biological processes. Atomic force microscopy (AFM) is highly sensitive to membrane surface potential in electrolyte solutions. With fully characterized probe tips, AFM can perform quantitative electrostatic analysis of lipid membranes. Electrostatic interactions between Silicon nitride probes and supported zwitterionic dioleoylphosphatidylcholine (DOPC) bilayer with a variable fraction of anionic dioleoylphosphatidylserine (DOPS) were measured by AFM. Classical Gouy-Chapman theory was used to model the membrane electrostatics. The nonlinear Poisson-Boltzmann equation was numerically solved with finite element method to provide the potential distribution around the AFM tips. Theoretical tip-sample electrostatic interactions were calculated with the surface integral of both Maxwell and osmotic stress tensors on tip surface. The measured forces were interpreted with theoretical forces and the resulting surface charge densities of the membrane surfaces were in quantitative agreement with the Gouy-Chapman-Stern model of membrane charge regulation. It was demonstrated that the AFM can quantitatively detect membrane surface potential at a separation of several screening lengths, and that the AFM probe only perturbs the membrane surface potential by external field created by the internai membrane dipole moment. The analysis yields a dipole moment of 1.5 Debye per lipid with a dipole potential of +275 mV for supported DOPC membranes. This new ability to quantitatively measure the membrane dipole density in a noninvasive manner will be useful in identifying the biological effects of the dipole potential. Finally, heterogeneous model membranes were studied with fluid electric force microscopy (FEFM). Electrostatic mapping was demonstrated with 50 nm resolution. The capabilities of quantitative electrostatic measurement and lateral charge density mapping make AFM a unique and powerful

  9. Measurement and correlation of solubility of cefmenoxime hydrochloride in pure solvents and binary solvent mixtures

    International Nuclear Information System (INIS)

    Wang, Jinxiu; Xie, Chuang; Yin, Qiuxiang; Tao, Linggang; Lv, Jun; Wang, Yongli; He, Fang; Hao, Hongxun

    2016-01-01

    Highlights: • Solubility of cefmenoxime hydrochloride in pure and binary solvents was determined. • The experimental solubility data were correlated by thermodynamic models. • A model was employed to calculate the melting temperature of cefmenoxime hydrochloride. • Mixing thermodynamic properties of cefmenoxime hydrochloride were calculated. - Abstract: The solubility of cefmenoxime hydrochloride in pure solvents and binary solvent mixtures was measured at temperatures from (283.15 to 313.15) K by using the UV spectroscopic method. The results reveal that the solubility of cefmenoxime hydrochloride increases with increasing temperature in all solvent selected. The solubility of cefmenoxime hydrochloride reaches its maximum value when the mole fraction of isopropanol is 0.2 in the binary solvent mixtures of (isopropanol + water). The modified Apelblat equation and the NRTL model were successfully used to correlate the experimental solubility in pure solvents while the modified Apelblat equation, the CNIBS/R–K model and the Jouyban–Acree model were applied to correlate the solubility in binary solvent mixtures. In addition, the mixing thermodynamic properties of cefmenoxime hydrochloride in different solvents were also calculated based on the NRTL model and experimental solubility data.

  10. Ionic strength independence of charge distributions in solvation of biomolecules

    Energy Technology Data Exchange (ETDEWEB)

    Virtanen, J. J. [Department of Chemistry, University of Chicago, Chicago, Illinois 60637 (United States); James Franck Institute, University of Chicago, Chicago, Illinois 60637 (United States); Sosnick, T. R. [Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637 (United States); Computation Institute, University of Chicago, Chicago, Illinois 60637 (United States); Freed, K. F. [Department of Chemistry, University of Chicago, Chicago, Illinois 60637 (United States); James Franck Institute, University of Chicago, Chicago, Illinois 60637 (United States); Computation Institute, University of Chicago, Chicago, Illinois 60637 (United States)

    2014-12-14

    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.

  11. Ionic strength independence of charge distributions in solvation of biomolecules

    International Nuclear Information System (INIS)

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

    2014-01-01

    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

  12. Frequency chirpings in Alfven continuum

    Science.gov (United States)

    Wang, Ge; Berk, Herb; Breizman, Boris; Zheng, Linjin

    2017-10-01

    We have used a self-consistent mapping technique to describe both the nonlinear wave-energetic particle resonant interaction and its spatial mode structure that depends upon the resonant energetic particle pressure. At the threshold for the onset of the energetic particle mode (EPM), strong chirping emerges in the lower continuum close to the TAE gap and then, driven by strong continuum damping, chirps rapidly to lower frequencies in the Alfven continuum. An adiabatic theory was developed that accurately replicated the results from the simulation where the nonlinearity was only due to the EPM resonant particles. The results show that the EPM-trapped particles have their action conserved during the time of rapid chirping. This adiabaticity enabled wave trapped particles to be confined within their separatrix, and produce even larger resonant structures, that can produce a large amplitude mode far from linearly predicted frequencies. In the present work we describe the effect of additional MHD nonlinearity to this calculation. We studied how the zonal flow component and its nonlinear feedback to the fundamental frequency and found that the MHD nonlinearity doesn't significantly alter the frequency chirping response that is predicted by the calculation that neglects the MHD nonlinearity.

  13. Accelerating electrostatic surface potential calculation with multi-scale approximation on graphics processing units.

    Science.gov (United States)

    Anandakrishnan, Ramu; Scogland, Tom R W; Fenley, Andrew T; Gordon, John C; Feng, Wu-chun; Onufriev, Alexey V

    2010-06-01

    Tools that compute and visualize biomolecular electrostatic surface potential have been used extensively for studying biomolecular function. However, determining the surface potential for large biomolecules on a typical desktop computer can take days or longer using currently available tools and methods. Two commonly used techniques to speed-up these types of electrostatic computations are approximations based on multi-scale coarse-graining and parallelization across multiple processors. This paper demonstrates that for the computation of electrostatic surface potential, these two techniques can be combined to deliver significantly greater speed-up than either one separately, something that is in general not always possible. Specifically, the electrostatic potential computation, using an analytical linearized Poisson-Boltzmann (ALPB) method, is approximated using the hierarchical charge partitioning (HCP) multi-scale method, and parallelized on an ATI Radeon 4870 graphical processing unit (GPU). The implementation delivers a combined 934-fold speed-up for a 476,040 atom viral capsid, compared to an equivalent non-parallel implementation on an Intel E6550 CPU without the approximation. This speed-up is significantly greater than the 42-fold speed-up for the HCP approximation alone or the 182-fold speed-up for the GPU alone. Copyright (c) 2010 Elsevier Inc. All rights reserved.

  14. Orbital dynamics in a storage ring with electrostatic bending

    International Nuclear Information System (INIS)

    Mane, S.R.

    2008-01-01

    A storage ring where electrostatic fields contribute to the bending and focusing of the orbital motion has some novel features because, unlike a magnetostatic field, an electrostatic field can change the kinetic energy of the particles. I present analytical formulas to calculate the linear focusing gradient, dispersion, momentum compaction and natural chromaticity for a storage ring with a radial electrostatic field. I solve the formulas explicitly for a weak focusing model.

  15. The Indigo Molecule Revisited Again: Assessment of the Minnesota Family of Density Functionals for the Prediction of Its Maximum Absorption Wavelengths in Various Solvents

    Directory of Open Access Journals (Sweden)

    Francisco Cervantes-Navarro

    2013-01-01

    Full Text Available The Minnesota family of density functionals (M05, M05-2X, M06, M06L, M06-2X, and M06-HF were evaluated for the calculation of the UV-Vis spectra of the indigo molecule in solvents of different polarities using time-dependent density functional theory (TD-DFT and the polarized continuum model (PCM. The maximum absorption wavelengths predicted for each functional were compared with the known experimental results.

  16. Solvent effect on 14 N NMR shielding of glycine, serine, leucine, and ...

    African Journals Online (AJOL)

    The polarizable continuum model (PCM) is employed to describe the system in the ... order nonlinear mixed electric and magnetic effects in condensed phase are ... of the solvent reaction field rather than on the change of molecular geometry ...

  17. Computational Approach for Studying Optical Properties of DNA Systems in Solution

    DEFF Research Database (Denmark)

    Nørby, Morten Steen; Svendsen, Casper Steinmann; Olsen, Jógvan Magnus Haugaard

    2016-01-01

    In this paper we present a study of the methodological aspects regarding calculations of optical properties for DNA systems in solution. Our computational approach will be built upon a fully polarizable QM/MM/Continuum model within a damped linear response theory framework. In this approach...... the environment is given a highly advanced description in terms of the electrostatic potential through the polarizable embedding model. Furthermore, bulk solvent effects are included in an efficient manner through a conductor-like screening model. With the aim of reducing the computational cost we develop a set...... of averaged partial charges and distributed isotropic dipole-dipole polarizabilities for DNA suitable for describing the classical region in ground-state and excited-state calculations. Calculations of the UV-spectrum of the 2-aminopurine optical probe embedded in a DNA double helical structure are presented...

  18. Perspectives on electrostatics and conformational motions in enzyme catalysis.

    Science.gov (United States)

    Hanoian, Philip; Liu, C Tony; Hammes-Schiffer, Sharon; Benkovic, Stephen

    2015-02-17

    CONSPECTUS: Enzymes are essential for all living organisms, and their effectiveness as chemical catalysts has driven more than a half century of research seeking to understand the enormous rate enhancements they provide. Nevertheless, a complete understanding of the factors that govern the rate enhancements and selectivities of enzymes remains elusive, due to the extraordinary complexity and cooperativity that are the hallmarks of these biomolecules. We have used a combination of site-directed mutagenesis, pre-steady-state kinetics, X-ray crystallography, nuclear magnetic resonance (NMR), vibrational and fluorescence spectroscopies, resonance energy transfer, and computer simulations to study the implications of conformational motions and electrostatic interactions on enzyme catalysis in the enzyme dihydrofolate reductase (DHFR). We have demonstrated that modest equilibrium conformational changes are functionally related to the hydride transfer reaction. Results obtained for mutant DHFRs illustrated that reductions in hydride transfer rates are correlated with altered conformational motions, and analysis of the evolutionary history of DHFR indicated that mutations appear to have occurred to preserve both the hydride transfer rate and the associated conformational changes. More recent results suggested that differences in local electrostatic environments contribute to finely tuning the substrate pKa in the initial protonation step. Using a combination of primary and solvent kinetic isotope effects, we demonstrated that the reaction mechanism is consistent across a broad pH range, and computer simulations suggested that deprotonation of the active site Tyr100 may play a crucial role in substrate protonation at high pH. Site-specific incorporation of vibrational thiocyanate probes into the ecDHFR active site provided an experimental tool for interrogating these microenvironments and for investigating changes in electrostatics along the DHFR catalytic cycle

  19. GroPBS: Fast Solver for Implicit Electrostatics of Biomolecules

    Directory of Open Access Journals (Sweden)

    Franziska eBertelshofer

    2015-11-01

    Full Text Available Knowledge about the electrostatic potential on the surface of biomolecules or biomembranes under physiological conditions is an important step in the attempt to characterize the physico-chemical properties of these molecules and in particular also their interactions with each other. Additionally, knowledge about solution electrostatics may guide also the design of molecules with specified properties. However, explicit water models come at a high computational cost, rendering them unsuitable for large design studies or for docking purposes. Implicit models with the water phase treated as a continuum require the numerical solution of the Poisson-Boltzmann Equation (PBE. Here, we present a new flexible program for the numerical solution of the PBE, allowing for different geometries, and the explicit and implicit inclusion of membranes. It involves a discretization of space and the computation of the molecular surface. The PBE is solved using finite differences, the resulting set of equations is solved using a Gauss-Seidel method. It is shown for the example of the sucrose transporter ScrY that the implicit inclusion of a surrounding membrane has a strong effect also on the electrostatics within the pore region and thus need to be carefully considered e.g. in design studies on membrane proteins.

  20. Orthogonal Electric Field Measurements near the Green Fluorescent Protein Fluorophore through Stark Effect Spectroscopy and pKa Shifts Provide a Unique Benchmark for Electrostatics Models.

    Science.gov (United States)

    Slocum, Joshua D; First, Jeremy T; Webb, Lauren J

    2017-07-20

    Measurement of the magnitude, direction, and functional importance of electric fields in biomolecules has been a long-standing experimental challenge. pK a shifts of titratable residues have been the most widely implemented measurements of the local electrostatic environment around the labile proton, and experimental data sets of pK a shifts in a variety of systems have been used to test and refine computational prediction capabilities of protein electrostatic fields. A more direct and increasingly popular technique to measure electric fields in proteins is Stark effect spectroscopy, where the change in absorption energy of a chromophore relative to a reference state is related to the change in electric field felt by the chromophore. While there are merits to both of these methods and they are both reporters of local electrostatic environment, they are fundamentally different measurements, and to our knowledge there has been no direct comparison of these two approaches in a single protein. We have recently demonstrated that green fluorescent protein (GFP) is an ideal model system for measuring changes in electric fields in a protein interior caused by amino acid mutations using both electronic and vibrational Stark effect chromophores. Here we report the changes in pK a of the GFP fluorophore in response to the same mutations and show that they are in excellent agreement with Stark effect measurements. This agreement in the results of orthogonal experiments reinforces our confidence in the experimental results of both Stark effect and pK a measurements and provides an excellent target data set to benchmark diverse protein electrostatics calculations. We used this experimental data set to test the pK a prediction ability of the adaptive Poisson-Boltzmann solver (APBS) and found that a simple continuum dielectric model of the GFP interior is insufficient to accurately capture the measured pK a and Stark effect shifts. We discuss some of the limitations of this

  1. Aqueous Solvation of Polyalanine α-Helices with Specific Water Molecules and with the CPCM and SM5.2 Aqueous Continuum Models using Density Functional Theory

    OpenAIRE

    Marianski, Mateusz; Dannenberg, J. J.

    2012-01-01

    We present density functional theory (DFT) calculations at the X3LYP/D95(d,p) level on the solvation of polyalanine α-helices in water. The study includes the effects of discrete water molecules and the CPCM and AMSOL SM5.2 solvent continuum model both separately and in combination. We find that individual water molecules cooperatively hydrogen-bond to both the C- and N-termini of the helix, which results in increases in the dipole moment of the helix/water complex to more than the vector sum...

  2. Lattice gravity near the continuum limit

    International Nuclear Information System (INIS)

    Feinberg, G.; Friedberg, R.; Lee, T.D.; Ren, H.C.

    1984-01-01

    We prove that the lattice gravity always approaches the usual continuum limit when the link length l -> 0, provided that certain general boundary conditions are satisfied. This result holds for any lattice, regular or irregular. Furthermore, for a given lattice, the deviation from its continuum limit can be expressed as a power series in l 2 . General formulas for such a perturbative calculation are given, together with a number of illustrative examples, including the graviton propagator. The lattice gravity satisfies all the invariance properties of Einstein's theory of general relativity. In addition, it is symmetric under a new class of transformations that are absent in the usual continuum theory. The possibility that the lattice theory (with a nonzero l) may be more fundamental is discussed. (orig.)

  3. Interplay of Electrostatics and Hydrophobic Effects in the Metamorphic Protein Human Lymphotactin.

    Science.gov (United States)

    Korkmaz, Elif Nihal; Volkman, Brian F; Cui, Qiang

    2015-07-30

    The human lymphotactin (hLtn) is a protein that features two native states both of which are physiologically relevant: it is a monomer (hLtn10) at 10 °C with 200 mM salt and a dimer (hLtn40) at 40 °C and without salt. Here we focus on the networks of electrostatic and hydrophobic interactions that display substantial changes upon the conversion from hLtn10 to hLtn40 since they are expected to modulate the relative stability of the two folds. In addition to the Arg 23-Arg 43 interaction discussed in previous work, we find several other like-charge pairs that are likely important to the stability of hLtn10. Free energy perturbation calculations are carried out to explicitly evaluate the contribution of the Arg 23-Arg 43 interaction to the hLtn10 stability. hLtn40 features a larger number of salt bridges, and a set of hydrophobic residues undergo major changes in the solvent accessible surface area between hLtn10 and hLtn40, pointing to their importance to the relative stability of the two folds. We also discuss the use of explicit and implicit solvent simulations for characterizing the conformational ensembles under different solution conditions.

  4. Electrostatic Transport and Manipulation of Lunar Soil and Dust

    International Nuclear Information System (INIS)

    Kawamoto, Hiroyuki

    2008-01-01

    Transport and manipulation technologies of lunar soil and dust are under development utilizing the electrostatic force. Transport of particles is realized by an electrostatic conveyer consisting of parallel electrodes. Four-phase traveling electrostatic wave was applied to the electrodes to transport particles upon the conveyer and it was demonstrated that particles were efficiently transported under conditions of low frequency, high voltage, and the application of rectangular wave. Not only linear but also curved and closed transport was demonstrated. Numerical investigation was carried out with a three-dimensional hard-sphere model of the Distinct Element Method to clarify the mechanism of the transport and to predict performances in the lunar environment. This technology is expected to be utilized not only for the transport of bulk soil but also for the cleaning of a solar panel and an optical lens. Another technology is an electrostatic manipulation system to manipulate single particle. A manipulator consisted of two parallel pin electrodes. When voltage was applied between the electrodes, electrophoresis force generated in non-uniform electrostatic field was applied to the particle near the tip of the electrode. The particle was captured by the application of the voltage and released from the manipulator by turning off the voltage. It was possible to manipulate not only insulative but also conductive particles. Three-dimensional electrostatic field calculation was conducted to calculate the electrophoresis force and the Coulomb force

  5. Solvent effect on redox properties of hexanethiolate monolayer-protected gold nanoclusters.

    Science.gov (United States)

    Su, Bin; Zhang, Meiqin; Shao, Yuanhua; Girault, Hubert H

    2006-11-02

    The capacitance of monolayer-protected gold nanoclusters (MPCs), C(MPC), in solution has been theoretically reconsidered from an electrostatic viewpoint, in which an MPC is considered as an isolated charged sphere within two dielectric layers, the intrinsic coating monolayer, and the bulk solvent. The model predicts that the bulk solvent provides an important contribution to C(MPC) and influences the redox properties of MPCs. This theoretical prediction is then examined experimentally by comparing the redox properties of MPCs in four organic solvents: 1,2-dichloroethane (DCE), dichloromethane (DCM), chlorobenzene (CB), and toluene (TOL), in all of which MPCs have excellent solubility. Furthermore, this set of organic solvents features a dielectric constant in a range from 10.37 (DCE) to 2.38 (TOL), which is wide enough to probe the solvent effect. In these organic solvents, tetrahexylammonium bis(trifluoromethylsulfonyl)imide (THATf2N) is used as the supporting electrolyte. Cyclic and differential pulse voltammetric results provide concrete evidence that, despite the monolayer protection, the solvent plays a significant effect on the properties of MPCs in solution.

  6. Gamma-ray continuum spectra from heavy ion reactions

    International Nuclear Information System (INIS)

    Beene, J.R.; Halbert, M.L.; Hensley, D.C.; Sarantites, D.G.; Westerberg, L.W.; Geoffroy, K.; Woodward, R.

    1979-01-01

    A detailed quantitative analysis of the yrast continuum was attempted by subtracting the underlying statistical continnuum in a way that makes allowance for ignorance of its detailed shape. This procedure makes it possible to obtain the moment of inertia as a function of spin over a wide range of spins. The results of this continuum spectra shape analysis can be used to calculate the first and second moments of the continuum multiplicity distribution. Continuum spectra were taken during the bombardment of 150 Nd by 115- and 130-MeV beams of 20 Ne, also the first and second moments of the γ-ray multiplicity distribution as a function of the gamma energy. The moment of inertia versus spin and the deduced Yrast continuua are shown. 10 references

  7. Solvent extraction: the coordination chemistry behind extractive metallurgy.

    Science.gov (United States)

    Wilson, A Matthew; Bailey, Phillip J; Tasker, Peter A; Turkington, Jennifer R; Grant, Richard A; Love, Jason B

    2014-01-07

    The modes of action of the commercial solvent extractants used in extractive hydrometallurgy are classified according to whether the recovery process involves the transport of metal cations, M(n+), metalate anions, MXx(n-), or metal salts, MXx into a water-immiscible solvent. Well-established principles of coordination chemistry provide an explanation for the remarkable strengths and selectivities shown by most of these extractants. Reagents which achieve high selectivity when transporting metal cations or metal salts into a water-immiscible solvent usually operate in the inner coordination sphere of the metal and provide donor atom types or dispositions which favour the formation of particularly stable neutral complexes that have high solubility in the hydrocarbons commonly used in recovery processes. In the extraction of metalates, the structures of the neutral assemblies formed in the water-immiscible phase are usually not well defined and the cationic reagents can be assumed to operate in the outer coordination spheres. The formation of secondary bonds in the outer sphere using, for example, electrostatic or H-bonding interactions are favoured by the low polarity of the water-immiscible solvents.

  8. Electron capture to the continuum from atomic hydrogen

    International Nuclear Information System (INIS)

    Glass, G.A.; Engar, P.; Berry, S.D.; Breinig, M.; Deserio, R.; Elston, S.B.; Sellin, I.A.

    1984-01-01

    The first known measurement of the differential cross section for electron capture to the continuum(ECC) from atomic hydrogen is presented. A 12 MeV beam of C 6+ ions traversed a static target of atomic hydrogen produced by an electron impact heated dissociation oven. The resulting ECC spectrum was obtained with a channel electron multiplier detector mounted at the exit of a 160 0 spherical sector electrostatic spectrometer with an angular acceptance of 2 0 . The ECC spectrum clearly shows the asymmetry generally associated with ECC spectra from gaseous targets. The ratio of the singly differential cross section of H to that of H 2 was found to be 0.80. 16 references, 3 figures

  9. Electrostatic field in inhomogeneous dielectric media. I. Indirect boundary element method

    International Nuclear Information System (INIS)

    Goel, N.S.; Gang, F.; Ko, Z.

    1995-01-01

    A computationally fast method is presented for calculating electrostatic field in arbitrary inhomogeneous dielectric media with open boundary condition. The method involves dividing the whole space into cubical cells and then finding effective dielectric parameters for interfacial cells consisting of several dielectrics. The electrostatic problem is then solved using either the indirect boundary element method described in this paper or the so-called volume element method described in the companion paper. Both methods are tested for accuracy by comparing the numerically calculated electrostatic fields against those analytically obtained for a dielectric sphere and dielectric ellipsoid in a uniform field and for a dielectric sphere in a point charge field

  10. A New Approach for Studying Bond Rupture/Closure of a Spiro Benzopyran Photochromic Material: Reactivity Descriptors Derived from Frontier Orbitals and DFT Computed Electrostatic Potential Energy Surface Maps

    Directory of Open Access Journals (Sweden)

    M. S. A. Abdel-Mottaleb

    2016-01-01

    Full Text Available This paper focuses on computations technique within the framework of the TD-DFT theory for studying the relationship between structure-properties of reversible conversion of photochromic materials. Specifically, we report on 1′,3′-dihydro-8-methoxy-1′,3′,3′-trimethyl-6-nitrospiro[2H-1-benzopyran-2,2′-(2H-indole] (SP and its isomers. TD-DFT calculated UV-Vis electronic spectra of the closed and open isomers of this photochromic material are in excellent agreement with the experimental results. Moreover, this paper reports on the results of theoretical investigations of reactivity indices that may govern the conversion between spiropyrans and its isomers. In addition, the solvent and rigidity of the medium significantly control the thermal bleaching of the photogenerated colored isomers and hence the switch ability pattern of the photochromic material. The effect of molecular structure computed by DFT in gas-phase and solvents on Cspiro-O bond length has been shown to correlate with photochromic properties. For this compound, DFT optimized geometry could be used to predict photochromism. Furthermore, in an attempt to predict the driving force for MC → SP, this work explores, for the first time, profitable exploitation of the calculated and visualized mapped electrostatic potential energy surfaces (ESP map. Interestingly, it seems that the electrostatic potential forces over the molecular fragments govern spirobond rupture/closure reactions. Thermodynamically, all-trans-colored isomer (CTT is the most stable merocyanine-like form.

  11. An improved fast multipole method for electrostatic potential calculations in a class of coarse-grained molecular simulations

    International Nuclear Information System (INIS)

    Poursina, Mohammad; Anderson, Kurt S.

    2014-01-01

    This paper presents a novel algorithm to approximate the long-range electrostatic potential field in the Cartesian coordinates applicable to 3D coarse-grained simulations of biopolymers. In such models, coarse-grained clusters are formed via treating groups of atoms as rigid and/or flexible bodies connected together via kinematic joints. Therefore, multibody dynamic techniques are used to form and solve the equations of motion of such coarse-grained systems. In this article, the approximations for the potential fields due to the interaction between a highly negatively/positively charged pseudo-atom and charged particles, as well as the interaction between clusters of charged particles, are presented. These approximations are expressed in terms of physical and geometrical properties of the bodies such as the entire charge, the location of the center of charge, and the pseudo-inertia tensor about the center of charge of the clusters. Further, a novel substructuring scheme is introduced to implement the presented far-field potential evaluations in a binary tree framework as opposed to the existing quadtree and octree strategies of implementing fast multipole method. Using the presented Lagrangian grids, the electrostatic potential is recursively calculated via sweeping two passes: assembly and disassembly. In the assembly pass, adjacent charged bodies are combined together to form new clusters. Then, the potential field of each cluster due to its interaction with faraway resulting clusters is recursively calculated in the disassembly pass. The method is highly compatible with multibody dynamic schemes to model coarse-grained biopolymers. Since the proposed method takes advantage of constant physical and geometrical properties of rigid clusters, improvement in the overall computational cost is observed comparing to the tradition application of fast multipole method

  12. An improved fast multipole method for electrostatic potential calculations in a class of coarse-grained molecular simulations

    Science.gov (United States)

    Poursina, Mohammad; Anderson, Kurt S.

    2014-08-01

    This paper presents a novel algorithm to approximate the long-range electrostatic potential field in the Cartesian coordinates applicable to 3D coarse-grained simulations of biopolymers. In such models, coarse-grained clusters are formed via treating groups of atoms as rigid and/or flexible bodies connected together via kinematic joints. Therefore, multibody dynamic techniques are used to form and solve the equations of motion of such coarse-grained systems. In this article, the approximations for the potential fields due to the interaction between a highly negatively/positively charged pseudo-atom and charged particles, as well as the interaction between clusters of charged particles, are presented. These approximations are expressed in terms of physical and geometrical properties of the bodies such as the entire charge, the location of the center of charge, and the pseudo-inertia tensor about the center of charge of the clusters. Further, a novel substructuring scheme is introduced to implement the presented far-field potential evaluations in a binary tree framework as opposed to the existing quadtree and octree strategies of implementing fast multipole method. Using the presented Lagrangian grids, the electrostatic potential is recursively calculated via sweeping two passes: assembly and disassembly. In the assembly pass, adjacent charged bodies are combined together to form new clusters. Then, the potential field of each cluster due to its interaction with faraway resulting clusters is recursively calculated in the disassembly pass. The method is highly compatible with multibody dynamic schemes to model coarse-grained biopolymers. Since the proposed method takes advantage of constant physical and geometrical properties of rigid clusters, improvement in the overall computational cost is observed comparing to the tradition application of fast multipole method.

  13. Improved continuum lowering calculations in screened hydrogenic model with l-splitting for high energy density systems

    Science.gov (United States)

    Ali, Amjad; Shabbir Naz, G.; Saleem Shahzad, M.; Kouser, R.; Aman-ur-Rehman; Nasim, M. H.

    2018-03-01

    The energy states of the bound electrons in high energy density systems (HEDS) are significantly affected due to the electric field of the neighboring ions. Due to this effect bound electrons require less energy to get themselves free and move into the continuum. This phenomenon of reduction in potential is termed as ionization potential depression (IPD) or the continuum lowering (CL). The foremost parameter to depict this change is the average charge state, therefore accurate modeling for CL is imperative in modeling atomic data for computation of radiative and thermodynamic properties of HEDS. In this paper, we present an improved model of CL in the screened hydrogenic model with l-splitting (SHML) proposed by G. Faussurier and C. Blancard, P. Renaudin [High Energy Density Physics 4 (2008) 114] and its effect on average charge state. We propose the level charge dependent calculation of CL potential energy and inclusion of exchange and correlation energy in SHML. By doing this, we made our model more relevant to HEDS and free from CL empirical parameter to the plasma environment. We have implemented both original and modified model of SHML in our code named OPASH and benchmark our results with experiments and other state-of-the-art simulation codes. We compared our results of average charge state for Carbon, Beryllium, Aluminum, Iron and Germanium against published literature and found a very reasonable agreement between them.

  14. An experimental study on anti-electrostatic gauge rulers

    International Nuclear Information System (INIS)

    Lou, Renjie; Dai, Liping; Sun, Hong

    2013-01-01

    The process of oil filling will produce electrostatic phenomena which may cause fire accidents. There were no reports about research on the danger of static electricity generation in the process of gauging operation to date. This paper presents an experiment on charge transferring quantity of gauge rulers, and calculates the charge transferring quantity of an anti-electrostatic gauge ruler and a metal one, respectively. The results indicate that the charge transferring quantity can be more than 0.1 μC for a metal gauge ruler, while it is less than 0.1 μC for an antistatic gauge ruler. Therefore, this experimental research proves that using an anti-electrostatic gauge ruler is safer than using a metal one. This study also provides some theoretical and experimental evidence for making anti-electrostatic gauge rulers.

  15. Calculation of phonon dispersion in carbon nanotubes using a continuum-atomistic finite element approach

    Directory of Open Access Journals (Sweden)

    Michael J. Leamy

    2011-12-01

    Full Text Available Dispersion calculations are presented for cylindrical carbon nanotubes using a manifold-based continuum-atomistic finite element formulation combined with Bloch analysis. The formulated finite elements allow any (n,m chiral nanotube, or mixed tubes formed by periodically-repeating heterojunctions, to be examined quickly and accurately using only three input parameters (radius, chiral angle, and unit cell length and a trivial structured mesh, thus avoiding the tedious geometry generation and energy minimization tasks associated with ab initio and lattice dynamics-based techniques. A critical assessment of the technique is pursued to determine the validity range of the resulting dispersion calculations, and to identify any dispersion anomalies. Two small anomalies in the dispersion curves are documented, which can be easily identified and therefore rectified. They include difficulty in achieving a zero energy point for the acoustic twisting phonon, and a branch veering in nanotubes with nonzero chiral angle. The twisting mode quickly restores its correct group velocity as wavenumber increases, while the branch veering is associated with a rapid exchange of eigenvectors at the veering point, which also lessens its impact. By taking into account the two noted anomalies, accurate predictions of acoustic and low-frequency optical branches can be achieved out to the midpoint of the first Brillouin zone.

  16. Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding.

    Science.gov (United States)

    Katkova, E V; Onufriev, A V; Aguilar, B; Sulimov, V B

    2017-03-01

    In this study several commonly used implicit solvent models are compared with respect to their accuracy of estimating solvation energies of small molecules and proteins, as well as desolvation penalty in protein-ligand binding. The test set consists of 19 small proteins, 104 small molecules, and 15 protein-ligand complexes. We compared predicted hydration energies of small molecules with their experimental values; the results of the solvation and desolvation energy calculations for small molecules, proteins and protein-ligand complexes in water were also compared with Thermodynamic Integration calculations based on TIP3P water model and Amber12 force field. The following implicit solvent (water) models considered here are: PCM (Polarized Continuum Model implemented in DISOLV and MCBHSOLV programs), GB (Generalized Born method implemented in DISOLV program, S-GB, and GBNSR6 stand-alone version), COSMO (COnductor-like Screening Model implemented in the DISOLV program and the MOPAC package) and the Poisson-Boltzmann model (implemented in the APBS program). Different parameterizations of the molecules were examined: we compared MMFF94 force field, Amber12 force field and the quantum-chemical semi-empirical PM7 method implemented in the MOPAC package. For small molecules, all of the implicit solvent models tested here yield high correlation coefficients (0.87-0.93) between the calculated solvation energies and the experimental values of hydration energies. For small molecules high correlation (0.82-0.97) with the explicit solvent energies is seen as well. On the other hand, estimated protein solvation energies and protein-ligand binding desolvation energies show substantial discrepancy (up to 10kcal/mol) with the explicit solvent reference. The correlation of polar protein solvation energies and protein-ligand desolvation energies with the corresponding explicit solvent results is 0.65-0.99 and 0.76-0.96 respectively, though this difference in correlations is caused

  17. Mechanical behavior analysis on electrostatically actuated rectangular microplates

    Science.gov (United States)

    Li, Zhikang; Zhao, Libo; Jiang, Zhuangde; Ye, Zhiying; Dai, Lu; Zhao, Yulong

    2015-03-01

    Microplates are widely used in various MEMS devices based on electrostatic actuation such as MEMS switches, micro pumps and capacitive micromachined ultrasonic transducers (CMUTs). Accurate predictions for the mechanical behavior of the microplate under electrostatic force are important not only for the design and optimization of these electrostatic devices but also for their operation. This paper presents a novel reduced-order model for electrostatically actuated rectangular and square microplates with a new method to treat the nonlinear electrostatic force. The model was developed using Galerkin method which turned the partial-differential equation governing the microplates into an ordinary equation system. Using this model and cosine-like deflection functions, explicit expressions were established for the deflection and pull-in voltage of the rectangular and square microplates. The theoretical results were well validated with the finite element method simulations and experimental data of literature. The expressions for the deflection analysis are able to predict the deflection up to the pull-in position with an error less than 5.0%. The expressions for the pull-in voltage analysis can determine the pull-in voltages with errors less than 1.0%. Additionally, the method to calculate the capacitance variation of the electrostatically actuated microplates was proposed. These theoretical analyses are helpful for design and optimization of electrostatically actuated microdevices.

  18. Nuclear structure investigations with inclusion of continuum states

    International Nuclear Information System (INIS)

    Rotter, I.

    1983-09-01

    The influence of the continuum on the properties of discrete nuclear states is reviewed. It is described on the basis of a continuum shell model. The coupling of the discrete states to the continuum results in an additional term to the Hamiltonian, commonly used in the study of nuclear structure, and an additional term to the wavefunction of the discrete state. These additional terms characterise finite nuclei in contrast to nuclear matter. They result in some symmetry violation of the residual nuclear interaction such as charge symmetry violation, and describe the nuclear surface, respectively. The energies and widths of resonance states result from the complex eigenvalues of the Hamiltonian. The partial widths are shown to be factorisable into a spectroscopic factor and into a penetration factor if the spectroscopic factor is large. An expression for the S-matrix is derived in which instead of the so-called resonance parameters, functions appear which are calculated in the framework of the model. The line shape of resonances is also influenced by these functions. As an extreme case, a resonance may have the appearance of a cusp. The conclusions drawn are supported by the results of numerical calculations performed in the continuum shell model for light nuclei with realistic shell model wavefunctions. (author)

  19. THE INFLUENCE OF THE SOLVENT ON THE THERMODYNAMICS OF ION ASSOCIATION

    Directory of Open Access Journals (Sweden)

    Vitalii Chumak

    2011-03-01

    Full Text Available Abstract. Some approaches which allow to divide thermodynamic functions of the ion associationprocess in two components have been developed. The first component belongs to the process, the second oneis caused by the temperature dependence of the dielectric permittivity of the solvent. The theory is confirmedby numerous examples of the ion association process of different electrolytes in the binary mixed solvents.Keywords: covalent part of the constant of ionic association, electrostatic part of the constant of ionicassociation, enthalpy of the chemical equilibria in solution, enthropy of the chemical equilibria in solution,ionic association, ionic equilibrias, the equilibrium constant.

  20. Photoinduced intramolecular charge transfer (ICT) reaction in trans-methyl p-(dimethylamino) cinnamate: A combined fluorescence measurement and quantum chemical calculations

    Energy Technology Data Exchange (ETDEWEB)

    Chakraborty, Amrita [Department of Chemistry, University of Calcutta, 92, A. P. C. Road, Kolkata 700009 (India); Kar, Samiran [Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032 (India); Guchhait, Nikhil [Department of Chemistry, University of Calcutta, 92, A. P. C. Road, Kolkata 700009 (India)], E-mail: nikhilg@postmark.net

    2006-01-05

    The photophysical behaviour of trans-methyl p-(dimethylamino) cinnamate (t-MDMAC) donor-acceptor system has been investigated by steady-state absorption and emission spectroscopy and quantum chemical calculations. The molecule t-MDMAC shows an emission from the locally excited state in non-polar solvents. In addition to weak local emission, a strong solvent dependent red shifted fluorescence in polar aprotic solvents is attributed to highly polar intramolecular charge transfer state. However, the formation of hydrogen-bonded clusters with polar protic solvents has been suggested from a linear correlation between the observed red shifted fluorescence band maxima with hydrogen bonding parameters ({alpha}). Calculations by ab initio and density functional theory show that the lone pair electron at nitrogen center is out of plane of the benzene ring in the global minimum ground state structure. In the gas phase, a potential energy surface along the twist coordinate at the donor (-NMe{sub 2}) and acceptor (-CH = CHCOOMe) sites shows stabilization of S{sub 1} state and destabilization S{sub 2} and S{sub 0} states. A similar potential energy calculation along the twist coordinate in acetonitrile solvent using non-equilibrium polarized continuum model also shows more stabilization of S{sub 1} state relative to other states and supports solvent dependent red shifted emission properties. In all types of calculations it is found that the nitrogen lone pair is delocalized over the benzene ring in the global minimum ground state and is localized on the nitrogen centre at the 90 deg. twisted configuration. The S{sub 1} energy state stabilization along the twist coordinate at the donor site and localized nitrogen lone pair at the perpendicular configuration support well the observed dual fluorescence in terms of proposed twisted intramolecular charge transfer (TICT) model.

  1. Quantum mechanics/molecular mechanics modeling of photoelectron spectra: the carbon 1s core-electron binding energies of ethanol-water solutions.

    Science.gov (United States)

    Löytynoja, T; Niskanen, J; Jänkälä, K; Vahtras, O; Rinkevicius, Z; Ågren, H

    2014-11-20

    Using ethanol-water solutions as illustration, we demonstrate the capability of the hybrid quantum mechanics/molecular mechanics (QM/MM) paradigm to simulate core photoelectron spectroscopy: the binding energies and the chemical shifts. An integrated approach with QM/MM binding energy calculations coupled to preceding molecular dynamics sampling is adopted to generate binding energies averaged over the solute-solvent configurations available at a particular temperature and pressure and thus allowing for a statistical assessment with confidence levels for the final binding energies. The results are analyzed in terms of the contributions in the molecular mechanics model-electrostatic, polarization, and van der Waals-with atom or bond granulation of the corresponding MM charge and polarizability force-fields. The role of extramolecular charge transfer screening of the core-hole and explicit hydrogen bonding is studied by extending the QM core to cover the first solvation shell. The results are compared to those obtained from pure electrostatic and polarizable continuum models. Particularly, the dependence of the carbon 1s binding energies with respect to the ethanol concentration is studied. Our results indicate that QM/MM can be used as an all-encompassing model to study photoelectron binding energies and chemical shifts in solvent environments.

  2. Continuum radiation of argon plasma

    International Nuclear Information System (INIS)

    D'Yachkov, L.G.

    1995-01-01

    A simple completely analytical method of the calculation of radiative continuum of plasmas is derived and an analysis of experimental data on continuum radiation of argon plasma is made. The method is based on the semiclassical quantum defect theory. To calculate radial matrix elements of dipole transitions the asymptotic expansion in powers of E c /ω 2/3 , with an accuracy to the linear term, where E, is the arithmetic mean of the initial and final energies of the transition, is used. This expansion has the same form for free-free, free-bound and bound-bound transitions. If the quantum defects are also approximated by a linear function of energy, the integration over the electron energy (the Maxwell-Boltzmann distribution is assumed) can be performed in analytical form. For Rydberg states the sum of photoionization continua can be replaced by an integral. We have calculated the absorption coefficient pf argon plasma. The photoionization cross section is calculated for all the states of 4s, 5s, 6s, 4p, 5p, 3d, 4d, 4s', 5s', 6s', 4p', 5p', 3d' and 4d' configurations taking into account P-coupling and multiplet splitting (56 states). Other excited states are allowed for by the integral formula together with free-free transitions

  3. Calculation of liquid-liquid phase separation in a ternary system of a polymer in a mixture of a solvent and a nonsolvent

    NARCIS (Netherlands)

    Altena, Frank W.; Smolders, C.A.

    1982-01-01

    A numerical method for the calculation of the binodal of liquid-liquid phase separation in a ternary system is described. The Flory-Huggins theory for three-component systems is used. Binodals are calculated for polymer/solvent/nonsolvent systems which are used in the preparation of asymmetric

  4. Consequences of inelastic discrete-level neutron-collision mechanics for inelastic continuum scattering

    Energy Technology Data Exchange (ETDEWEB)

    Hoogenboom, J.E. (Technische Hogeschool Delft (Netherlands))

    1983-01-01

    From the collision mechanics of inelastic discrete-level scattering several properties are derived for the secondary-neutron energy distribution (SNED) for inelastic continuum scattering, when conceived as scattering with continuously-distributed inelastic levels. Using assumptions about the level density and neutron cross section the SNED can be calculated and some examples are shown. A formula is derived to calculate from a given inelastic continuum SNED a function, which is proportional to the level density and the neutron cross section. From this relation further conditions follow for the SNED. Representations for the inelastic continuum SNED currently in use do not, in general, satisfy most of the derived conditions.

  5. Consequences of inelastic discrete-level neutron-collision mechanics for inelastic continuum scattering

    International Nuclear Information System (INIS)

    Hoogenboom, J.E.

    1983-01-01

    From the collision mechanics of inelastic discrete-level scattering several properties are derived for the secondary-neutron energy distribution (SNED) for inelastic continuum scattering, when conceived as scattering with continuously-distributed inelastic levels. Using assumptions about the level density and neutron cross section the SNED can be calculated and some examples are shown. A formula is derived to calculate from a given inelastic continuum SNED a function, which is proportional to the level density and the neutron cross section. From this relation further conditions follow for the SNED. Representations for the inelastic continuum SNED currently in use do not, in general, satisfy most of the derived conditions. (author)

  6. Biological Applications of Hybrid Quantum Mechanics/Molecular Mechanics Calculation

    Directory of Open Access Journals (Sweden)

    Jiyoung Kang

    2012-01-01

    Full Text Available Since in most cases biological macromolecular systems including solvent water molecules are remarkably large, the computational costs of performing ab initio calculations for the entire structures are prohibitive. Accordingly, QM calculations that are jointed with MM calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structures of biological macromolecules. A UNIX-shell-based interface program connecting the quantum mechanics (QMs and molecular mechanics (MMs calculation engines, GAMESS and AMBER, was developed in our lab. The system was applied to a metalloenzyme, azurin, and PU.1-DNA complex; thereby, the significance of the environmental effects on the electronic structures of the site of interest was elucidated. Subsequently, hybrid QM/MM molecular dynamics (MD simulation using the calculation system was employed for investigation of mechanisms of hydrolysis (editing reaction in leucyl-tRNA synthetase complexed with the misaminoacylated tRNALeu, and a novel mechanism of the enzymatic reaction was revealed. Thus, our interface program can play a critical role as a powerful tool for state-of-the-art sophisticated hybrid ab initio QM/MM MD simulations of large systems, such as biological macromolecules.

  7. Counterintuitive electron localisation from density-functional theory with polarisable solvent models

    Energy Technology Data Exchange (ETDEWEB)

    Dale, Stephen G., E-mail: sdale@ucmerced.edu [Chemistry and Chemical Biology, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California 95343 (United States); Johnson, Erin R., E-mail: erin.johnson@dal.ca [Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2 (Canada)

    2015-11-14

    Exploration of the solvated electron phenomena using density-functional theory (DFT) generally results in prediction of a localised electron within an induced solvent cavity. However, it is well known that DFT favours highly delocalised charges, rendering the localisation of a solvated electron unexpected. We explore the origins of this counterintuitive behaviour using a model Kevan-structure system. When a polarisable-continuum solvent model is included, it forces electron localisation by introducing a strong energetic bias that favours integer charges. This results in the formation of a large energetic barrier for charge-hopping and can cause the self-consistent field to become trapped in local minima thus converging to stable solutions that are higher in energy than the ground electronic state. Finally, since the bias towards integer charges is caused by the polarisable continuum, these findings will also apply to other classical polarisation corrections, as in combined quantum mechanics and molecular mechanics (QM/MM) methods. The implications for systems beyond the solvated electron, including cationic DNA bases, are discussed.

  8. 40 CFR 63.5753 - How do I calculate the combined organic HAP content of aluminum wipedown solvents and aluminum...

    Science.gov (United States)

    2010-07-01

    ... HAP content of aluminum wipedown solvents and aluminum recreational boat surface coatings? 63.5753... Standards for Hazardous Air Pollutants for Boat Manufacturing Standards for Aluminum Recreational Boat Surface Coating Operations § 63.5753 How do I calculate the combined organic HAP content of aluminum...

  9. Comet Halley: An optical continuum study

    International Nuclear Information System (INIS)

    Hoban, S.M.

    1989-01-01

    From an analysis of narrowband CCD images of Comet Halley from 1986 January, March, and April, certain dust structures which are redder than the remainder of the dust coma have become apparent. Mie calculations suggest that this reddening is due to an enhancement of particles with sizes comparable to the observing wavelengths. Although the mass range derived from the calculations presented here is somewhat uncertain as a result of the limitations of Mie theory, these values are in the expected range derived from the calculations presented here is somewhat uncertain as a result of particle sizes which would be both sensitive to radiation pressure and significantly reddened with respect to the solar spectrum at the observing wavelengths. Thus, the red envelopes are plausibly the result of size sorting by solar radiation pressure. The red jets observed on 1986 January 10, March 1 and March 9 can then be explained by the enhanced dust flux at the jet sources, and the subsequent trapping of a relative excess of intermediate mass (i.e. red) particles into the jets which are visible in the continuum images. Analysis of narrowband photometry of the optical continuum of Comet Halley reveals no correlation between the color of the dust and heliocentric distance, phase angle, strength of the continuum or gas-to-dust ratio. The photometric data are thus consistent with a post-ejection sorting mechanism. Chemical inhomogeneities of the nucleus are therefore not necessary to explain the observed structure in the color of the dust in Comet Halley

  10. Effect of solvent on proton location and dynamic behavior in short intramolecular hydrogen bonds studied by molecular dynamics simulations and NMR experiments

    International Nuclear Information System (INIS)

    Mori, Yukie; Masuda, Yuichi

    2015-01-01

    H nuclei monitoring the nuclear magnetic relaxation times of 1 H. The experimental results indicated that the H-bond geometry of 2 is influenced by the interactions with dimethylsulfoxide, suggesting the formation of a bifurcated H-bond, which was supported by the DFT calculations. The MD simulations for the methanol solution of 2 showed that the asymmetry of the OH distance is correlated with the asymmetry in the electrostatic field of the solvent, although the correlation is weaker than that for the methanol solution of 1. The lower sensitivity of 2 to the solvent is attributed to the smaller number of oxygen atoms and the less negative electrostatic potential at the proton-accepting sites. The present study indicates that the specific interactions with protic solvents or strong H-bond-accepting solvents affect the geometry and dynamic behavior of short intramolecular H-bonds

  11. Effect of solvent on proton location and dynamic behavior in short intramolecular hydrogen bonds studied by molecular dynamics simulations and NMR experiments

    Energy Technology Data Exchange (ETDEWEB)

    Mori, Yukie, E-mail: mori.yukie@ocha.ac.jp; Masuda, Yuichi

    2015-09-08

    }O and {sup 1}H nuclei monitoring the nuclear magnetic relaxation times of {sup 1}H. The experimental results indicated that the H-bond geometry of 2 is influenced by the interactions with dimethylsulfoxide, suggesting the formation of a bifurcated H-bond, which was supported by the DFT calculations. The MD simulations for the methanol solution of 2 showed that the asymmetry of the OH distance is correlated with the asymmetry in the electrostatic field of the solvent, although the correlation is weaker than that for the methanol solution of 1. The lower sensitivity of 2 to the solvent is attributed to the smaller number of oxygen atoms and the less negative electrostatic potential at the proton-accepting sites. The present study indicates that the specific interactions with protic solvents or strong H-bond-accepting solvents affect the geometry and dynamic behavior of short intramolecular H-bonds.

  12. Complex calculation and improvement of beam shaping and accelerating system of the ''Sokol'' small-size electrostatic accelerator

    International Nuclear Information System (INIS)

    Simonenko, A.V.; Pistryak, V.M.; Zats, A.V.; Levchenko, Yu.Z.; Kuz'menko, V.V.

    1987-01-01

    Features of charged particle accelerated beam shaping in the electrostatic part of the ''Sokol'' small-size accelerator are considered in complex taking into account the electrode real geometry. Effect of the extracting, accelerating electorde potential and accelerator total voltage on beam behaviour is investigated. A modified variation of the beam shaping system, allowing to decrease 2 times the required interval of accelerating electrode potential adjustment and to decrease the beam size in the starting acceleration region, is presented. It permits to simplify the construction and to improve accelerator operation. Comparison of experimental and calculational data on the beam in the improved accelerator variation is carried out. Effect of peripheral parts of accelerating tube electrodes on the beam is investigated

  13. Electronic excitations in a dielectric continuum solvent with quantum Monte Carlo: Acrolein in water

    NARCIS (Netherlands)

    Floris, F.M.; Filippi, Claudia; Amovilli, C.

    2014-01-01

    We investigate here the vertical n → π* and π → π* transitions of s-trans-acrolein in aqueous solution by means of a polarizable continuum model (PCM) we have developed for the treatment of the solute at the quantum Monte Carlo (QMC) level of the theory. We employ the QMC approach which allows us to

  14. Excitation of electrostatic ion cyclotron wave in electron beam plasma system

    International Nuclear Information System (INIS)

    Fukumura, Takashi; Takamoto, Teruo

    1984-01-01

    The electrostatic ion cyclotron waves excited in an electron beam plasma system was investigated. The excitation condition of the waves was calculated by using Harris type dispersion relation under some assumption, and its comparison with the experimental result was made. Beam plasma discharge is a kind of RF discharge, and it is caused by the waves generated by the interaction of electron beam with plasma. It was shown that electrostatic ion cyclotron waves seemed to be the most probable as excited waves. But the excitation mechanism of these waves has not been concretely investigated. In this study, the excitation condition of electrostatic ion cyclotron waves was calculated as described above. The experimental apparatus and the results of potential, electric field and ion saturation current in beam plasma, electron drift motion in azimuthal direction and the waves excited in beam plasma are reported. The frequency of oscillation observed in beam plasma corresponds to the harmonics or subharmonics of ion cyclotron frequency. The calculation of Harris type dispersion relation, the numerical calculation and the comparison of the experimental result with the calculated result are described. (Kako, I.)

  15. Extraction of uranium with TBP in an electrostatic apparatus

    International Nuclear Information System (INIS)

    Kalbasi, M.

    1980-10-01

    An experimental investigation into the utilization of electrostatic energy for solvent extraction of metallic species has been made. Drops were formed at a single nozzle and charged electrically by applying a high d.c. voltage to the nozzle which was arranged to form part of a parallel disc electrode system. After the drops left this electrode zone they travelled through a metallic pipe the purpose of which was to screen the drops from the external electrostatic forces. The liquid system employed in the present work was aqueous uranyl nitrate solution as a dispersed phase and organic tri-n-butyl phosphate (TBP)-diluent as a continuous phase. Uncharged drops were studied in the presence and absence of nitric acid salting agent and in addition both discrete and spray regimes were examined with charged drops. Size, velocity, oscillation motion, charge leakage, actual potential gradient and mass transfer coefficients (reaction rate constants) were studied. A cine camera was used to study the velocity and oscillatory motion of the charged drops moving in the continuous phase in the presence and absence of an electric field. The results of this work suggest that both hydrodynamic and electrostatic forces are responsible for the liquid-liquid extraction rate increase. (author)

  16. Mechanical behavior analysis on electrostatically actuated rectangular microplates

    International Nuclear Information System (INIS)

    Li, Zhikang; Zhao, Libo; Jiang, Zhuangde; Ye, Zhiying; Zhao, Yulong; Dai, Lu

    2015-01-01

    Microplates are widely used in various MEMS devices based on electrostatic actuation such as MEMS switches, micro pumps and capacitive micromachined ultrasonic transducers (CMUTs). Accurate predictions for the mechanical behavior of the microplate under electrostatic force are important not only for the design and optimization of these electrostatic devices but also for their operation. This paper presents a novel reduced-order model for electrostatically actuated rectangular and square microplates with a new method to treat the nonlinear electrostatic force. The model was developed using Galerkin method which turned the partial-differential equation governing the microplates into an ordinary equation system. Using this model and cosine-like deflection functions, explicit expressions were established for the deflection and pull-in voltage of the rectangular and square microplates. The theoretical results were well validated with the finite element method simulations and experimental data of literature. The expressions for the deflection analysis are able to predict the deflection up to the pull-in position with an error less than 5.0%. The expressions for the pull-in voltage analysis can determine the pull-in voltages with errors less than 1.0%. Additionally, the method to calculate the capacitance variation of the electrostatically actuated microplates was proposed. These theoretical analyses are helpful for design and optimization of electrostatically actuated microdevices. (paper)

  17. Comparison of experimental and DFT-calculated NMR chemical shifts of 2-amino and 2-hydroxyl substituted phenyl benzimidazoles, benzoxazoles and benzothiazoles in four solvents using the IEF-PCM solvation model.

    Science.gov (United States)

    Pierens, Gregory K; Venkatachalam, T K; Reutens, David C

    2016-04-01

    A comparative study of experimental and calculated NMR chemical shifts of six compounds comprising 2-amino and 2-hydroxy phenyl benzoxazoles/benzothiazoles/benzimidazoles in four solvents is reported. The benzimidazoles showed interesting spectral characteristics, which are discussed. The proton and carbon chemical shifts were similar for all solvents. The largest chemical shift deviations were observed in benzene. The chemical shifts were calculated with density functional theory using a suite of four functionals and basis set combinations. The calculated chemical shifts revealed a good match to the experimentally observed values in most of the solvents. The mean absolute error was used as the primary metric. The use of an additional metric is suggested, which is based on the order of chemical shifts. The DP4 probability measures were also used to compare the experimental and calculated chemical shifts for each compound in the four solvents. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

  18. New Distributed Multipole Methods for Accurate Electrostatics for Large-Scale Biomolecular Simultations

    Science.gov (United States)

    Sagui, Celeste

    2006-03-01

    An accurate and numerically efficient treatment of electrostatics is essential for biomolecular simulations, as this stabilizes much of the delicate 3-d structure associated with biomolecules. Currently, force fields such as AMBER and CHARMM assign ``partial charges'' to every atom in a simulation in order to model the interatomic electrostatic forces, so that the calculation of the electrostatics rapidly becomes the computational bottleneck in large-scale simulations. There are two main issues associated with the current treatment of classical electrostatics: (i) how does one eliminate the artifacts associated with the point-charges (e.g., the underdetermined nature of the current RESP fitting procedure for large, flexible molecules) used in the force fields in a physically meaningful way? (ii) how does one efficiently simulate the very costly long-range electrostatic interactions? Recently, we have dealt with both of these challenges as follows. In order to improve the description of the molecular electrostatic potentials (MEPs), a new distributed multipole analysis based on localized functions -- Wannier, Boys, and Edminston-Ruedenberg -- was introduced, which allows for a first principles calculation of the partial charges and multipoles. Through a suitable generalization of the particle mesh Ewald (PME) and multigrid method, one can treat electrostatic multipoles all the way to hexadecapoles all without prohibitive extra costs. The importance of these methods for large-scale simulations will be discussed, and examplified by simulations from polarizable DNA models.

  19. Engineering Design of Electrostatic Quadrupole for ISOL Beam Lines

    International Nuclear Information System (INIS)

    Kim, H. S.; Kwon, H. J.; Cho, Y. S.

    2014-01-01

    In the ISOL system, the RI beam should be transported from the target ion source to post accelerator through various analyzing and charge-breeding systems such as PS (pre-seperator), HRMS (High Resolution Mass Seperator), RF cooler and A/q separator. A reference particle for the beam dynamics calculation is 132 Sn 1+ . After charge breeder system, the charge state is boosted from +1 to +19 with ECR charge breeder and to +33 with EBIS charge breeder. Because the beam energy is as low as 50 keV, the electrostatic optics was adopted rather than the magnetic optics. The electrostatic quadrupole triplets were used for the beam focusing and the electrostatic bender is used for 90-degree bending. In this paper, the design procedure and engineering design of the electrostatic quadrupole are presented

  20. 3DRISM-HI-D2MSA: an improved analytic theory to compute solvent structure around hydrophobic solutes with proper treatment of solute–solvent electrostatic interactions

    KAUST Repository

    Cao, Siqin

    2017-12-22

    The 3D reference interaction site model (3DRISM) is a powerful tool to study the thermodynamic and structural properties of liquids. However, for hydrophobic solutes, the inhomogeneity of the solvent density around them poses a great challenge to the 3DRISM theory. To address this issue, we have previously introduced the hydrophobic-induced density inhomogeneity theory (HI) for purely hydrophobic solutes. To further consider the complex hydrophobic solutes containing partial charges, here we propose the D2MSA closure to incorporate the short-range and long-range interactions with the D2 closure and the mean spherical approximation, respectively. We demonstrate that our new theory can compute the solvent distributions around real hydrophobic solutes in water and complex organic solvents that agree well with the explicit solvent molecular dynamics simulations.

  1. 3DRISM-HI-D2MSA: an improved analytic theory to compute solvent structure around hydrophobic solutes with proper treatment of solute–solvent electrostatic interactions

    KAUST Repository

    Cao, Siqin; Zhu, Lizhe; Huang, Xuhui

    2017-01-01

    The 3D reference interaction site model (3DRISM) is a powerful tool to study the thermodynamic and structural properties of liquids. However, for hydrophobic solutes, the inhomogeneity of the solvent density around them poses a great challenge to the 3DRISM theory. To address this issue, we have previously introduced the hydrophobic-induced density inhomogeneity theory (HI) for purely hydrophobic solutes. To further consider the complex hydrophobic solutes containing partial charges, here we propose the D2MSA closure to incorporate the short-range and long-range interactions with the D2 closure and the mean spherical approximation, respectively. We demonstrate that our new theory can compute the solvent distributions around real hydrophobic solutes in water and complex organic solvents that agree well with the explicit solvent molecular dynamics simulations.

  2. 3DRISM-HI-D2MSA: an improved analytic theory to compute solvent structure around hydrophobic solutes with proper treatment of solute–solvent electrostatic interactions

    Science.gov (United States)

    Cao, Siqin; Zhu, Lizhe; Huang, Xuhui

    2018-04-01

    The 3D reference interaction site model (3DRISM) is a powerful tool to study the thermodynamic and structural properties of liquids. However, for hydrophobic solutes, the inhomogeneity of the solvent density around them poses a great challenge to the 3DRISM theory. To address this issue, we have previously introduced the hydrophobic-induced density inhomogeneity theory (HI) for purely hydrophobic solutes. To further consider the complex hydrophobic solutes containing partial charges, here we propose the D2MSA closure to incorporate the short-range and long-range interactions with the D2 closure and the mean spherical approximation, respectively. We demonstrate that our new theory can compute the solvent distributions around real hydrophobic solutes in water and complex organic solvents that agree well with the explicit solvent molecular dynamics simulations.

  3. Nonlinear behaviour of cantilevered carbon nanotube resonators based on a new nonlinear electrostatic load model

    Science.gov (United States)

    Farokhi, Hamed; Païdoussis, Michael P.; Misra, Arun K.

    2018-04-01

    The present study examines the nonlinear behaviour of a cantilevered carbon nanotube (CNT) resonator and its mass detection sensitivity, employing a new nonlinear electrostatic load model. More specifically, a 3D finite element model is developed in order to obtain the electrostatic load distribution on cantilevered CNT resonators. A new nonlinear electrostatic load model is then proposed accounting for the end effects due to finite length. Additionally, a new nonlinear size-dependent continuum model is developed for the cantilevered CNT resonator, employing the modified couple stress theory (to account for size-effects) together with the Kelvin-Voigt model (to account for nonlinear damping); the size-dependent model takes into account all sources of nonlinearity, i.e. geometrical and inertial nonlinearities as well as nonlinearities associated with damping, small-scale, and electrostatic load. The nonlinear equation of motion of the cantilevered CNT resonator is obtained based on the new models developed for the CNT resonator and the electrostatic load. The Galerkin method is then applied to the nonlinear equation of motion, resulting in a set of nonlinear ordinary differential equations, consisting of geometrical, inertial, electrical, damping, and size-dependent nonlinear terms. This high-dimensional nonlinear discretized model is solved numerically utilizing the pseudo-arclength continuation technique. The nonlinear static and dynamic responses of the system are examined for various cases, investigating the effect of DC and AC voltages, length-scale parameter, nonlinear damping, and electrostatic load. Moreover, the mass detection sensitivity of the system is examined for possible application of the CNT resonator as a nanosensor.

  4. SUCCESS AND PITFALLS OF THE DIELECTRIC CONTINUUM MODEL IN QUANTUM-CHEMICAL CALCULATIONS

    NARCIS (Netherlands)

    DEVRIES, AH; VANDUIJNEN, PT; JUFFER, AH

    1993-01-01

    Recently we presented an extension of the direct reaction field (DRF) method, in which a quantum system and a set of point charges and interacting polarizabilities are embedded in a continuum that is characterized by a dielectric constant epsilon and a finite ionic strength. The reaction field of

  5. Continuum Mechanics

    CERN Document Server

    Romano, Antonio

    2010-01-01

    This book offers a broad overview of the potential of continuum mechanics to describe a wide range of macroscopic phenomena in real-world problems. Building on the fundamentals presented in the authors' previous book, Continuum Mechanics using Mathematica(R), this new work explores interesting models of continuum mechanics, with an emphasis on exploring the flexibility of their applications in a wide variety of fields.Specific topics, which have been chosen to show the power of continuum mechanics to characterize the experimental behavior of real phenomena, include: * various aspects of nonlin

  6. Rational redesign of inhibitors of furin/kexin processing proteases by electrostatic mutations.

    Science.gov (United States)

    Cai, Xiao-hui; Zhang, Qing; Ding, Da-fu

    2004-12-01

    To model the three-dimensional structure and investigate the interaction mechanism of the proprotein convertase furin/kexin and their inhibitors (eglin c mutants). The three-dimensional complex structures of furin/kexin with its inhibitors, eglin c mutants, were generated by modeller program using the newly published X-ray crystallographical structures of mouse furin and yeast kexin as templates. The electrostatic interaction energy of each complex was calculated and the results were compared with the experimentally determined inhibition constants to find the correlation between them. High quality models of furin/kexin-eglin c mutants were obtained and used for calculation of the electrostatic interaction energies between the proteases and their inhibitors. The calculated electrostatic energies of interaction showed a linear correlation to the experimental inhibition constants. The modeled structures give good explanations of the specificity of eglin c mutants to furin/kexin. The electrostatic interactions play important roles in inhibitory activity of eglin c mutants to furin/kexin. The results presented here provided quantitative structural and functional information concerning the role of the charge-charge interactions in the binding of furin/kexin and their inhibitors.

  7. Lightweight space radiator with leakage control by internal electrostatic fields

    International Nuclear Information System (INIS)

    Kim, H.; Bankoff, S.G.; Miksis, M.J.

    1991-01-01

    An electrostatic liquid film space radiator is proposed. This will employ an internal electrostatic field to prevent leakage of the liquid-metal coolant out of a puncture. This overcomes the major disadvantage of membrane radiators, which is their vulnerability to micrometeorite impacts. Calculations show that leaks of liquid lithium at 700 degree K can easily be stopped from punctures which are several mm in diameter, with very large safety factors. The basic idea lends itself to a variety of radiator concepts, both rotating and non-rotating. Some typical film thickness and pressure calculations in the presence of an electric field are shown

  8. A versatile electrostatic trap with open optical access

    Science.gov (United States)

    Li, Sheng-Qiang; Yin, Jian-Ping

    2018-04-01

    A versatile electrostatic trap with open optical access for cold polar molecules in weak-field-seeking state is proposed in this paper. The trap is composed of a pair of disk electrodes and a hexapole. With the help of a finite element software, the spatial distribution of the electrostatic field is calculated. The results indicate that a three-dimensional closed electrostatic trap is formed. Taking ND3 molecules as an example, the dynamic process of loading and trapping is simulated. The results show that when the velocity of the molecular beam is 10 m/s and the loading time is 0.9964 ms, the maximum loading efficiency reaches 94.25% and the temperature of the trapped molecules reaches about 30.3 mK. A single well can be split into two wells, which is of significant importance to the precision measurement and interference of matter waves. This scheme, in addition, can be further miniaturized to construct one-dimensional, two-dimensional, and three-dimensional spatial electrostatic lattices.

  9. Predicting the equilibrium solubility of solid polycyclic aromatic hydrocarbons and dibenzothiophene using a combination of MOSCED plus molecular simulation or electronic structure calculations

    Science.gov (United States)

    Phifer, Jeremy R.; Cox, Courtney E.; da Silva, Larissa Ferreira; Nogueira, Gabriel Gonçalves; Barbosa, Ana Karolyne Pereira; Ley, Ryan T.; Bozada, Samantha M.; O'Loughlin, Elizabeth J.; Paluch, Andrew S.

    2017-06-01

    Methods to predict the equilibrium solubility of non-electrolyte solids are important for the design of novel separation processes. Here we demonstrate how conventional molecular simulation free energy calculations or electronic structure calculations in a continuum solvent, here SMD or SM8, can be used to predict parameters for the MOdified Separation of Cohesive Energy Density (MOSCED) method. The method is applied to the solutes naphthalene, anthracene, phenanthrene, pyrene and dibenzothiophene, compounds of interested to the petroleum industry and for environmental remediation. Adopting the melting point temperature and enthalpy of fusion of these compounds from experiment, we are able to predict equilibrium solubilities. Comparing to a total of 422 non-aqueous and 193 aqueous experimental solubilities, we find the proposed method is able to well correlate the data. The use of MOSCED is additionally advantageous as it is a solubility parameter-based method useful for intuitive solvent selection and formulation.

  10. Material Science Smart Coatings

    Energy Technology Data Exchange (ETDEWEB)

    Rubinstein, A. I. [Univ. of Nebraska Medical Center, Omaha, NE (United States); Sabirianov, R. F. [Univ. of Nebraska Medical Center, Omaha, NE (United States); Namavar, Fereydoon [Univ. of Nebraska Medical Center, Omaha, NE (United States)

    2014-07-01

    The contribution of electrostatic interactions to the free energy of binding between model protein and a ceramic implant surface in the aqueous solvent, considered in the framework of the nonlocal electrostatic model, is calculated as a function of the implant low-frequency dielectric constant. We show that the existence of a dynamically ordered (low-dielectric) interfacial solvent layer at the protein-solvent and ceramic-solvent interface markedly increases charging energy of the protein and ceramic implant, and consequently makes the electrostatic contribution to the protein-ceramic binding energy more favorable (attractive). Our analysis shows that the corresponding electrostatic energy between protein and oxide ceramics depends nonmonotonically on the dielectric constant of ceramic, εC. Obtained results indicate that protein can attract electrostatically to the surface if ceramic material has a moderate εC below or about 35 (in particularly ZrO2 or Ta2O5). This is in contrast to classical (local) consideration of the solvent, which demonstrates an unfavorable electrostatic interaction of protein with typical metal oxide ceramic materials (εC>10). Thus, a solid implant coated by combining oxide ceramic with a reduced dielectric constant can be beneficial to strengthen the electrostatic binding of the protein-implant complex.

  11. Competing processes of whistler and electrostatic instabilities in the magnetosphere

    International Nuclear Information System (INIS)

    Omura, Y.; Matsumoto, H.

    1987-01-01

    Competing processes of whistler mode and electrostatic mode instabilities induced by an electron beam are studied by a linear growth rate analysis and by an electromagnetic particle simulation. In addition to a background cold plasma we assumed an electron beam drifting along a static magnetic field. We studied excitation of whistler and electrostatic mode waves in the direction of the static magnetic field. We first calculated linear growth rates for the whistler mode and electrostatic mode instabilities, assuming various possible parameters in the equatorial magnetosphere. We found that the growth rate for the electrostatic instability is always larger than that of the whistler mode instability. A short simulation run with a monoenergetic electron beam demonstrates that a monoenergetic beam can hardly give energy to whistler mode waves as a result of competition with faster growing electrostatic waves, because the beam electrons are trapped and diffused by the electrostatic waves, and hence the growth rates for whistler mode waves become very small. A long simulation run starting with a warm electron beam demonstrates that whistler mode waves are excited in spite of the small growth rates and the coexisting quasi-linear electrostatic diffusion process

  12. Expansion of continuum functions on resonance wave functions and amplitudes

    International Nuclear Information System (INIS)

    Bang, J.; Gareev, F.A.; Gizzatkulov, M.H.; Goncharov, S.A.

    1978-01-01

    To overcome difficulties encountered with wave functions of continuum spectrum (for example, in a shell model with continuum) the pole expansion (by the Mittag-Leffler theorem) of wave functions, scattering amplitudes and the Green functions with positive energies are considered. It is shown that resonance functions (the Gamov functions) form a complete set over which the continuum functions could be expanded. The general view of these expansions for final potentials and for the Coulomb repulsion potential are obtained and discussed. It is shown that the application of the method to nuclear structure calculations leads to simple algebraic equations

  13. Dissolution of covalent adaptable network polymers in organic solvent

    Science.gov (United States)

    Yu, Kai; Yang, Hua; Dao, Binh H.; Shi, Qian; Yakacki, Christopher M.

    2017-12-01

    It was recently reported that thermosetting polymers can be fully dissolved in a proper organic solvent utilizing a bond-exchange reaction (BER), where small molecules diffuse into the polymer, break the long polymer chains into short segments, and eventually dissolve the network when sufficient solvent is provided. The solvent-assisted dissolution approach was applied to fully recycle thermosets and their fiber composites. This paper presents the first multi-scale modeling framework to predict the dissolution kinetics and mechanics of thermosets in organic solvent. The model connects the micro-scale network dynamics with macro-scale material properties: in the micro-scale, a model is developed based on the kinetics of BERs to describe the cleavage rate of polymer chains and evolution of chain segment length during the dissolution. The micro-scale model is then fed into a continuum-level model with considerations of the transportation of solvent molecules and chain segments in the system. The model shows good prediction on conversion rate of functional groups, degradation of network mechanical properties, and dissolution rate of thermosets during the dissolution. It identifies the underlying kinetic factors governing the dissolution process, and reveals the influence of different material and processing variables on the dissolution process, such as time, temperature, catalyst concentration, and chain length between cross-links.

  14. On the electronic structure of Barrelene-based rigid organic donor-acceptor systems. An INDO model study including solvent effects

    International Nuclear Information System (INIS)

    Fox, T.; Kotzian, M.; Roesch, N.

    1992-01-01

    The authors present an INDO/S Molecular-orbital investigation of organic molecules containing a barrelene moiety that provides a rigid link between an aromatic donor and a maleic ester acceptor group. Molecules of this type have recently been synthesized and characterized spectroscopically. The authors discuss the ground state and various excited states both in vacuo and in solution. Solvent effects are incorporated by use of an electrostatic cavity model which is not restricted to a spherical cavity, but allows for a cavity shape that is adapted to the solute molecule. The calculations indicate low-lying charge-transfer (CT) excitations in the region of the first aromatic transitions, even in the gas phase

  15. The modification of the terminal electrostatic field of HI-13 tandem accelerator

    International Nuclear Information System (INIS)

    Li Tao; Guan Xialing

    1993-01-01

    The calculation of electrostatic field of terminal and its neighbour region for HI-13 tandem accelerator is made. The limit terminal voltage without tubes is evaluated. Using elliptical cross section in stead of circular ones for the first six equipotential rings, the electrostatic field of this region are modified

  16. Pairing in the BCS and LN approximations using continuum single particle level density

    International Nuclear Information System (INIS)

    Id Betan, R.M.; Repetto, C.E.

    2017-01-01

    Understanding the properties of drip line nuclei requires to take into account the correlations with the continuum spectrum of energy of the system. This paper has the purpose to show that the continuum single particle level density is a convenient way to consider the pairing correlation in the continuum. Isospin mean-field and isospin pairing strength are used to find the Bardeen–Cooper–Schrieffer (BCS) and Lipkin–Nogami (LN) approximate solutions of the pairing Hamiltonian. Several physical properties of the whole chain of the Tin isotope, as gap parameter, Fermi level, binding energy, and one- and two-neutron separation energies, were calculated and compared with other methods and with experimental data when they exist. It is shown that the use of the continuum single particle level density is an economical way to include explicitly the correlations with the continuum spectrum of energy in large scale mass calculation. It is also shown that the computed properties are in good agreement with experimental data and with more sophisticated treatment of the pairing interaction.

  17. ThermoData Engine: Extension to Solvent Design and Multi-component Process Stream Property Calculations with Uncertainty Analysis

    DEFF Research Database (Denmark)

    Diky, Vladimir; Chirico, Robert D.; Muzny, Chris

    ThermoData Engine (TDE, NIST Standard Reference Databases 103a and 103b) is the first product that implements the concept of Dynamic Data Evaluation in the fields of thermophysics and thermochemistry, which includes maintaining the comprehensive and up-to-date database of experimentally measured...... property values and expert system for data analysis and generation of recommended property values at the specified conditions along with uncertainties on demand. The most recent extension of TDE covers solvent design and multi-component process stream property calculations with uncertainty analysis...... variations). Predictions can be compared to the available experimental data, and uncertainties are estimated for all efficiency criteria. Calculations of the properties of multi-component streams including composition at phase equilibria (flash calculations) are at the heart of process simulation engines...

  18. BCS equations in the continuum

    International Nuclear Information System (INIS)

    Sandulescu, N.; Liotta, R. J.; Wyss, R.

    1998-01-01

    The properties of nuclei close to the drip line are significantly influenced by the continuum part of the single-particle spectrum. The main role is played by the resonant states which are largely confined in the region of nuclear potential and therefore stronger coupled with the bound states in an excitation process. Resonant states are also important in the nuclei beyond the drip line. In this case the decay properties of the nucleus can be directly related to the widths of the narrow resonances occupied by the unbound nucleons. The aim of this work is to propose an alternative for evaluating the effect of the resonant part of single-particle spectrum on the pairing correlations calculated within the BCS approximation. We estimated the role of resonances in the case of the isotope 170 Sn. The Resonant-BCS (RBCS) equations are solved for the case of a seniority force. The BCS approximation based on a seniority force cannot be applied in the case of a nucleus immersed in a box if all discrete states simulating the continuum are considered. In such a case the pairing correlations will increase with the number of states in the box. In our case one can still apply a seniority force with RBCS because the effect of the continuum appears here through a finite number of physical resonances, well defined by the given mean field. Because these resonances have a spatial distribution concentrated within the region of the nuclear potential, one expects that the localization probability of nucleons, far out from the nuclear surface, to be small. The gap obtained taking correctly the contribution of resonances, according to RBCS equations, is about 1.3 MeV, while pairing gap calculated only with the bound single-particle spectrum has the value Δ = 1.10 MeV. If we introduce also the resonant states, neglecting completely their widths, the gap will increase to the value Δ = 1.880 MeV. Therefore, one cannot estimate properly the pairing correlations by supplementing the spectrum

  19. Relativistic continuum random phase approximation in spherical nuclei

    International Nuclear Information System (INIS)

    Daoutidis, Ioannis

    2009-01-01

    Covariant density functional theory is used to analyze the nuclear response in the external multipole fields. The investigations are based on modern functionals with zero range and density dependent coupling constants. After a self-consistent solution of the Relativistic Mean Field (RMF) equations for the nuclear ground states multipole giant resonances are studied within the Relativistic Random Phase Approximation (RRPA), the small amplitude limit of the time-dependent RMF. The coupling to the continuum is treated precisely by calculating the single particle Greens-function of the corresponding Dirac equation. In conventional methods based on a discretization of the continuum this was not possible. The residual interaction is derived from the same RMF Lagrangian. This guarantees current conservation and a precise decoupling of the Goldstone modes. For nuclei with open shells pairing correlations are taken into account in the framework of BCS theory and relativistic quasiparticle RPA. Continuum RPA (CRPA) presents a robust method connected with an astonishing reduction of the numerical effort as compared to conventional methods. Modes of various multipolarities and isospin are investigated, in particular also the newly discovered Pygmy modes in the vicinity of the neutron evaporation threshold. The results are compared with conventional discrete RPA calculations as well as with experimental data. We find that the full treatment of the continuum is essential for light nuclei and the study of resonances in the neighborhood of the threshold. (orig.)

  20. Modeling of Continuum Manipulators Using Pythagorean Hodograph Curves.

    Science.gov (United States)

    Singh, Inderjeet; Amara, Yacine; Melingui, Achille; Mani Pathak, Pushparaj; Merzouki, Rochdi

    2018-05-10

    Research on continuum manipulators is increasingly developing in the context of bionic robotics because of their many advantages over conventional rigid manipulators. Due to their soft structure, they have inherent flexibility, which makes it a huge challenge to control them with high performances. Before elaborating a control strategy of such robots, it is essential to reconstruct first the behavior of the robot through development of an approximate behavioral model. This can be kinematic or dynamic depending on the conditions of operation of the robot itself. Kinematically, two types of modeling methods exist to describe the robot behavior; quantitative methods describe a model-based method, and qualitative methods describe a learning-based method. In kinematic modeling of continuum manipulator, the assumption of constant curvature is often considered to simplify the model formulation. In this work, a quantitative modeling method is proposed, based on the Pythagorean hodograph (PH) curves. The aim is to obtain a three-dimensional reconstruction of the shape of the continuum manipulator with variable curvature, allowing the calculation of its inverse kinematic model (IKM). It is noticed that the performances of the PH-based kinematic modeling of continuum manipulators are considerable regarding position accuracy, shape reconstruction, and time/cost of the model calculation, than other kinematic modeling methods, for two cases: free load manipulation and variable load manipulation. This modeling method is applied to the compact bionic handling assistant (CBHA) manipulator for validation. The results are compared with other IKMs developed in case of CBHA manipulator.

  1. Relativistic continuum random phase approximation in spherical nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Daoutidis, Ioannis

    2009-10-01

    Covariant density functional theory is used to analyze the nuclear response in the external multipole fields. The investigations are based on modern functionals with zero range and density dependent coupling constants. After a self-consistent solution of the Relativistic Mean Field (RMF) equations for the nuclear ground states multipole giant resonances are studied within the Relativistic Random Phase Approximation (RRPA), the small amplitude limit of the time-dependent RMF. The coupling to the continuum is treated precisely by calculating the single particle Greens-function of the corresponding Dirac equation. In conventional methods based on a discretization of the continuum this was not possible. The residual interaction is derived from the same RMF Lagrangian. This guarantees current conservation and a precise decoupling of the Goldstone modes. For nuclei with open shells pairing correlations are taken into account in the framework of BCS theory and relativistic quasiparticle RPA. Continuum RPA (CRPA) presents a robust method connected with an astonishing reduction of the numerical effort as compared to conventional methods. Modes of various multipolarities and isospin are investigated, in particular also the newly discovered Pygmy modes in the vicinity of the neutron evaporation threshold. The results are compared with conventional discrete RPA calculations as well as with experimental data. We find that the full treatment of the continuum is essential for light nuclei and the study of resonances in the neighborhood of the threshold. (orig.)

  2. Relativistic mean field calculations in neutron-rich nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Gangopadhyay, G.; Bhattacharya, Madhubrata [Department of Physics, University of Calcutta, 92 Acharya Prafulla Chandra Road, Kolkata 700 009 (India); Roy, Subinit [Saha Institute of Nuclear Physics, Block AF, Sector 1, Kolkata- 700 064 (India)

    2014-08-14

    Relativistic mean field calculations have been employed to study neutron rich nuclei. The Lagrange's equations have been solved in the co-ordinate space. The effect of the continuum has been effectively taken into account through the method of resonant continuum. It is found that BCS approximation performs as well as a more involved Relativistic Continuum Hartree Bogoliubov approach. Calculations reveal the possibility of modification of magic numbers in neutron rich nuclei. Calculation for low energy proton scattering cross sections shows that the present approach reproduces the density in very light neutron rich nuclei.

  3. Microencapsulation and Electrostatic Processing Method

    Science.gov (United States)

    Morrison, Dennis R. (Inventor); Mosier, Benjamin (Inventor)

    2000-01-01

    Methods are provided for forming spherical multilamellar microcapsules having alternating hydrophilic and hydrophobic liquid layers, surrounded by flexible, semi-permeable hydrophobic or hydrophilic outer membranes which can be tailored specifically to control the diffusion rate. The methods of the invention rely on low shear mixing and liquid-liquid diffusion process and are particularly well suited for forming microcapsules containing both hydrophilic and hydrophobic drugs. These methods can be carried out in the absence of gravity and do not rely on density-driven phase separation, mechanical mixing or solvent evaporation phases. The methods include the process of forming, washing and filtering microcapsules. In addition, the methods contemplate coating microcapsules with ancillary coatings using an electrostatic field and free fluid electrophoresis of the microcapsules. The microcapsules produced by such methods are particularly useful in the delivery of pharmaceutical compositions.

  4. Negative adsorption due to electrostatic exclusion of micelles.

    Science.gov (United States)

    Somasundaran, P; Ananthapadmanabhan, K P; Deo, Puspendu

    2005-10-15

    Interactions of surfactants with solid substrates are important in the controlling of processes such as flotation, coating, flocculation and sedimentation. These interactions usually lead to adsorption on solids, but can also result in an exclusion of the reagents with dire consequences. In this work electrostatic exclusion of negatively charged dodecylbenzene sulfonate micelles from quartz/water, Bio-Sil/water and alumina/water interfaces has been investigated as a function of pH and ionic strength. Measurable negative adsorption of these surfactants from similarly charged solid/liquid interface was observed in the micellar region. In the case of porous samples with large surface area, comparison of pore size with the micelle size is necessary to avoid any erroneous conclusions regarding the role of electrostatic exclusion in a given system. A theoretical model for the electrostatic exclusion of micelles is developed and used to calculate the adsorption of negatively charged dodecylbenzene sulfonate on negatively charged quartz (pH 7), silica (Bio-Sil A, pH 3) and alumina (pH 11) in the micellar concentration region. The micellar exclusion values calculated using the model are in excellent agreement with the experimental results.

  5. Effects of organic solvents on hyaluronic acid nanoparticles obtained by precipitation and chemical crosslinking.

    Science.gov (United States)

    Bicudo, Rafaela Costa Souza; Santana, Maria Helena Andrade

    2012-03-01

    Hyaluronic acid is a hydrophilic mucopolysaccharide composed of alternating units of D-glucuronic acid and N-acetylglucosamine. It is used in many medical, pharmaceutical, and cosmetic applications, as sponges, films, or particle formulations. Hyaluronic acid nanoparticles can be synthesized free of oil and surfactants by nanoprecipitation in organic solvents, followed by chemical crosslinking. The organic solvent plays an important role in particles size and structure. Therefore, this study aimed to investigate the influence of acetone, ethanol, and isopropyl alcohol on the synthesis and physico-chemical properties of hyaluronic acid nanoparticles. Particles were crosslinked with adipic hydrazide and chloride carbodiimide under controlled conditions. The nanoparticles obtained with all three studied solvents were moderately electrostatically stable. Experiments with acetone produced the smallest particle size (120.44 nm) and polydispersity (0.27). The size and polydispersity of hyaluronic acid nanoparticles correlated with the surface tension between water and the organic solvents, not with the thermodynamic affinity of water for the organic solvents.

  6. Encapsulation of cisplatin as an anti-cancer drug into boron-nitride and carbon nanotubes: Molecular simulation and free energy calculation

    Energy Technology Data Exchange (ETDEWEB)

    Roosta, Sara [Molecular Simulation Research Laboratory, Department of Chemistry, Iran University of Science & Technology, Tehran (Iran, Islamic Republic of); Hashemianzadeh, Seyed Majid, E-mail: hashemianzadeh@iust.ac.ir [Molecular Simulation Research Laboratory, Department of Chemistry, Iran University of Science & Technology, Tehran (Iran, Islamic Republic of); Ketabi, Sepideh, E-mail: sepidehketabi@yahoo.com [Department of Chemistry, East Tehran Branch, Islamic Azad University, Tehran (Iran, Islamic Republic of)

    2016-10-01

    Encapsulation of cisplatin anticancer drug into the single walled (10, 0) carbon nanotube and (10, 0) boron-nitride nanotube was investigated by quantum mechanical calculations and Monte Carlo Simulation in aqueous solution. Solvation free energies and complexation free energies of the cisplatin@ carbon nanotube and cisplatin@ boron-nitride nanotube complexes was determined as well as radial distribution functions of entitled compounds. Solvation free energies of cisplatin@ carbon nanotube and cisplatin@ boron-nitride nanotube were − 4.128 kcal mol{sup −1} and − 2457.124 kcal mol{sup −1} respectively. The results showed that cisplatin@ boron-nitride nanotube was more soluble species in water. In addition electrostatic contribution of the interaction of boron- nitride nanotube complex and solvent was − 281.937 kcal mol{sup −1} which really more than Van der Waals and so the electrostatic interactions play a distinctive role in the solvation free energies of boron- nitride nanotube compounds. On the other hand electrostatic part of the interaction of carbon nanotube complex and solvent were almost the same as Van der Waals contribution. Complexation free energies were also computed to study the stability of related structures and the free energies were negative (− 374.082 and − 245.766 kcal mol{sup −1}) which confirmed encapsulation of drug into abovementioned nanotubes. However, boron-nitride nanotubes were more appropriate for encapsulation due to their larger solubility in aqueous solution. - Highlights: • Solubility of cisplatin@ boron-nitride nanotube is larger than cisplatin@ carbon nanotube. • Boron- nitride nanotube complexes have larger electrostatic contribution in solvation free energy. • Complexation free energies confirm encapsulation of drug into the nanotubes in aqueous solution. • Boron- nitride nanotubes are appropriate drug delivery systems compared with carbon nanotubes.

  7. Encapsulation of cisplatin as an anti-cancer drug into boron-nitride and carbon nanotubes: Molecular simulation and free energy calculation

    International Nuclear Information System (INIS)

    Roosta, Sara; Hashemianzadeh, Seyed Majid; Ketabi, Sepideh

    2016-01-01

    Encapsulation of cisplatin anticancer drug into the single walled (10, 0) carbon nanotube and (10, 0) boron-nitride nanotube was investigated by quantum mechanical calculations and Monte Carlo Simulation in aqueous solution. Solvation free energies and complexation free energies of the cisplatin@ carbon nanotube and cisplatin@ boron-nitride nanotube complexes was determined as well as radial distribution functions of entitled compounds. Solvation free energies of cisplatin@ carbon nanotube and cisplatin@ boron-nitride nanotube were − 4.128 kcal mol"−"1 and − 2457.124 kcal mol"−"1 respectively. The results showed that cisplatin@ boron-nitride nanotube was more soluble species in water. In addition electrostatic contribution of the interaction of boron- nitride nanotube complex and solvent was − 281.937 kcal mol"−"1 which really more than Van der Waals and so the electrostatic interactions play a distinctive role in the solvation free energies of boron- nitride nanotube compounds. On the other hand electrostatic part of the interaction of carbon nanotube complex and solvent were almost the same as Van der Waals contribution. Complexation free energies were also computed to study the stability of related structures and the free energies were negative (− 374.082 and − 245.766 kcal mol"−"1) which confirmed encapsulation of drug into abovementioned nanotubes. However, boron-nitride nanotubes were more appropriate for encapsulation due to their larger solubility in aqueous solution. - Highlights: • Solubility of cisplatin@ boron-nitride nanotube is larger than cisplatin@ carbon nanotube. • Boron- nitride nanotube complexes have larger electrostatic contribution in solvation free energy. • Complexation free energies confirm encapsulation of drug into the nanotubes in aqueous solution. • Boron- nitride nanotubes are appropriate drug delivery systems compared with carbon nanotubes.

  8. Plasma and BIAS Modeling: Self-Consistent Electrostatic Particle-in-Cell with Low-Density Argon Plasma for TiC

    Directory of Open Access Journals (Sweden)

    Jürgen Geiser

    2011-01-01

    processes. In this paper we present a new model taken into account a self-consistent electrostatic-particle in cell model with low density Argon plasma. The collision model are based of Monte Carlo simulations is discussed for DC sputtering in lower pressure regimes. In order to simulate transport phenomena within sputtering processes realistically, a spatial and temporal knowledge of the plasma density and electrostatic field configuration is needed. Due to relatively low plasma densities, continuum fluid equations are not applicable. We propose instead a Particle-in-cell (PIC method, which allows the study of plasma behavior by computing the trajectories of finite-size particles under the action of an external and self-consistent electric field defined in a grid of points.

  9. Nonlocal continuum field theories

    CERN Document Server

    2002-01-01

    Nonlocal continuum field theories are concerned with material bodies whose behavior at any interior point depends on the state of all other points in the body -- rather than only on an effective field resulting from these points -- in addition to its own state and the state of some calculable external field. Nonlocal field theory extends classical field theory by describing the responses of points within the medium by functionals rather than functions (the "constitutive relations" of classical field theory). Such considerations are already well known in solid-state physics, where the nonlocal interactions between the atoms are prevalent in determining the properties of the material. The tools developed for crystalline materials, however, do not lend themselves to analyzing amorphous materials, or materials in which imperfections are a major part of the structure. Nonlocal continuum theories, by contrast, can describe these materials faithfully at scales down to the lattice parameter. This book presents a unif...

  10. Compact electrostatic comb actuator

    Science.gov (United States)

    Rodgers, M. Steven; Burg, Michael S.; Jensen, Brian D.; Miller, Samuel L.; Barnes, Stephen M.

    2000-01-01

    A compact electrostatic comb actuator is disclosed for microelectromechanical (MEM) applications. The actuator is based upon a plurality of meshed electrostatic combs, some of which are stationary and others of which are moveable. One or more restoring springs are fabricated within an outline of the electrostatic combs (i.e. superposed with the moveable electrostatic combs) to considerably reduce the space required for the actuator. Additionally, a truss structure is provided to support the moveable electrostatic combs and prevent bending or distortion of these combs due to unbalanced electrostatic forces or external loading. The truss structure formed about the moveable electrostatic combs allows the spacing between the interdigitated fingers of the combs to be reduced to about one micron or less, thereby substantially increasing the number of active fingers which can be provided in a given area. Finally, electrostatic shields can be used in the actuator to substantially reduce unwanted electrostatic fields to further improve performance of the device. As a result, the compact electrostatic comb actuator of the present invention occupies only a fraction of the space required for conventional electrostatic comb actuators, while providing a substantial increase in the available drive force (up to one-hundred times).

  11. Equations of motion for anisotropic nonlinear elastic continuum in gravitational field

    International Nuclear Information System (INIS)

    Sokolov, S.N.

    1994-01-01

    Equations of motion for anisotropic nonlinear elastic continuum in the gravitational field are written in the form convenient for numerical calculations. The energy-stress tensor is expressed through scalar and tensor products of three vectors frozen in the continuum. Examples of expansion of the energy-stress tensor into scalar and tensor invariants corresponding to some crystal classes are given. 47 refs

  12. Continuum contributions to dipole oscillator-strength sum rules for hydrogen in finite basis sets

    DEFF Research Database (Denmark)

    Oddershede, Jens; Ogilvie, John F.; Sauer, Stephan P. A.

    2017-01-01

    Calculations of the continuum contributions to dipole oscillator sum rules for hydrogen are performed using both exact and basis-set representations of the stick spectra of the continuum wave function. We show that the same results are obtained for the sum rules in both cases, but that the conver......Calculations of the continuum contributions to dipole oscillator sum rules for hydrogen are performed using both exact and basis-set representations of the stick spectra of the continuum wave function. We show that the same results are obtained for the sum rules in both cases......, but that the convergence towards the final results with increasing excitation energies included in the sum over states is slower in the basis-set cases when we use the best basis. We argue also that this conclusion most likely holds also for larger atoms or molecules....

  13. Ionic magnetic fluids in polar solvents with tuned counter-ions

    Energy Technology Data Exchange (ETDEWEB)

    Lopes Filomeno, C. [Sorbonne Universités, UPMC Univ Paris 06, CNRS, Lab. PHENIX, Paris (France); Grupo de Fluidos Complexos Inst. de Quimica, Univ. de Brasília, Brasília (DF) (Brazil); Kouyaté, M. [Sorbonne Universités, UPMC Univ Paris 06, CNRS, Lab. PHENIX, Paris (France); Cousin, F. [Lab. Léon Brillouin – CE-Saclay, Gif-sur-Yvette (France); Demouchy, G. [Sorbonne Universités, UPMC Univ Paris 06, CNRS, Lab. PHENIX, Paris (France); Dpt de physique, Univ. de Cergy Pontoise, Cergy-Pontoise (France); Dubois, E.; Michot, L.; Mériguet, G. [Sorbonne Universités, UPMC Univ Paris 06, CNRS, Lab. PHENIX, Paris (France); Perzynski, R., E-mail: regine.perzynski@upmc.fr [Sorbonne Universités, UPMC Univ Paris 06, CNRS, Lab. PHENIX, Paris (France); Peyre, V.; Sirieix-Plénet, J. [Sorbonne Universités, UPMC Univ Paris 06, CNRS, Lab. PHENIX, Paris (France); Tourinho, F.A. [Grupo de Fluidos Complexos Inst. de Quimica, Univ. de Brasília, Brasília (DF) (Brazil)

    2017-06-01

    The aim of the present study is to propose a new reproducible method for preparing colloidal dispersions of electrostatically charged nanoparticles (NPs) in polar solvents with different kinds of counter-ions. Maghemite NPs are here dispersed in solvents of different dielectric constant, namely water, dimethylsulfoxide (DMSO) and an ionic liquid, ethylammonium nitrate (EAN). If the existence of a NP superficial charge happens to be necessary for the colloidal stability of the dispersions in these three solvents, the standard DLVO theory cannot be used any more to describe the colloidal stability in EAN. The structure of the dispersions and the strength of the interparticle repulsion are investigated by small angle X-ray scattering measurements, in association with Ludwig–Soret coefficient determinations. Specificities, associated to the nature of the counter-ions are identified in this work on the colloidal stability, on the interparticle repulsion and on the Ludwig–Soret coefficient. - Highlights: • A controlled synthesis of ionic magnetic fluids in three polar solvents is proposed. • Colloidal repulsion in the magnetic fluids depends on the counter-ion nature. • Soret coefficient of citrate-coated maghemite nanoparticles is probed in water-pH7. • Thermophilicity of nanoparticles depends on the nature of their counter-ions. • Nanoparticles dressed with same counter-ions have solvent-dependent thermoproperties.

  14. Interpreting the Coulomb-field approximation for generalized-Born electrostatics using boundary-integral equation theory.

    Science.gov (United States)

    Bardhan, Jaydeep P

    2008-10-14

    The importance of molecular electrostatic interactions in aqueous solution has motivated extensive research into physical models and numerical methods for their estimation. The computational costs associated with simulations that include many explicit water molecules have driven the development of implicit-solvent models, with generalized-Born (GB) models among the most popular of these. In this paper, we analyze a boundary-integral equation interpretation for the Coulomb-field approximation (CFA), which plays a central role in most GB models. This interpretation offers new insights into the nature of the CFA, which traditionally has been assessed using only a single point charge in the solute. The boundary-integral interpretation of the CFA allows the use of multiple point charges, or even continuous charge distributions, leading naturally to methods that eliminate the interpolation inaccuracies associated with the Still equation. This approach, which we call boundary-integral-based electrostatic estimation by the CFA (BIBEE/CFA), is most accurate when the molecular charge distribution generates a smooth normal displacement field at the solute-solvent boundary, and CFA-based GB methods perform similarly. Conversely, both methods are least accurate for charge distributions that give rise to rapidly varying or highly localized normal displacement fields. Supporting this analysis are comparisons of the reaction-potential matrices calculated using GB methods and boundary-element-method (BEM) simulations. An approximation similar to BIBEE/CFA exhibits complementary behavior, with superior accuracy for charge distributions that generate rapidly varying normal fields and poorer accuracy for distributions that produce smooth fields. This approximation, BIBEE by preconditioning (BIBEE/P), essentially generates initial guesses for preconditioned Krylov-subspace iterative BEMs. Thus, iterative refinement of the BIBEE/P results recovers the BEM solution; excellent agreement

  15. Solvent primitive model of an electric double layer in slit-like pores: microscopic structure, adsorption and capacitance from a density functional approach

    Directory of Open Access Journals (Sweden)

    O. Pizio

    2014-06-01

    Full Text Available We investigate the electric double layer formed between charged walls of a slit-like pore and a solvent primitive model (SPM for electrolyte solution. The recently developed version of the weighted density functional approach for electrostatic interparticle interaction is applied to the study of the density profiles, adsorption and selectivity of adsorption of ions and solvent species. Our principal focus, however, is in the dependence of differential capacitance on the applied voltage, on the electrode and on the pore width. We discuss the properties of the model with respect to the behavior of a primitive model, i.e., in the absence of a hard-sphere solvent. We observed that the differential capacitance of the SPM on the applied electrostatic potential has the camel-like shape unless the ion fraction is high. Moreover, it is documented that the dependence of differential capacitance of the SPM on the pore width is oscillatory, which is in close similarity to the primitive model.

  16. Caustic-Side Solvent Extraction: Chemical and Physical Properties of the Optimized Solvent

    Energy Technology Data Exchange (ETDEWEB)

    Delmau, L.H.

    2002-10-08

    This work was undertaken to optimize the solvent used in the Caustic Side Solvent Extraction (CSSX) process and to measure key chemical and physical properties related to its performance in the removal of cesium from the alkaline high-level salt waste stored in tanks at the Savannah River Site. The need to adjust the solvent composition arose from the prior discovery that the previous baseline solvent was supersaturated with respect to the calixarene extractant. The following solvent-component concentrations in Isopar{reg_sign} L diluent are recommended: 0.007 M calix[4]arene-bis(tert-octylbenzo-crown-6) (BOBCalixC6) extractant, 0.75 M 1-(2,2,3,3-tetrafluoropropoxy)-3-(4-sec-butylphenoxy)-2-propanol (Cs-7SB) phase modifier, and 0.003 M tri-n-octylamine (TOA) stripping aid. Criteria for this selection included BOBCalixC6 solubility, batch cesium distribution ratios (D{sub Cs}), calculated flowsheet robustness, third-phase formation, coalescence rate (dispersion numbers), and solvent density. Although minor compromises within acceptable limits were made in flowsheet robustness and solvent density, significant benefits were gained in lower risk of third-phase formation and lower solvent cost. Data are also reported for the optimized solvent regarding the temperature dependence of D{sub Cs} in extraction, scrubbing, and stripping (ESS); ESS performance on recycle; partitioning of BOBCalixC6, Cs-7SB, and TOA to aqueous process solutions; partitioning of organic anions; distribution of metals; solvent phase separation at low temperatures; solvent stability to elevated temperatures; and solvent density and viscosity. Overall, the technical risk of the CSSX process has been reduced by resolving previously identified issues and raising no new issues.

  17. Long range Debye-Hückel correction for computation of grid-based electrostatic forces between biomacromolecules

    International Nuclear Information System (INIS)

    Mereghetti, Paolo; Martinez, Michael; Wade, Rebecca C

    2014-01-01

    Brownian dynamics (BD) simulations can be used to study very large molecular systems, such as models of the intracellular environment, using atomic-detail structures. Such simulations require strategies to contain the computational costs, especially for the computation of interaction forces and energies. A common approach is to compute interaction forces between macromolecules by precomputing their interaction potentials on three-dimensional discretized grids. For long-range interactions, such as electrostatics, grid-based methods are subject to finite size errors. We describe here the implementation of a Debye-Hückel correction to the grid-based electrostatic potential used in the SDA BD simulation software that was applied to simulate solutions of bovine serum albumin and of hen egg white lysozyme. We found that the inclusion of the long-range electrostatic correction increased the accuracy of both the protein-protein interaction profiles and the protein diffusion coefficients at low ionic strength. An advantage of this method is the low additional computational cost required to treat long-range electrostatic interactions in large biomacromolecular systems. Moreover, the implementation described here for BD simulations of protein solutions can also be applied in implicit solvent molecular dynamics simulations that make use of gridded interaction potentials

  18. Theoretical investigation of redox species in condensed phase

    Indian Academy of Sciences (India)

    WINTEC

    enced by the conformation of the solvents in its immediate vicinity, and ... geometry in the presence of static solvent molecules; ... (3) averaging over different solvent conformations starting from the ..... Calculation of electrostatic interactions in proteins. Downloaded .... defines the water-accessible surface, was chosen. Peri-.

  19. Optics elements for modeling electrostatic lenses and accelerator components: III. Electrostatic deflectors

    International Nuclear Information System (INIS)

    Brown, T.A.; Gillespie, G.H.

    2000-01-01

    Ion-beam optics models for simulating electrostatic prisms (deflectors) of different geometries have been developed for the envelope (matrix) computer code TRACE 3-D as a part of the development of a suite of electrostatic beamline element models which includes lenses, acceleration columns, quadrupoles and prisms. The models for electrostatic prisms are described in this paper. The electrostatic prism model options allow the first-order modeling of cylindrical, spherical and toroidal electrostatic deflectors. The application of these models in the development of ion-beam transport systems is illustrated through the modeling of a spherical electrostatic analyzer as a component of the new low-energy beamline at the Center for Accelerator Mass Spectrometry. Although initial tests following installation of the new beamline showed that the new spherical electrostatic analyzer was not behaving as predicted by these first-order models, operational conditions were found under which the analyzer now works properly as a double-focusing spherical electrostatic prism

  20. The strong influence of the solvent on the electron spin resonance spectra of semiquinone radical anions

    DEFF Research Database (Denmark)

    Spanget-Larsen, Jens

    2013-01-01

    ). The proton hyperfine constants predicted for the chrysazin semiquinone radical anion were highly sensitive to the assumed dielectric constant ε of the solvent continuum, inverting the relative magnitudes of the hyperfine constants and thereby leading to agreement with the observed data published by Stegmann...

  1. Double-continuum wave functions and double-photoionization cross sections of two-electron systems

    International Nuclear Information System (INIS)

    Tiwary, S.N.

    1996-09-01

    The present review briefly presents the growing experimental as well as theoretical interests in recent years in the double-continuum wave functions and double-photoionization cross sections of two-electron systems. The validity of existing double-continuum wave functions is analyzed and the importance of electronic correlations in both the initial as well as final states wave functions involved in the transition amplitude for double-photoionization process is demonstrated. At present, we do not have comprehensive and practical double-continuum wave functions which account the full correlation of two-electron in the continuum. Basic difficulties in making accurate theoretical calculations of double ionization by a single high energy photon especially in the vicinity of the threshold, where the correlation plays an important role, are discussed. Illuminating, illustrative and representative examples are presented in order to show the present status and the progress in this field. Future challenges and directions, in high-precision double-photoionization cross sections calculations, have been discussed and suggested. (author). 133 refs, 9 figs

  2. Potential of mean force for ion pairs in non-aqueous solvents. Comparison of polarizable and non-polarizable MD simulations

    Science.gov (United States)

    Odinokov, A. V.; Leontyev, I. V.; Basilevsky, M. V.; Petrov, N. Ch.

    2011-01-01

    Potentials of mean force (PMF) are calculated for two model ion pairs in two non-aqueous solvents. Standard non-polarizable molecular dynamics simulation (NPMD) and approximate polarizable simulation (PMD) are implemented and compared as tools for monitoring PMF profiles. For the polar solvent (dimethylsulfoxide, DMSO) the PMF generated in terms of the NPMD reproduces fairly well the refined PMD-PMF profile. For the non-polar solvent (benzene) the conventional NPMD computation proves to be deficient. The validity of the correction found in terms of the approximate PMD approach is verified by its comparison with the result of the explicit PMD computation in benzene. The shapes of the PMF profiles in DMSO and in benzene are quite different. In DMSO, owing to dielectric screening, the PMF presents a flat plot with a shallow minimum positioned in the vicinity of the van der Waals contact of the ion pair. For the benzene case, the observed minimum proves to be unexpectedly deep, which manifests the formation of a tightly-binded contact ion pair. This remarkable effect arises owing to the strong electrostatic interaction that is incompletely screened by a non-polar medium. The PMFs for the binary benzene/DMSO mixtures display intermediate behaviour depending on the DMSO content.

  3. On the Impact of Electrostatic Correlations on the Double-Layer Polarization of a Spherical Particle in an Alternating Current Field.

    Science.gov (United States)

    Alidoosti, Elaheh; Zhao, Hui

    2018-05-15

    At concentrated electrolytes, the ion-ion electrostatic correlation effect is considered an important factor in electrokinetics. In this paper, we compute, in theory and simulation, the dipole moment for a spherical particle (charged, dielectric) under the action of an alternating electric field using the modified continuum Poisson-Nernst-Planck (PNP) model by Bazant et al. [ Double Layer in Ionic Liquids: Overscreening Versus Crowding . Phys. Rev. Lett. 2011 , 106 , 046102 ] We investigate the dependency of the dipole moment in terms of frequency and its variation with such quantities like ζ-potential, electrostatic correlation length, and double-layer thickness. With thin electric double layers, we develop simple models through performing an asymptotic analysis of the modified PNP model. We also present numerical results for an arbitrary Debye screening length and electrostatic correlation length. From the results, we find a complicated impact of electrostatic correlations on the dipole moment. For instance, with increasing the electrostatic correlation length, the dipole moment decreases and reaches a minimum and then it goes up. This is because of initially decreasing of surface conduction and finally increasing due to the impact of ion-ion electrostatic correlations on ion's convection and migration. Also, we show that in contrast to the standard PNP model, the modified PNP model can qualitatively explain the data from the experimental results in multivalent electrolytes.

  4. Effects of continuum breakdown on hypersonic aerothermodynamics for reacting flow

    Science.gov (United States)

    Holman, Timothy D.; Boyd, Iain D.

    2011-02-01

    This study investigates the effects of continuum breakdown on the surface aerothermodynamic properties (pressure, stress, and heat transfer rate) of a sphere in a Mach 25 flow of reacting air in regimes varying from continuum to a rarefied gas. Results are generated using both continuum [computational fluid dynamics (CFD)] and particle [direct simulation Monte Carlo (DSMC)] approaches. The DSMC method utilizes a chemistry model that calculates the backward rates from an equilibrium constant. A preferential dissociation model is modified in the CFD method to better compare with the vibrationally favored dissociation model that is utilized in the DSMC method. Tests of these models are performed to confirm their validity and to compare the chemistry models in both numerical methods. This study examines the effect of reacting air flow on continuum breakdown and the surface properties of the sphere. As the global Knudsen number increases, the amount of continuum breakdown in the flow and on the surface increases. This increase in continuum breakdown significantly affects the surface properties, causing an increase in the differences between CFD and DSMC. Explanations are provided for the trends observed.

  5. Optics Elements for Modeling Electrostatic Lenses and Accelerator Components: III. Electrostatic Deflectors

    International Nuclear Information System (INIS)

    Brown, T.A.; Gillespie, G.H.

    1999-01-01

    Ion-beam optics models for simulating electrostatic prisms (deflectors) of different geometries have been developed for the computer code TRACE 3-D. TRACE 3-D is an envelope (matrix) code, which includes a linear space charge model, that was originally developed to model bunched beams in magnetic transport systems and radiofrequency (RF) accelerators. Several new optical models for a number of electrostatic lenses and accelerator columns have been developed recently that allow the code to be used for modeling beamlines and accelerators with electrostatic components. The new models include a number of options for: (1) Einzel lenses, (2) accelerator columns, (3) electrostatic prisms, and (4) electrostatic quadrupoles. A prescription for setting up the initial beam appropriate to modeling 2-D (continuous) beams has also been developed. The models for electrostatic prisms are described in this paper. The electrostatic prism model options allow the modeling of cylindrical, spherical, and toroidal electrostatic deflectors. The application of these models in the development of ion-beam transport systems is illustrated through the modeling of a spherical electrostatic analyzer as a component of the new low energy beamline at CAMS

  6. Fast electrostatic force calculation on parallel computer clusters

    International Nuclear Information System (INIS)

    Kia, Amirali; Kim, Daejoong; Darve, Eric

    2008-01-01

    The fast multipole method (FMM) and smooth particle mesh Ewald (SPME) are well known fast algorithms to evaluate long range electrostatic interactions in molecular dynamics and other fields. FMM is a multi-scale method which reduces the computation cost by approximating the potential due to a group of particles at a large distance using few multipole functions. This algorithm scales like O(N) for N particles. SPME algorithm is an O(NlnN) method which is based on an interpolation of the Fourier space part of the Ewald sum and evaluating the resulting convolutions using fast Fourier transform (FFT). Those algorithms suffer from relatively poor efficiency on large parallel machines especially for mid-size problems around hundreds of thousands of atoms. A variation of the FMM, called PWA, based on plane wave expansions is presented in this paper. A new parallelization strategy for PWA, which takes advantage of the specific form of this expansion, is described. Its parallel efficiency is compared with SPME through detail time measurements on two different computer clusters

  7. Large electrostatic accelerators

    International Nuclear Information System (INIS)

    Jones, C.M.

    1984-01-01

    The paper is divided into four parts: a discussion of the motivation for the construction of large electrostatic accelerators, a description and discussion of several large electrostatic accelerators which have been recently completed or are under construction, a description of several recent innovations which may be expected to improve the performance of large electrostatic accelerators in the future, and a description of an innovative new large electrostatic accelerator whose construction is scheduled to begin next year

  8. Towards an improved continuum theory for phase transformations

    International Nuclear Information System (INIS)

    Tijssens, M.G.A.; James, R.D.

    2003-01-01

    We develop a continuum theory for martensitic phase transformations in which explicit use is made of atomistic calculations based on density functional theory. Following the work of Rabe and coworkers, branches of the phonon-dispersion relation with imaginary frequencies are selected to construct a localized basis tailored to the symmetry of the crystal lattice. This so-called Wannier basis helps to construct an effective Hamiltonian of a particularly simple form. We extend the methodology by incorporating finite deformations and passing the effective Hamiltonian fully to continuum level. The developments so far are implemented on the shape memory material NiTi

  9. FreeSASA: An open source C library for solvent accessible surface area calculations [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Simon Mitternacht

    2016-02-01

    Full Text Available Calculating solvent accessible surface areas (SASA is a run-of-the-mill calculation in structural biology. Although there are many programs available for this calculation, there are no free-standing, open-source tools designed for easy tool-chain integration. FreeSASA is an open source C library for SASA calculations that provides both command-line and Python interfaces in addition to its C API. The library implements both Lee and Richards’ and Shrake and Rupley’s approximations, and is highly configurable to allow the user to control molecular parameters, accuracy and output granularity. It only depends on standard C libraries and should therefore be easy to compile and install on any platform. The library is well-documented, stable and efficient. The command-line interface can easily replace closed source legacy programs, with comparable or better accuracy and speed, and with some added functionality.

  10. Electrostatic field distributions in the Harwell Tandem accelerator

    International Nuclear Information System (INIS)

    Read, P.M.

    1981-11-01

    The electrostatic field distributions in the Harwell Tandem accelerator have been precisely calculated using the electrostatics program FINALE. The results indicate that the accelerator which presently has an upper voltage limit of 6.5 MV has the potential to operate at 8 MV. Such an upgrade could be achieved by a modification to the high voltage terminal. Replacement of the existing accelerator tubes with accelerator tubes capable of a gradient of 1.8 MV/m would also be required. The existing stack may also require replacement. The terminal modification itself would reduce the terminal to tank breakdown frequency. (author)

  11. AESOP: A Python Library for Investigating Electrostatics in Protein Interactions.

    Science.gov (United States)

    Harrison, Reed E S; Mohan, Rohith R; Gorham, Ronald D; Kieslich, Chris A; Morikis, Dimitrios

    2017-05-09

    Electric fields often play a role in guiding the association of protein complexes. Such interactions can be further engineered to accelerate complex association, resulting in protein systems with increased productivity. This is especially true for enzymes where reaction rates are typically diffusion limited. To facilitate quantitative comparisons of electrostatics in protein families and to describe electrostatic contributions of individual amino acids, we previously developed a computational framework called AESOP. We now implement this computational tool in Python with increased usability and the capability of performing calculations in parallel. AESOP utilizes PDB2PQR and Adaptive Poisson-Boltzmann Solver to generate grid-based electrostatic potential files for protein structures provided by the end user. There are methods within AESOP for quantitatively comparing sets of grid-based electrostatic potentials in terms of similarity or generating ensembles of electrostatic potential files for a library of mutants to quantify the effects of perturbations in protein structure and protein-protein association. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  12. Retinal Photoisomerization in Rhodopsin: Electrostatic and Steric Catalysis

    International Nuclear Information System (INIS)

    Tomasello, Gaia; Altoe, Piero; Stenta, Marco; Olaso-Gonzalez, Gloria; Garavelli, Marco; Orlandi, Giorgio

    2007-01-01

    Excited state QM(CASPT2//CASSCF)/MM(GAFF) calculations, by our recently developed code COBRAMM (Computations at Bologna Relating Ab-initio and Molecular Mechanic Methods), were carried out in rhodopsin to investigate on the steric and electrostatic effects in retinal photoisomerization catalysis due to the β-ionone ring and glutammate 181 (GLU 181), respectively. The excited state photoisomerization channel has been mapped and a new christallographyc structure (2.2 Aa resolution) has been used for this purpose. Two different set-ups have been used to evaluate the electrostatic effects of GLU 181 (which is very close to the central double bond of the chromophore): the first with a neutral GLU 181 (as commonly accepted), the second with a negatively charged (i.e. deprotonated) GLU 181 (as very recent experimental findings seem to suggest). On the other hand, β-ionone ring steric effects were evaluated by calculating the photoisomerization path of a modified chromophore, where the ring double bond has been saturated. Spectroscopic properties were calculated and compared with the available experimental data

  13. Continuum Lowering and Fermi-Surface Rising in Strongly Coupled and Degenerate Plasmas

    International Nuclear Information System (INIS)

    Hu, S. X.

    2017-01-01

    Here, continuum lowering is a well-known and important physics concept that describes the ionization potential depression (IPD) in plasmas caused by thermal-/pressure-induced ionization of outer-shell electrons. The existing IPD models are often used to characterize plasma conditions and to gauge opacity calculations. Recent precision measurements have revealed deficits in our understanding of continuum lowering in dense hot plasmas. However, these investigations have so far been limited to IPD in strongly coupled but nondegenerate plasmas. Here, we report a first-principles study of the K-edge shifting in both strongly coupled and fully degenerate carbon plasmas, with quantum molecular dynamics (QMD) calculations based on the all-electron density-functional theory (DFT). The resulted K-edge shifting versus plasma density, as a probe to the continuum lowering and the Fermi-surface rising, is found to be significantly different from predictions of existing IPD models. In contrast, a simple model of “single atom in box” (SAIB), developed in this work, accurately predicts K-edge locations as what ab-initio calculations provide.

  14. Nanoparticle electrostatic loss within corona needle charger during particle-charging process

    International Nuclear Information System (INIS)

    Huang Chenghsiung; Alonso, Manuel

    2011-01-01

    A numerical investigation has been carried out to examine the electrostatic loss of nanoparticles in a corona needle charger. Two-dimensional flow field, electric field, particle charge, and particle trajectory were simulated to obtain the electrostatic deposition loss at different conditions. Simulation of particle trajectories shows that the number of charges per particle during the charging process depends on the particle diameter, radial position from the symmetry axis, applied voltage, Reynolds number, and axial distance along the charger. The numerical results of nanoparticle electrostatic loss agreed fairly well with available experimental data. The results reveal that the electrostatic loss of nanoparticles increases with increasing applied voltage and electrical mobility of particles; and with decreasing particle diameter and Reynolds number. A regression equation closely fitted the obtained numerical results for different conditions. The equation is useful for directly calculating the electrostatic loss of nanoparticles in the corona needle charger during particle-charging process.

  15. A Combined Synthetic and DFT Study on the Catalyst-Free and Solvent-Assisted Synthesis of 1,3,4-Oxadiazole-2-thiol Derivatives

    Directory of Open Access Journals (Sweden)

    Mohammad Soleiman-Beigi

    2013-01-01

    Full Text Available A novel practical and efficient catalyst-free method for the synthesis of 5-substituted 1,3,4-oxadiazole-2-thiols has been developed, which is assisted by reaction solvent (DMF. The solvent effects on product selectivity were studied based on Onsager’s reaction field theory of electrostatic solvation. The ab initio theoretical studies on the effect of solvents on the process also supported the suitability of DMF as the reaction medium for the preparation of 1,3,4-oxadiazole-2-thiol derivatives.

  16. Location of protons in N-H···N hydrogen-bonded systems: a theoretical study on intramolecular pyridine-dihydropyridine and pyridine-pyridinium pairs.

    Science.gov (United States)

    Mori, Yukie; Takano, Keiko

    2012-08-21

    Two-dimensional potential energy surfaces (PESs) were calculated for the degenerate intramolecular proton transfer (PT) in two N-H···N hydrogen-bonded systems, (Z)-2-(2-pyridylmethylidene)-1,2-dihydropyridine (1) and monoprotonated di(2-pyridyl) ether (2), at the MP2/cc-pVDZ level of theory. The calculated PES had two minima in both cases. The energy barrier in 1 was higher than the zero-point energy (ZPE) level, while that in 2 was close to the ZPE. Vibrational wavefunctions were obtained by solving time-independent Schrödinger equations with the calculated PESs. The maximum points of the probability density were shifted from the energy minima towards the region where the covalent N-H bond was elongated and the N···N distance shortened. The effects of a polar solvent on the PES were investigated with the continuum or cluster models in such a way that the solute-solvent electrostatic interactions could be taken into account under non-equilibrated conditions. A solvated contact ion-pair was modelled by a cluster consisting of one cation 2, one chloride ion and 26 molecules of acetonitrile. The calculation with this model suggested that the bridging proton is localised in the deeper well due to the significant asymmetry of the PES and the high potential barrier.

  17. An assessment of anti-neutrino mass determination via electrostatic measurements of tritium beta-decay

    International Nuclear Information System (INIS)

    Le Bas, P.A.

    1984-01-01

    Data on the mass of the anti-neutrino determined via electrostatic measurements of tritium beta-decay are assessed. Relativistic calculations concerning the finite mass of the electron anti-neutrino and the recoil of the nucleus, are given for the theoretical end-point spectrum of tritium beta-decay. The specifications are given for an electrostatic Spherical Retarding Beta-Spectrometer, and an electrostatic Cylindrical Mirror Analyser, both used in the tritium beta-decay experiment. The electrostatic measurements lead to a value of less than 50 ev (90% C.L.) for the electron anti-neutrino mass. These results are discussed in terms of the resolution of the electrostatic equipment and the Monte Carlo simulations of the data collection. (UK)

  18. SIRAH: a structurally unbiased coarse-grained force field for proteins with aqueous solvation and long-range electrostatics.

    Science.gov (United States)

    Darré, Leonardo; Machado, Matías Rodrigo; Brandner, Astrid Febe; González, Humberto Carlos; Ferreira, Sebastián; Pantano, Sergio

    2015-02-10

    Modeling of macromolecular structures and interactions represents an important challenge for computational biology, involving different time and length scales. However, this task can be facilitated through the use of coarse-grained (CG) models, which reduce the number of degrees of freedom and allow efficient exploration of complex conformational spaces. This article presents a new CG protein model named SIRAH, developed to work with explicit solvent and to capture sequence, temperature, and ionic strength effects in a topologically unbiased manner. SIRAH is implemented in GROMACS, and interactions are calculated using a standard pairwise Hamiltonian for classical molecular dynamics simulations. We present a set of simulations that test the capability of SIRAH to produce a qualitatively correct solvation on different amino acids, hydrophilic/hydrophobic interactions, and long-range electrostatic recognition leading to spontaneous association of unstructured peptides and stable structures of single polypeptides and protein-protein complexes.

  19. Electrostatics of proteins in dielectric solvent continua. II. Hamiltonian reaction field dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Bauer, Sebastian; Tavan, Paul; Mathias, Gerald, E-mail: gerald.mathias@physik.uni-muenchen.de [Lehrstuhl für BioMolekulare Optik, Ludig-Maximilians Universität München, Oettingenstr. 67, 80538 München (Germany)

    2014-03-14

    In Paper I of this work [S. Bauer, G. Mathias, and P. Tavan, J. Chem. Phys. 140, 104102 (2014)] we have presented a reaction field (RF) method, which accurately solves the Poisson equation for proteins embedded in dielectric solvent continua at a computational effort comparable to that of polarizable molecular mechanics (MM) force fields. Building upon these results, here we suggest a method for linearly scaling Hamiltonian RF/MM molecular dynamics (MD) simulations, which we call “Hamiltonian dielectric solvent” (HADES). First, we derive analytical expressions for the RF forces acting on the solute atoms. These forces properly account for all those conditions, which have to be self-consistently fulfilled by RF quantities introduced in Paper I. Next we provide details on the implementation, i.e., we show how our RF approach is combined with a fast multipole method and how the self-consistency iterations are accelerated by the use of the so-called direct inversion in the iterative subspace. Finally we demonstrate that the method and its implementation enable Hamiltonian, i.e., energy and momentum conserving HADES-MD, and compare in a sample application on Ac-Ala-NHMe the HADES-MD free energy landscape at 300 K with that obtained in Paper I by scanning of configurations and with one obtained from an explicit solvent simulation.

  20. Electrostatics in Chemistry

    Indian Academy of Sciences (India)

    Electrostatics in Chemistry. 3. Molecular Electrostatic Potential: Visualization and Topography. Shridhar R Gadre and Pravin K Bhadane. 1 1. Basic Principles, Resona- nce, Vol.4, No.2, 11-19, 1999. 2. Electrostatic Potentials of. Atoms, Ions and Molecules,. Resonance, Vol.4, No.5, 40-51,. 1999. Topographical features of the ...

  1. Direct and solvent-assisted thione–thiol tautomerism in 5-(thiophen-2-yl)-1,3,4-oxadiazole-2(3H)-thione: Experimental and molecular modeling study

    Energy Technology Data Exchange (ETDEWEB)

    Burcu Arslan, N. [Department of Computer Education and Instructional Technology, Faculty of Education, Giresun University, 28100 Giresun (Turkey); Özdemir, Namık, E-mail: namiko@omu.edu.tr [Department of Physics, Faculty of Arts and Sciences, Ondokuz Mayıs University, 55139 Samsun (Turkey); Dayan, Osman, E-mail: osmandayan@comu.edu.tr [Laboratory of Inorganic Synthesis and Molecular Catalysis, Çanakkale Onsekiz Mart University, 17020 Çanakkale (Turkey); Dege, Necmi [Department of Physics, Faculty of Arts and Sciences, Ondokuz Mayıs University, 55139 Samsun (Turkey); Koparır, Metin [Department of Chemistry, Faculty of Science, Fırat University, 23169 Elazığ (Turkey); Koparır, Pelin [Department of Chemistry, Forensic Medicine Institute, 44000 Malatya (Turkey); Muğlu, Halit [Department of Chemistry, Faculty of Arts and Sciences, Kastamonu University, 37200 Kastamonu (Turkey)

    2014-08-17

    Graphical abstract: - Highlights: • The molecule exists in the thione form in the solid state. • FT-IR and NMR data support the thione form. • The anti-thione conformer has the lowest energy. • The barrier height increases with increasing polarity of the solvent. • Multiple methanol or water-assisted thione–thiol tautomerism may happen. - Abstract: The compound has been synthesized and characterized by IR, NMR and X-ray diffraction. Quantum chemical calculations at B3LYP/6−311++G(d,p) level were performed to study the molecular and spectroscopic properties, conformational equilibrium, thione ↔ thiol tautomerism and intermolecular double proton transfer reaction of the compound. The obtained structural and spectroscopic results are well in agreement with the experimental data. The solvent effect on the proton transfer reaction was investigated in three solvents using the polarizable continuum model approximation and solvent-assisted mechanism. The anti-thione tautomer is the most stable isomer among the four possible structural forms both in the gas phase and in solution phase. A high tautomeric energy barrier is found for the tautomerism between the anti and syn forms of the compound, indicating a quite disfavored process. Although the presence of one methanol or water solvent molecule significantly lowers the energy barrier, it is not adequate for the reaction to occur.

  2. Continuum description for jointed media

    International Nuclear Information System (INIS)

    Thomas, R.K.

    1982-04-01

    A general three-dimensional continuum description is presented for a material containing regularly spaced and approximately parallel jointing planes within a representative elementary volume. Constitutive relationships are introduced for linear behavior of the base material and nonlinear normal and shear behavior across jointing planes. Furthermore, a fracture permeability tensor is calculated so that deformation induced alterations to the in-situ values can be measured. Examples for several strain-controlled loading paths are presented

  3. VHDL-AMS modelling and simulation of a planar electrostatic micromotor

    Science.gov (United States)

    Endemaño, A.; Fourniols, J. Y.; Camon, H.; Marchese, A.; Muratet, S.; Bony, F.; Dunnigan, M.; Desmulliez, M. P. Y.; Overton, G.

    2003-09-01

    System level simulation results of a planar electrostatic micromotor, based on analytical models of the static and dynamic torque behaviours, are presented. A planar variable capacitance (VC) electrostatic micromotor designed, fabricated and tested at LAAS (Toulouse) in 1995 is simulated using the high level language VHDL-AMS (VHSIC (very high speed integrated circuits) hardware description language-analog mixed signal). The analytical torque model is obtained by first calculating the overlaps and capacitances between different electrodes based on a conformal mapping transformation. Capacitance values in the order of 10-16 F and torque values in the order of 10-11 N m have been calculated in agreement with previous measurements and simulations from this type of motor. A dynamic model has been developed for the motor by calculating the inertia coefficient and estimating the friction-coefficient-based values calculated previously for other similar devices. Starting voltage results obtained from experimental measurement are in good agreement with our proposed simulation model. Simulation results of starting voltage values, step response, switching response and continuous operation of the micromotor, based on the dynamic model of the torque, are also presented. Four VHDL-AMS blocks were created, validated and simulated for power supply, excitation control, micromotor torque creation and micromotor dynamics. These blocks can be considered as the initial phase towards the creation of intellectual property (IP) blocks for microsystems in general and electrostatic micromotors in particular.

  4. Research and simulation of intense pulsed beam transfer in electrostatic accelerate tube

    International Nuclear Information System (INIS)

    Li Chaolong; Shi Haiquan; Lu Jianqin

    2012-01-01

    To study intense pulsed beam transfer in electrostatic accelerate tube, the matrix method was applied to analyze the transport matrixes in electrostatic accelerate tube of non-intense pulsed beam and intense pulsed beam, and a computer code was written for the intense pulsed beam transporting in electrostatic accelerate tube. Optimization techniques were used to attain the given optical conditions and iteration procedures were adopted to compute intense pulsed beam for obtaining self-consistent solutions in this computer code. The calculations were carried out by using ACCT, TRACE-3D and TRANSPORT for different beam currents, respectively. The simulation results show that improvement of the accelerating voltage ratio can enhance focusing power of electrostatic accelerate tube, reduce beam loss and increase the transferring efficiency. (authors)

  5. Ewald Electrostatics for Mixtures of Point and Continuous Line Charges.

    Science.gov (United States)

    Antila, Hanne S; Tassel, Paul R Van; Sammalkorpi, Maria

    2015-10-15

    Many charged macro- or supramolecular systems, such as DNA, are approximately rod-shaped and, to the lowest order, may be treated as continuous line charges. However, the standard method used to calculate electrostatics in molecular simulation, the Ewald summation, is designed to treat systems of point charges. We extend the Ewald concept to a hybrid system containing both point charges and continuous line charges. We find the calculated force between a point charge and (i) a continuous line charge and (ii) a discrete line charge consisting of uniformly spaced point charges to be numerically equivalent when the separation greatly exceeds the discretization length. At shorter separations, discretization induces deviations in the force and energy, and point charge-point charge correlation effects. Because significant computational savings are also possible, the continuous line charge Ewald method presented here offers the possibility of accurate and efficient electrostatic calculations.

  6. Free Energy, Enthalpy and Entropy from Implicit Solvent End-Point Simulations.

    Science.gov (United States)

    Fogolari, Federico; Corazza, Alessandra; Esposito, Gennaro

    2018-01-01

    Free energy is the key quantity to describe the thermodynamics of biological systems. In this perspective we consider the calculation of free energy, enthalpy and entropy from end-point molecular dynamics simulations. Since the enthalpy may be calculated as the ensemble average over equilibrated simulation snapshots the difficulties related to free energy calculation are ultimately related to the calculation of the entropy of the system and in particular of the solvent entropy. In the last two decades implicit solvent models have been used to circumvent the problem and to take into account solvent entropy implicitly in the solvation terms. More recently outstanding advancement in both implicit solvent models and in entropy calculations are making the goal of free energy estimation from end-point simulations more feasible than ever before. We review briefly the basic theory and discuss the advancements in light of practical applications.

  7. Free Energy, Enthalpy and Entropy from Implicit Solvent End-Point Simulations

    Directory of Open Access Journals (Sweden)

    Federico Fogolari

    2018-02-01

    Full Text Available Free energy is the key quantity to describe the thermodynamics of biological systems. In this perspective we consider the calculation of free energy, enthalpy and entropy from end-point molecular dynamics simulations. Since the enthalpy may be calculated as the ensemble average over equilibrated simulation snapshots the difficulties related to free energy calculation are ultimately related to the calculation of the entropy of the system and in particular of the solvent entropy. In the last two decades implicit solvent models have been used to circumvent the problem and to take into account solvent entropy implicitly in the solvation terms. More recently outstanding advancement in both implicit solvent models and in entropy calculations are making the goal of free energy estimation from end-point simulations more feasible than ever before. We review briefly the basic theory and discuss the advancements in light of practical applications.

  8. Ion optics of a high resolution multipassage mass spectrometer with electrostatic ion mirrors

    Energy Technology Data Exchange (ETDEWEB)

    Sakurai, T [Osaka Univ. (Japan). Dept. of Physics; Baril, M [Departement de Physique, Faculte des Sciences et de Genie, Universite Laval, Ste-Foy, Quebec G1K 7P4 (Canada)

    1995-09-01

    Ion trajectories in an electrostatic ion mirror are calculated. The interferences of the extended fringing fields of the mirror with finite aperture are studied. The results of the calculations are represented by three transfer matrices, which describe ion trajectories under the effects of a fringing field at the entrances, of an idealized mirror region, and of a fringing field at the exit. The focusing effects and ion-optical properties of mass spectrometers with electrostatic ion mirrors can be evaluated by using these transfer matrices. A high performance multipassage mass spectrometer is designed. The system has one magnet and four electrostatic sector analyzers and two ion mirrors. The double focusing condition and stigmatic focusing condition are achieved in any passage of the system. The mass resolution increases linearly with the number of passages in a magnet. (orig.).

  9. Fabrication of a New Electrostatic Linear Actuator

    Science.gov (United States)

    Matsunaga, Takashi; Kondoh, Kazuya; Kumagae, Michihiro; Kawata, Hiroaki; Yasuda, Masaaki; Murata, Kenji; Yoshitake, Masaaki

    2000-12-01

    We propose a new electrostatic linear actuator with a large stroke and a new process for fabricating the actuator. A moving slider with many teeth on both sides is suspended above lower electrodes on a substrate by two bearings. A photoresist is used as a sacrificial layer. Both the slider and the bearings are fabricated by Ni electroplating. The bearings are fabricated by the self-alignment technique. Bearings with 0.6 μm clearance can be easily fabricated. All processes are performed at low temperatures up to 110°C. It is confirmed that the slider can be moved mechanically, and also can be moved by about 10 μm when a voltage pulse of 50 V is applied between the slider and the lower electrodes when the slider is upside down. However, the slider cannot move continuously because of friction. We also calculate the electrostatic force acting on one slider tooth. The simulation result shows that the reduction of the electrostatic force to the vertical direction is very important for mechanical movement of the actuator.

  10. Defining the contributions of permanent electrostatics, Pauli repulsion, and dispersion in density functional theory calculations of intermolecular interaction energies

    Energy Technology Data Exchange (ETDEWEB)

    Horn, Paul R., E-mail: prhorn@berkeley.edu; Mao, Yuezhi; Head-Gordon, Martin, E-mail: mhg@cchem.berkeley.edu [Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA and Chemical Sciences Division Lawrence Berkeley National Laboratory Berkeley, California 94720 (United States)

    2016-03-21

    In energy decomposition analysis of Kohn-Sham density functional theory calculations, the so-called frozen (or pre-polarization) interaction energy contains contributions from permanent electrostatics, dispersion, and Pauli repulsion. The standard classical approach to separate them suffers from several well-known limitations. We introduce an alternative scheme that employs valid antisymmetric electronic wavefunctions throughout and is based on the identification of individual fragment contributions to the initial supersystem wavefunction as determined by an energetic optimality criterion. The density deformations identified with individual fragments upon formation of the initial supersystem wavefunction are analyzed along with the distance dependence of the new and classical terms for test cases that include the neon dimer, ammonia borane, water-Na{sup +}, water-Cl{sup −}, and the naphthalene dimer.

  11. Electrostatic septum in a high intensity electron accelerator

    International Nuclear Information System (INIS)

    Koechlin, F.

    1987-01-01

    Calculations of beam power losses and equilibrium temperatures of the wires of an electrostatic septum have been carried out. The occurrence of an electromagnetic shower has been examined in the case of a metal foil septum and the longitudinal profile of the beam power losses is given

  12. Thermodynamic properties of L-Theanine in different solvents

    International Nuclear Information System (INIS)

    Zhou, Fuli; Hou, Baohong; Tao, Xiaolong; Hu, Xiaoxue; Huang, Qiaoyin; Zhang, Zaixiang; Wang, Yongli; Hao, Hongxun

    2017-01-01

    Highlights: • The solubility data of L-Theanine in different solvents were measured by using an equilibrium method. • Several models were used to correlate the experimental solubility data. • The mixing thermodynamic properties were calculated. - Abstract: The solubility data of L-Theanine in pure water and three kinds of water + organic solvent mxitures were measured in temperature ranges from (278.15 to 13.15) K by using an equilibrium method. The results show that the solubility of L-Theanine increases with the increasing of temperature in all selected solvents. The modified Apelblat equation and the λ-h model were applied to correlate the solubility data in pure water, while the modified Apelblat equation, the λ-h model, the NRTL model and the Jouyban–Acree model were applied to correlate the solubility data in binary solvent mixtures. Furthermore, the mixing thermodynamic properties of L-Theanine in different solvents were also calculated based on the NRTL model and experimental solubility data.

  13. Continuum Vlasov Simulation in Four Phase-space Dimensions

    Science.gov (United States)

    Cohen, B. I.; Banks, J. W.; Berger, R. L.; Hittinger, J. A.; Brunner, S.

    2010-11-01

    In the VALHALLA project, we are developing scalable algorithms for the continuum solution of the Vlasov-Maxwell equations in two spatial and two velocity dimensions. We use fourth-order temporal and spatial discretizations of the conservative form of the equations and a finite-volume representation to enable adaptive mesh refinement and nonlinear oscillation control [1]. The code has been implemented with and without adaptive mesh refinement, and with electromagnetic and electrostatic field solvers. A goal is to study the efficacy of continuum Vlasov simulations in four phase-space dimensions for laser-plasma interactions. We have verified the code in examples such as the two-stream instability, the weak beam-plasma instability, Landau damping, electron plasma waves with electron trapping and nonlinear frequency shifts [2]^ extended from 1D to 2D propagation, and light wave propagation.^ We will report progress on code development, computational methods, and physics applications. This work was performed under the auspices of the U.S. DOE by LLNL under contract no. DE-AC52-07NA27344. This work was funded by the Lab. Dir. Res. and Dev. Prog. at LLNL under project tracking code 08-ERD-031. [1] J.W. Banks and J.A.F. Hittinger, to appear in IEEE Trans. Plas. Sci. (Sept., 2010). [2] G.J. Morales and T.M. O'Neil, Phys. Rev. Lett. 28,417 (1972); R. L. Dewar, Phys. Fluids 15,712 (1972).

  14. Electrostatics of cysteine residues in proteins: Parameterization and validation of a simple model

    Science.gov (United States)

    Salsbury, Freddie R.; Poole, Leslie B.; Fetrow, Jacquelyn S.

    2013-01-01

    One of the most popular and simple models for the calculation of pKas from a protein structure is the semi-macroscopic electrostatic model MEAD. This model requires empirical parameters for each residue to calculate pKas. Analysis of current, widely used empirical parameters for cysteine residues showed that they did not reproduce expected cysteine pKas; thus, we set out to identify parameters consistent with the CHARMM27 force field that capture both the behavior of typical cysteines in proteins and the behavior of cysteines which have perturbed pKas. The new parameters were validated in three ways: (1) calculation across a large set of typical cysteines in proteins (where the calculations are expected to reproduce expected ensemble behavior); (2) calculation across a set of perturbed cysteines in proteins (where the calculations are expected to reproduce the shifted ensemble behavior); and (3) comparison to experimentally determined pKa values (where the calculation should reproduce the pKa within experimental error). Both the general behavior of cysteines in proteins and the perturbed pKa in some proteins can be predicted reasonably well using the newly determined empirical parameters within the MEAD model for protein electrostatics. This study provides the first general analysis of the electrostatics of cysteines in proteins, with specific attention paid to capturing both the behavior of typical cysteines in a protein and the behavior of cysteines whose pKa should be shifted, and validation of force field parameters for cysteine residues. PMID:22777874

  15. Effects of electrostatic interactions on ligand dissociation kinetics

    Science.gov (United States)

    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.

  16. An implicit boundary integral method for computing electric potential of macromolecules in solvent

    Science.gov (United States)

    Zhong, Yimin; Ren, Kui; Tsai, Richard

    2018-04-01

    A numerical method using implicit surface representations is proposed to solve the linearized Poisson-Boltzmann equation that arises in mathematical models for the electrostatics of molecules in solvent. The proposed method uses an implicit boundary integral formulation to derive a linear system defined on Cartesian nodes in a narrowband surrounding the closed surface that separates the molecule and the solvent. The needed implicit surface is constructed from the given atomic description of the molecules, by a sequence of standard level set algorithms. A fast multipole method is applied to accelerate the solution of the linear system. A few numerical studies involving some standard test cases are presented and compared to other existing results.

  17. Modifications of the SEPHIS computer code for calculating the Purex solvent extraction system

    International Nuclear Information System (INIS)

    Watson, S.B.; Rainey, R.H.

    1975-12-01

    The SEPHIS computer program was developed to simulate the countercurrent solvent extraction. This report gives modifications in the program which result in improved fit to experimental data, a decrease in computer storage requirements, and a decrease in execution time. Methods for applying the computer program to practical solvent extraction problems are explained

  18. Extension of the multiconfiguration Hartree-Fock program for continuum functions

    International Nuclear Information System (INIS)

    Fischer, C.F.; Saha, H.P.

    1984-01-01

    The wave function of an outer electron coupled to a core, possibly with correlation included in the core, is similar to a multiconfiguration Hartree-Fock (MCHF) wavefunction, except that the radial function of the electron is a continuum function, and different numerical procedures are required for determining it. Only a single continuum function is allowed, and the orbitals defining the wave function of the core and bound channels are assumed to be fixed. The coefficients in the expansion of the wave function of the core are also fixed and are the result of a bound state calculation for the core. Under these assumptions, the equation for the radial wave function of the electron is solved iteratively. The asymptotic phase shift is evaluated. In order to test the accuracy of the procedure, calculations were performed for the scattering of electrons by neutral hydrogen. Some results of a photo-ionization calculation are compared, and for an electron transition in nitrogen

  19. Proton emission with a screened electrostatic barrier

    Energy Technology Data Exchange (ETDEWEB)

    Budaca, R. [Horia Hulubei National Institute of Physics and Nuclear Engineering, Bucharest-Magurele (Romania); Academy of Romanian Scientists, Bucharest (Romania); Budaca, A.I. [Horia Hulubei National Institute of Physics and Nuclear Engineering, Bucharest-Magurele (Romania)

    2017-08-15

    Half-lives of proton emission for Z ≥ 51 nuclei are calculated within a simple analytical model based on the WKB approximation for the barrier penetration probability which includes the centrifugal and overlapping effects besides the electrostatic repulsion. The model has a single free parameter associated to a Hulthen potential which emulates a Coulomb electrostatic interaction only at short distance. The agreement with experimental data is very good for most of the considered nuclei. Theoretical predictions are made for few cases with uncertain emitting state configuration or incomplete decay information. The model's assignment of the proton orbital momentum is in agreement with the differentiation of the experimental data by orbital momentum values realized with a newly introduced correlation formula. (orig.)

  20. Relationship between the electrostatic sensitivity of nitramines and their molecular structure

    Energy Technology Data Exchange (ETDEWEB)

    Hossein Keshavarz, Mohammad [Department of Chemistry, Malek-ashtar University of Technology, Shahin-shahr (Iran); Moghadas, Mohammad Hassan [Department of Mechanical Engineering, Malek-ashtar University of Technology, Shahin-shahr (Iran); Kavosh Tehrani, Masoud [Department of Physics, Malek-ashtar University of Technology, Shahin-shahr (Iran)

    2009-04-15

    In this paper, a new approach is introduced to predict the electrostatic sensitivity of nitramines on the basis of their molecular structure. The ratio of carbon to oxygen and the existence of two specific structural parameters can be used for the prediction of the electrostatic sensitivity of nitramines. The results are also compared with quantum mechanical computations from [9] so that the new method gives better predictions with respect to the measured data. Electrostatic sensitivities calculated by the new method for two new nitramines CL-20 [2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane] and TNAZ [1,3,3-trinitroazatidine] are also close to the experimental data. (Abstract Copyright [2009], Wiley Periodicals, Inc.)

  1. Anion-π aromatic neutral tweezers complexes: are they stable in polar solvents?

    Science.gov (United States)

    Sánchez-Lozano, Marta; Otero, Nicolás; Hermida-Ramón, Jose M; Estévez, Carlos M; Mandado, Marcos

    2011-03-17

    The impact of the solvent environment on the stabilization of the complexes formed by fluorine (T-F) and cyanide (T-CN) substituted tweezers with halide anions has been investigated theoretically. The study was carried out using computational methodologies based on density functional theory (DFT) and symmetry adapted perturbation theory (SAPT). Interaction energies were obtained at the M05-2X/6-31+G* level. The obtained results show a large stability of the complexes in solvents with large dielectric constant and prove the suitability of these molecular tweezers as potential hosts for anion recognition in solution. A detailed analysis of the effects of the solvent on the electron withdrawing ability of the substituents and its influence on the complex stability has been performed. In particular, the interaction energy in solution was split up into intermonomer and solvent-complex terms. In turn, the intermonomer interaction energy was partitioned into electrostatic, exchange, and polarization terms. Polar resonance structures in T-CN complexes are favored by polar solvents, giving rise to a stabilization of the intermonomer interaction, the opposite is found for T-F complexes. The solvent-complex energy increases with the polarity of the solvent in T-CN complexes, nonetheless the energy reaches a maximum and then decreases slowly in T-F complexes. An electron density analysis was also performed before and after complexation, providing an explanation to the trends followed by the interaction energies and their different components in solution.

  2. Web-based computational chemistry education with CHARMMing III: Reduction potentials of electron transfer proteins.

    Directory of Open Access Journals (Sweden)

    B Scott Perrin

    2014-07-01

    Full Text Available A module for fast determination of reduction potentials, E°, of redox-active proteins has been implemented in the CHARMM INterface and Graphics (CHARMMing web portal (www.charmming.org. The free energy of reduction, which is proportional to E°, is composed of an intrinsic contribution due to the redox site and an environmental contribution due to the protein and solvent. Here, the intrinsic contribution is selected from a library of pre-calculated density functional theory values for each type of redox site and redox couple, while the environmental contribution is calculated from a crystal structure of the protein using Poisson-Boltzmann continuum electrostatics. An accompanying lesson demonstrates a calculation of E°. In this lesson, an ionizable residue in a [4Fe-4S]-protein that causes a pH-dependent E° is identified, and the E° of a mutant that would test the identification is predicted. This demonstration is valuable to both computational chemistry students and researchers interested in predicting sequence determinants of E° for mutagenesis.

  3. Continuum extrapolation of moments of nucleon quark distributions in full QCD

    International Nuclear Information System (INIS)

    Dreher, P.; Brower, R.; Capitani, S.; Dolgov, D.; Edwards, R.; Eicker, N.; Heller, U.M.; Lippert, Th.; Negele, J.W.; Pochinsky, A.; Renner, D.B.; Schilling, K.

    2003-01-01

    Moments of light cone quark density, helicity, and transversity distributions are calculated in unquenched lattice QCD at β = 5.5 and β = 5.3 using Wilson fermions on 163 x 32 lattices. These results are combined with earlier calculations at β = 5.6 using SESAM configurations to study the continuum limit

  4. Structural transition of a homopolymer in solvents mixture

    International Nuclear Information System (INIS)

    Guettari, Moez; Aschi, Adel; Gomati, Riadh; Gharbi, Abdelhafidh

    2008-01-01

    The present work is aimed at studying the thermodynamic behaviour of a polymer in solvents mixture. Dynamic light scattering is used to measure the hydrodynamic radius of polyvinylpyrrolidone (M w = 360,000 g/mol), in water/methanol solvents mixture, versus the mixed solvents composition at 25 deg. C. Then, we show that the polymer conformation adopts the Coil-Globule-Coil structure when the methanol molar fraction X A is varied. This transition is attributed to solvent quality change which result from water and methanol complex formation. The polymer contraction rate calculated for each composition takes its maximum value at X A = 0.17. Hildebrand theory assuming the solvents mixture as an equivalent solvent was used to analyze the change in mixed solvents quality. These changes can be attributed to dispersive forces in solvents mixture

  5. Unexpected strong attraction in the presence of continuum bound state

    International Nuclear Information System (INIS)

    Delfino, A.; Frederico, T.

    1992-06-01

    The result of few-particle ground-state calculation employing a two-particle non-local potential supporting a continuum bound state in addition to a negative-energy bound state has occasionally revealed unexpected large attraction in producing a very strongly bound ground state. In the presence of the continuum bound state the difference of phase shift between zero and infinite energies has an extra jump of φ as in the presence of an additional bound state. The wave function of the continuum bound state is identical with that of a strongly bound negative-energy state, which leads us to postulate a pseudo bound state in the two-particle system in order to explain the unexpected attraction. The role of the Pauli forbidden states is expected to be similar to these pseudo states. (author)

  6. The response of electrostatic probes via the λ-function

    DEFF Research Database (Denmark)

    Rerup, T.O.; Crichton, George C; McAllister, Iain Wilson

    1994-01-01

    The response of an electrostatic probe is examined with reference to a planar spacer. The study involves the numerical calculation of the probe λ-function, from which response-related characteristic parameters can be derived. These parameters enable the probe detection sensitivity and spatial...

  7. Structure of DNA toroids and electrostatic attraction of DNA duplexes

    International Nuclear Information System (INIS)

    Cherstvy, A G

    2005-01-01

    DNA-DNA electrostatic attraction is considered as the driving force for the formation of DNA toroids in the presence of DNA condensing cations. This attraction comes from the DNA helical charge distribution and favours hexagonal toroidal cross-sections. The latter is in agreement with recent cryo-electron microscopy studies on DNA condensed with cobalt hexammine. We treat the DNA-DNA interactions within the modern theory of electrostatic interaction between helical macromolecules. The size and thickness of the toroids is calculated within a simple model; other models of stability of DNA toroids are discussed and compared

  8. Combine experimental and theoretical investigation on an alkaloid-Dimethylisoborreverine

    Science.gov (United States)

    Singh, Swapnil; Singh, Harshita; Karthick, T.; Agarwal, Parag; Erande, Rohan D.; Dethe, Dattatraya H.; Tandon, Poonam

    2016-01-01

    A combined experimental (FT-IR, 1H and 13C NMR) and theoretical approach is used to study the structure and properties of antimalarial drug dimethylisoborreverine (DMIB). Conformational analysis, has been performed by plotting one dimensional potential energy curve that was computed using density functional theory (DFT) with B3LYP/6-31G method and predicted conformer A1 as the most stable conformer. After full geometry optimization, harmonic wavenumbers were computed for conformer A1 at the DFT/B3LYP/6-311++G(d,P) level. A complete vibrational assignment of all the vibrational modes have been performed on the bases of the potential energy distribution (PED) and theoretical results were found to be in good agreement with the observed data. To predict the solvent effect, the UV-Vis spectra were calculated in different solvents by polarizable continuum model using TD-DFT method. Molecular docking studies were performed to test the biological activity of the sample using SWISSDOCK web server and Hex 8.0.0 software. The molecular electrostatic potential (MESP) was plotted to identify the reactive sites of the molecule. Natural bond orbital (NBO) analysis was performed to get a deep insight of intramolecular charge transfer. Thermodynamical parameters were calculated to predict the direction of chemical reaction.

  9. Alfven continuum and high-frequency eigenmodes in optimized stellarators

    International Nuclear Information System (INIS)

    Kolesnichenko, Ya.I.; Lutsenko, V.V.; Wobig, H.; Yakovenko, Yu.V.; Fesenyuk, O.P.

    2001-01-01

    An equation of shear Alfven eigenmodes (AE) in optimized stellarators of Wendelstein line (Helias configurations) is derived. The metric tensor coefficients, which are contained in this equation, are calculated analytically. Two numerical codes are developed: the first one, COBRA (COntinuum BRanches of Alfven waves), is intended for the investigation of the structure of Alfven continuum; the second, BOA (Branches Of Alfven modes), solves the eigenvalue problem. The family of possible gaps in Alfven continuum of a Helias configuration is obtained. It is predicted that there exist gaps which arise due to or are strongly affected by the variation of the shape of the plasma cross section along the large azimuth of the torus. In such gaps, discrete eigenmodes, namely, helicity-induced eigenmodes (HAE 21 ) and mirror-induced eigenmodes (MAE) are found. It is shown that plasma inhomogeneity may suppress the AEs with a wide region of localization

  10. SIMION, Electrostatic Lens Analysis and Design

    International Nuclear Information System (INIS)

    Dahl, David A.

    2001-01-01

    1 - Description of program or function: SIMION is an electrostatic lens analysis and design program. In SIMION an electrostatic lens is defined as a two-dimensional electrostatic potential array containing both electrode and non-electrode points. The potential array is refined using over-relaxation methods allowing voltage contours and ion trajectories to be computed and plotted. Planar and cylindrical symmetry assumptions allow the two-dimensional fields to support three-dimensional ion trajectory calculations. In addition, the user has the option of writing simple programs which can among other actions control field scale factors, dynamically adjust electrodes, and define explicit three-dimensional field functions (e.g. a quadrupole) used in lieu of array fields in specified portions of the potential array. Magnetic fields can be specified for computing ion trajectories in many electrostatic and magnetic field environments. An interactive graphics interface that uses a high resolution color display and mouse allows the user to view electrodes, trajectories, and contours on the screen prior to plotting, and a memory zoom feature permits expansion of selected areas in the current view. The mouse can be operated to edit the potential array, initialize voltage gradients, or resize the potential array. 2 - Method of solution: SIMION is designed to model the electrostatic fields and forces created by a collection of shaped electrodes given certain symmetry assumptions. The electrostatic fields are modeled as boundary value problem solutions of a Laplace elliptical partial differential equation. A finite difference technique called dynamically self-adjusting over-relaxation is applied to the two-dimensional potential array of points representing electrode and non-electrode regions to obtain a best estimate of the voltages for those points within the array that depict non-electrode regions. A standard fourth-order Runge-Kutta method is used for numerical integration of

  11. Electrostatics of cysteine residues in proteins: parameterization and validation of a simple model.

    Science.gov (United States)

    Salsbury, Freddie R; Poole, Leslie B; Fetrow, Jacquelyn S

    2012-11-01

    One of the most popular and simple models for the calculation of pK(a) s from a protein structure is the semi-macroscopic electrostatic model MEAD. This model requires empirical parameters for each residue to calculate pK(a) s. Analysis of current, widely used empirical parameters for cysteine residues showed that they did not reproduce expected cysteine pK(a) s; thus, we set out to identify parameters consistent with the CHARMM27 force field that capture both the behavior of typical cysteines in proteins and the behavior of cysteines which have perturbed pK(a) s. The new parameters were validated in three ways: (1) calculation across a large set of typical cysteines in proteins (where the calculations are expected to reproduce expected ensemble behavior); (2) calculation across a set of perturbed cysteines in proteins (where the calculations are expected to reproduce the shifted ensemble behavior); and (3) comparison to experimentally determined pK(a) values (where the calculation should reproduce the pK(a) within experimental error). Both the general behavior of cysteines in proteins and the perturbed pK(a) in some proteins can be predicted reasonably well using the newly determined empirical parameters within the MEAD model for protein electrostatics. This study provides the first general analysis of the electrostatics of cysteines in proteins, with specific attention paid to capturing both the behavior of typical cysteines in a protein and the behavior of cysteines whose pK(a) should be shifted, and validation of force field parameters for cysteine residues. Copyright © 2012 Wiley Periodicals, Inc.

  12. Structural transition of a homopolymer in solvents mixture

    Energy Technology Data Exchange (ETDEWEB)

    Guettari, Moez [Laboratoire de Physique de la Matiere Molle, Faculte des Sciences de Tunis, Campus Universitaire, 2092 Tunisia (Tunisia)], E-mail: gtarimoez@yahoo.fr; Aschi, Adel; Gomati, Riadh; Gharbi, Abdelhafidh [Laboratoire de Physique de la Matiere Molle, Faculte des Sciences de Tunis, Campus Universitaire, 2092 Tunisia (Tunisia)

    2008-07-01

    The present work is aimed at studying the thermodynamic behaviour of a polymer in solvents mixture. Dynamic light scattering is used to measure the hydrodynamic radius of polyvinylpyrrolidone (M{sub w} = 360,000 g/mol), in water/methanol solvents mixture, versus the mixed solvents composition at 25 deg. C. Then, we show that the polymer conformation adopts the Coil-Globule-Coil structure when the methanol molar fraction X{sub A} is varied. This transition is attributed to solvent quality change which result from water and methanol complex formation. The polymer contraction rate calculated for each composition takes its maximum value at X{sub A} = 0.17. Hildebrand theory assuming the solvents mixture as an equivalent solvent was used to analyze the change in mixed solvents quality. These changes can be attributed to dispersive forces in solvents mixture.

  13. Gels and lyotropic liquid crystals: using an imidazolium-based catanionic surfactant in binary solvents.

    Science.gov (United States)

    Cheng, Ni; Hu, Qiongzheng; Bi, Yanhui; Xu, Wenwen; Gong, Yanjun; Yu, Li

    2014-08-05

    The self-assembly behavior of an imidazolium-based catanionic surfactant, 1-butyl-3-methylimidazolium dodecylsulfate ([C4mim][C12H25SO4]), was investigated in water-ethylammonium nitrate (EAN) mixed solvents with different volume ratios. It is particular interesting that this simple surfactant could not only form lyotropic liquid crystals (LLC) with multimesophases, i.e., normal hexagonal (H1), lamellar liquid crystal (Lα), and reverse bicontinuous cubic phase (V2), in the water-rich environment but also act as an efficient low-molecular-weight gelator (LMWG) which gelated EAN-abundant binary media in a broad concentration range. The peculiar nanodisk cluster morphology of gels composed of similar bilayer units was first observed. FT-IR spectra and density functional theory (DFT) calculations reveal that strong H bonding and electrostatic interactions between EAN and the headgroups of [C4mim][C12H25SO4] are primarily responsible for gelation. The self-assembled gels displayed excellent mechanical strength and a thermoreversible sol-gel transition. It is for the first time that a rich variety of controllable ordered aggregates could be observed only by simply modulating the concentration of a single imidazolium-based catanionic surfactant or the ratio of mixed solvents. This environmentally friendly system is expected to have broad applications in various fields, such as materials science, drug delivery systems, and supramolecular chemistry.

  14. Large electrostatic accelerators

    Energy Technology Data Exchange (ETDEWEB)

    Jones, C.M.

    1984-01-01

    The increasing importance of energetic heavy ion beams in the study of atomic physics, nuclear physics, and materials science has partially or wholly motivated the construction of a new generation of large electrostatic accelerators designed to operate at terminal potentials of 20 MV or above. In this paper, the author briefly discusses the status of these new accelerators and also discusses several recent technological advances which may be expected to further improve their performance. The paper is divided into four parts: (1) a discussion of the motivation for the construction of large electrostatic accelerators, (2) a description and discussion of several large electrostatic accelerators which have been recently completed or are under construction, (3) a description of several recent innovations which may be expected to improve the performance of large electrostatic accelerators in the future, and (4) a description of an innovative new large electrostatic accelerator whose construction is scheduled to begin next year. Due to time and space constraints, discussion is restricted to consideration of only tandem accelerators.

  15. Large electrostatic accelerators

    International Nuclear Information System (INIS)

    Jones, C.M.

    1984-01-01

    The increasing importance of energetic heavy ion beams in the study of atomic physics, nuclear physics, and materials science has partially or wholly motivated the construction of a new generation of large electrostatic accelerators designed to operate at terminal potentials of 20 MV or above. In this paper, the author briefly discusses the status of these new accelerators and also discusses several recent technological advances which may be expected to further improve their performance. The paper is divided into four parts: (1) a discussion of the motivation for the construction of large electrostatic accelerators, (2) a description and discussion of several large electrostatic accelerators which have been recently completed or are under construction, (3) a description of several recent innovations which may be expected to improve the performance of large electrostatic accelerators in the future, and (4) a description of an innovative new large electrostatic accelerator whose construction is scheduled to begin next year. Due to time and space constraints, discussion is restricted to consideration of only tandem accelerators

  16. Electrostatic and electromagnetic instabilities associated with electrostatic shocks: Two-dimensional particle-in-cell simulation

    International Nuclear Information System (INIS)

    Kato, Tsunehiko N.; Takabe, Hideaki

    2010-01-01

    A two-dimensional electromagnetic particle-in-cell simulation with the realistic ion-to-electron mass ratio of 1836 is carried out to investigate the electrostatic collisionless shocks in relatively high-speed (∼3000 km s -1 ) plasma flows and also the influence of both electrostatic and electromagnetic instabilities, which can develop around the shocks, on the shock dynamics. It is shown that the electrostatic ion-ion instability can develop in front of the shocks, where the plasma is under counterstreaming condition, with highly oblique wave vectors as was shown previously. The electrostatic potential generated by the electrostatic ion-ion instability propagating obliquely to the shock surface becomes comparable with the shock potential and finally the shock structure is destroyed. It is also shown that in front of the shock the beam-Weibel instability gradually grows as well, consequently suggesting that the magnetic field generated by the beam-Weibel instability becomes important in long-term evolution of the shock and the Weibel-mediated shock forms long after the electrostatic shock vanished. It is also observed that the secondary electrostatic shock forms in the reflected ions in front of the primary electrostatic shock.

  17. Vibrational quasi-continuum in unimolecular multiphoton dissociation

    Energy Technology Data Exchange (ETDEWEB)

    Garcia Fernandez, P.; Gonzalez-Diaz, P.F.

    1987-04-01

    The vibrational quasi-continuum of the boron trifluoride molecule has been qualitatively studied and the formalism extended to treat N-normal-mode molecules. The anharmonic potential curves for the BF/sub 3/ normal modes have been calculated, and the computed anharmonicity constants have been tested against the fundamental frequencies. The potential curve of the wagging mode has been simulated by an internal rotation of one of the fluoride atoms. The vibrational-energy levels and wave functions have been calculated applying second-order perturbation theory. The quasi-continuum energy levels of BF/sub 3/ have been obtained by means of a method based in forming adequate linear combinations of wave functions belonging to the N-1 modes resulting from removing the i.r.-active mode;the associated energies have been minimized using a constrained minimization procedure. It has been found that the energy pattern of the N-1 vibrational modes possesses an energy density high enough for constituting a vibrational heat bath and, finally, it has been verified that the ''fictitious'' pattern of the active mode is included in the pattern of the N-1 modes.

  18. Thermodynamic equilibrium of hydroxyacetic acid in pure and binary solvent systems

    International Nuclear Information System (INIS)

    Huang, Qiaoyin; Xie, Chuang; Li, Yang; Su, Nannan; Lou, Yajing; Hu, Xiaoxue; Wang, Yongli; Bao, Ying; Hou, Baohong

    2017-01-01

    Highlights: • Solubility of hydroxyacetic acid in mono-solvents and binary solvent mixtures was measured. • Modified Apelblat, NRTL and Wilson model were used to correlate the solubility data in pure solvents. • CNIBS/R-K and Jouyban-Acree model were used to correlate the solubility in binary solvent mixtures. • The mixing properties were calculated based on the NRTL model. - Abstract: The solubility of hydroxyacetic acid in five pure organic solvents and two binary solvent mixtures were experimentally measured from 273.15 K to 313.15 K at atmospheric pressure (p = 0.1 MPa) by using a dynamic method. The order of solubility in pure organic solvents is ethanol > isopropanol > n-butanol > acetonitrile > ethyl acetate within the investigated temperature range, except for temperature lower than 278 K where the solubility of HA in ethyl acetate is slightly larger than that in acetonitrile. Furthermore, the solubility data in pure solvents were correlated with the modified Apelblat model, NRTL model, and Wilson model and that in the binary solvents mixtures were fitted to the CNIBS/R-K model and Jouyban-Acree model. Finally, the mixing thermodynamic properties of hydroxyacetic acid in pure and binary solvent systems were calculated and discussed.

  19. Characterization of zonal flow generation in weak electrostatic turbulence

    International Nuclear Information System (INIS)

    Negrea, M; Petrisor, I; Weyssow, B

    2008-01-01

    The influence of the diamagnetic Kubo number, which is proportional to the diamagnetic drift velocity, on the zonal flow generation by an anisotropic stochastic electrostatic potential is considered from a semi-analytic point of view. The analysis is performed in the weak turbulence limit and as an analytical tool the decorrelation trajectory method is used. It is shown that the fragmentation of the drift wave structures (a signature of the zonal flow generation) is influenced not only by the anisotropy parameter and the electrostatic Kubo number as expected, but also by the diamagnetic Kubo number. Global Lagrangian averages of characteristic quantities are calculated and interpreted

  20. The initial step of silicate versus aluminosilicate formation in zeolite synthesis: a reaction mechanism in water with a tetrapropylammonium template

    KAUST Repository

    Trinh, Thuat T.; Rozanska, Xavier; Delbecq, Franç oise; Sautet, Philippe

    2012-01-01

    is then compared to a simple calculation using an implicit continuum model for the solvent. The results underline the importance of an explicit and dynamical treatment of the water solvent, which plays a key role in assisting the reaction. © the Owner Societies

  1. A generalized Poisson and Poisson-Boltzmann solver for electrostatic environments

    International Nuclear Information System (INIS)

    Fisicaro, G.; Goedecker, S.; Genovese, L.; Andreussi, O.; Marzari, N.

    2016-01-01

    The computational study of chemical reactions in complex, wet environments is critical for applications in many fields. It is often essential to study chemical reactions in the presence of applied electrochemical potentials, taking into account the non-trivial electrostatic screening coming from the solvent and the electrolytes. As a consequence, the electrostatic potential has to be found by solving the generalized Poisson and the Poisson-Boltzmann equations for neutral and ionic solutions, respectively. In the present work, solvers for both problems have been developed. A preconditioned conjugate gradient method has been implemented for the solution of the generalized Poisson equation and the linear regime of the Poisson-Boltzmann, allowing to solve iteratively the minimization problem with some ten iterations of the ordinary Poisson equation solver. In addition, a self-consistent procedure enables us to solve the non-linear Poisson-Boltzmann problem. Both solvers exhibit very high accuracy and parallel efficiency and allow for the treatment of periodic, free, and slab boundary conditions. The solver has been integrated into the BigDFT and Quantum-ESPRESSO electronic-structure packages and will be released as an independent program, suitable for integration in other codes

  2. A generalized Poisson and Poisson-Boltzmann solver for electrostatic environments.

    Science.gov (United States)

    Fisicaro, G; Genovese, L; Andreussi, O; Marzari, N; Goedecker, S

    2016-01-07

    The computational study of chemical reactions in complex, wet environments is critical for applications in many fields. It is often essential to study chemical reactions in the presence of applied electrochemical potentials, taking into account the non-trivial electrostatic screening coming from the solvent and the electrolytes. As a consequence, the electrostatic potential has to be found by solving the generalized Poisson and the Poisson-Boltzmann equations for neutral and ionic solutions, respectively. In the present work, solvers for both problems have been developed. A preconditioned conjugate gradient method has been implemented for the solution of the generalized Poisson equation and the linear regime of the Poisson-Boltzmann, allowing to solve iteratively the minimization problem with some ten iterations of the ordinary Poisson equation solver. In addition, a self-consistent procedure enables us to solve the non-linear Poisson-Boltzmann problem. Both solvers exhibit very high accuracy and parallel efficiency and allow for the treatment of periodic, free, and slab boundary conditions. The solver has been integrated into the BigDFT and Quantum-ESPRESSO electronic-structure packages and will be released as an independent program, suitable for integration in other codes.

  3. A generalized Poisson and Poisson-Boltzmann solver for electrostatic environments

    Energy Technology Data Exchange (ETDEWEB)

    Fisicaro, G., E-mail: giuseppe.fisicaro@unibas.ch; Goedecker, S. [Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel (Switzerland); Genovese, L. [University of Grenoble Alpes, CEA, INAC-SP2M, L-Sim, F-38000 Grenoble (France); Andreussi, O. [Institute of Computational Science, Università della Svizzera Italiana, Via Giuseppe Buffi 13, CH-6904 Lugano (Switzerland); Theory and Simulations of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, Station 12, CH-1015 Lausanne (Switzerland); Marzari, N. [Theory and Simulations of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, Station 12, CH-1015 Lausanne (Switzerland)

    2016-01-07

    The computational study of chemical reactions in complex, wet environments is critical for applications in many fields. It is often essential to study chemical reactions in the presence of applied electrochemical potentials, taking into account the non-trivial electrostatic screening coming from the solvent and the electrolytes. As a consequence, the electrostatic potential has to be found by solving the generalized Poisson and the Poisson-Boltzmann equations for neutral and ionic solutions, respectively. In the present work, solvers for both problems have been developed. A preconditioned conjugate gradient method has been implemented for the solution of the generalized Poisson equation and the linear regime of the Poisson-Boltzmann, allowing to solve iteratively the minimization problem with some ten iterations of the ordinary Poisson equation solver. In addition, a self-consistent procedure enables us to solve the non-linear Poisson-Boltzmann problem. Both solvers exhibit very high accuracy and parallel efficiency and allow for the treatment of periodic, free, and slab boundary conditions. The solver has been integrated into the BigDFT and Quantum-ESPRESSO electronic-structure packages and will be released as an independent program, suitable for integration in other codes.

  4. Electrostatic coupling of ion pumps.

    Science.gov (United States)

    Nieto-Frausto, J; Lüger, P; Apell, H J

    1992-01-01

    In this paper the electrostatic interactions between membrane-embedded ion-pumps and their consequences for the kinetics of pump-mediated transport processes have been examined. We show that the time course of an intrinsically monomolecular transport reaction can become distinctly nonexponential, if the reaction is associated with charge translocation and takes place in an aggregate of pump molecules. First we consider the electrostatic coupling of a single dimer of ion-pumps embedded in the membrane. Then we apply the treatment to the kinetic analysis of light-driven proton transport by bacteriorhodopsin which forms two-dimensional hexagonal lattices. Finally, for the case of nonordered molecules, we also consider a model in which the pumps are randomly distributed over the nodes of a lattice. Here the average distance is equal to that deduced experimentally and the elemental size of the lattice is the effective diameter of one single pump. This latter model is applied to an aggregate of membrane-embedded Na, K- and Ca-pumps. In all these cases the electrostatic potential considered is the exact solution calculated from the method of electrical images for a plane membrane of finite thickness immersed in an infinite aqueous solution environment. The distributions of charges (ions or charged binding sites) are considered homogeneous or discrete in the membrane and/or in the external solution. In the case of discrete distributions we compare the results from a mean field approximation and a stochastic simulation.

  5. Spreadsheet algorithm for stagewise solvent extraction

    International Nuclear Information System (INIS)

    Leonard, R.A.; Regalbuto, M.C.

    1994-01-01

    The material balance and equilibrium equations for solvent extraction processes have been combined with computer spreadsheets in a new way so that models for very complex multicomponent multistage operations can be setup and used easily. A part of the novelty is the way in which the problem is organized in the spreadsheet. In addition, to facilitate spreadsheet setup, a new calculational procedure has been developed. The resulting Spreadsheet Algorithm for Stagewise Solvent Extraction (SASSE) can be used with either IBM or Macintosh personal computers as a simple yet powerful tool for analyzing solvent extraction flowsheets. 22 refs., 4 figs., 2 tabs

  6. Empirical equations of the solvent extraction of the energetic inputs, uranium and plutonium, calculated by using the program Microsoft Excel

    International Nuclear Information System (INIS)

    Bento, Dercio Lopes

    2006-01-01

    PUREX is one of the purification process for irradiated nuclear fuel. In the flowchart the program uses various uranium and plutonium extraction phases by using organic solvent contained in the aqueous phase obtained in the dissolution of the fuel element. A posterior extraction U and Pu are changed to the aqueous phase. So it is fundamental to know the distribution coefficient (dS), at the temperature (tc), of the substances among the two immiscible phases, for better calculation the suitable flowchart. A mathematical model was elaborated based on experimental data, for the calculation of the dS and applied to a referential band of substance concentrations in the aqueous phase (xS) and organic (yS). By using the program Excel, we personalized the empirical equations calculated by the root mean square. The relative deviation, among the calculated values and the experimental ones are the standards

  7. Determination and correlation of solubility and thermodynamic properties of pyraclostrobin in pure and binary solvents

    International Nuclear Information System (INIS)

    Yang, Peng; Du, Shichao; Qin, Yujia; Zhao, Kaifei; Li, Kangli; Hou, Baohong; Gong, Junbo

    2016-01-01

    Highlights: • The solubility data of pyraclostrobin in pure and binary solvents were determined and correlated. • The theory of solubility parameter was used to explain the cosolvency in binary solvents. • A modified mixing rule was proposed to calculate the solubility parameter of binary solvents. • The dissolution thermodynamic properties were calculated and discussed. - Abstract: The solubility of pyraclostrobin in five pure solvents and two binary solvent mixtures was measured from 283.15 K to 308.15 K using a static analytical method. Solubility in five pure solvents was well correlated by the modified Apelblat equation and Wilson model. While the CNIBS/R–K model was applied to correlate the solubility in two binary solvent mixtures, the correlation showed good agreement with experimental results. The solubility of pyraclostrobin reaches its maximum value at a certain cyclohexane mole fraction in the two binary solvent mixtures. The solubility parameter of pyraclostrobin was calculated by the Fedors method and a new modified mixing rule with preferable applicability was proposed to determine the solubility parameter of solvents. Then the co-solvency in the binary solvent mixtures can be explained based on the obtained solubility parameters. In a addition, the dissolution thermodynamic properties were calculated from the experimental values using the Wilson model.

  8. Calculation of spectral shifts in UV–visible region and photoresponsive behaviour of fluorinated liquid crystals: Effect of solvent and substituent

    International Nuclear Information System (INIS)

    Lakshmi Praveen, P.; Ojha, Durga P.

    2012-01-01

    The photoresponsive behaviour of fluorinated liquid crystals p-phenylene-4-methoxy benzoate-4-trifluoromethylbenzoate (FLUORO1), and 4-propyloxyphenyl-4-(4-trifluoromethylbenzoyloxy) benzoate (FLUORO2) has been systematically investigated using the CNDO/S + CI and INDO/S + CI methods. These methods have been employed to calculate/analyze the spectral shifts, and absorbance measurements in UV–visible region of the systems. The electronic transitions, absorption wavelength, HOMO (highest occupied molecular orbital), and LUMO (lowest unoccupied molecular orbital) energies have been calculated. Further, ultraviolet (UV) stability of the molecules has been discussed in the light of absorption wavelength and electronic transition oscillator strength (f). The effect of different solvent media and substituents on transition energies, oscillator strength, and other absorption parameters have also been reported. The present article provides valuable information regarding enhancing the UV stability of molecules by marinating their conductivity. Highlights: ► The strongest bands of FLUORO molecules can be assigned as π → π ∗ transitions. ► A small red-shift indicates a weak exciton coupling of chromophores. ► No n → π ∗ transition occurs due to the rigidity of the ring system of the molecules. ► The HOMO, LUMO, and E g values have been found to be independent of solvent effect.

  9. Solvent Role in the Formation of Electric Double Layers with Surface Charge Regulation: A Bystander or a Key Participant?

    Science.gov (United States)

    Fleharty, Mark E.; van Swol, Frank; Petsev, Dimiter N.

    2016-01-01

    The charge formation at interfaces involving electrolyte solutions is due to the chemical equilibrium between the surface reactive groups and the potential determining ions in the solution (i.e., charge regulation). In this Letter we report our findings that this equilibrium is strongly coupled to the precise molecular structure of the solution near the charged interface. The neutral solvent molecules dominate this structure due to their overwhelmingly large number. Treating the solvent as a structureless continuum leads to a fundamentally inadequate physical picture of charged interfaces. We show that a proper account of the solvent effect leads to an unexpected and complex system behavior that is affected by the molecular and ionic excluded volumes and van der Waals interactions.

  10. Continuum model for water movement in an unsaturated fractured rock mass

    International Nuclear Information System (INIS)

    Peters, R.R.; Klavetter, E.A.

    1988-01-01

    The movement of fluids in a fractured, porous medium has been the subject of considerable study. This paper presents a continuum model that may be used to evaluate the isothermal movement of water in an unsaturated, fractured, porous medium under slowly changing conditions. This continuum model was developed for use in evaluating the unsaturated zone at the Yucca Mountain site as a potential repository for high-level nuclear waste. Thus its development has been influenced by the conditions thought to be present at Yucca Mountain. A macroscopic approach and a microscopic approach are used to develop a continuum model to evaluate water movement in a fractured rock mass. Both approaches assume that the pressure head in the fractures and the matrix are identical in a plane perpendicular to flow. Both approaches lead to a single-flow equation for a fractured rock mass. The two approaches are used to calculate unsaturated hydrologic properties, i.e., relative permeability and saturation as a function of pressure head, for several types of tuff underlying Yucca Mountain, using the best available hydrologic data for the matrix and the fractures. Rock mass properties calculated by both approaches are similar

  11. Magnetosheath electrostatic turbulence

    International Nuclear Information System (INIS)

    Rodriguez, P.

    1979-01-01

    By using measurements with the University of Iowa plasma wave experiment on the Imp 6 satellite a study has been conducted of the spectrum of electrostatic plasma waves in the terrestrial magnetosheath. Electrostatic plasma wave turbulence is almost continuously present throughout the magnetosheath with broadband (20 Hz to 70 kHz) rms field intensities typically 0.01--1.0 mV m -1 . Peak intensities of about 1.0 mV m -1 near the electron plasma frequency (30--60 kHz) have been detected occasionally. Two or three components can usually be identified in the spectrum of magnetosheath electrostatic turbulence: a high-frequency (> or =30kHz) component peaking at the electron plasma frequency f/sub p/e, a low-frequency component with a broad intensity maximum below the nominal ion plasma frequency f/sub p/i (approx. f/sub p/e/43), and a less well defined intermediate component in the range f/sub p/i < f< f/sub p/e. The intensity distribution of magnetosheath electrostatic turbulence clearly shows that the low-frequency component is associated with the bow shock, suggesting that the ion heating begun at the shock continues into the downstream magnetosheath. Electrostatic waves below 1 kHz are polarized along the magnetic field direction, a result consistent with the polarization of electrostatic waves at the shock. The high- and intermediate-frequency components are features of the magnetosheath spectrum which are not characteristic of the shock spectrum but are often detected in the upstream solar wind. The intensity distribution of electrostatic turbulence at the magnetosheath plasma frequency has no apparent correlation with the shock, indicating that electron plasma oscillations are a general feature of the magnetosheath. The plasma wave noise shows a tendency to decrease toward the dawn and dusk regions, consistent with a general decrease in turbulence away from the subsolar magnetosheath

  12. Excited State Charge Transfer reaction with dual emission from 5-(4-dimethylamino-phenyl)-penta-2,4-dienenitrile: Spectral measurement and theoretical density functional theory calculation

    Science.gov (United States)

    Jana, Sankar; Dalapati, Sasanka; Ghosh, Shalini; Kar, Samiran; Guchhait, Nikhil

    2011-07-01

    The excited state intramolecular charge transfer process in donor-chromophore-acceptor system 5-(4-dimethylamino-phenyl)-penta-2,4-dienenitrile (DMAPPDN) has been investigated by steady state absorption and emission spectroscopy in combination with Density Functional Theory (DFT) calculations. This flexible donor acceptor molecule DMAPPDN shows dual fluorescence corresponding to emission from locally excited and charge transfer state in polar solvent. Large solvatochromic emission shift, effect of variation of pH and HOMO-LUMO molecular orbital pictures support excited state intramolecular charge transfer process. The experimental findings have been correlated with the calculated structure and potential energy surfaces based on the Twisted Intramolecular Charge Transfer (TICT) model obtained at DFT level using B3LYP functional and 6-31+G( d, p) basis set. The theoretical potential energy surfaces for the excited states have been generated in vacuo and acetonitrile solvent using Time Dependent Density Functional Theory (TDDFT) and Time Dependent Density Functional Theory Polarized Continuum Model (TDDFT-PCM) method, respectively. All the theoretical results show well agreement with the experimental observations.

  13. The effect of interface state continuum on the impedance spectroscopy of semiconductor heterojunctions

    International Nuclear Information System (INIS)

    Brus, V V

    2013-01-01

    A quantitative analysis of the impedance spectroscopy of semiconductor heterojunctions was carried out in the presence of interface state continuum at the heterojunction interface. A comparison of the impedance spectroscopy of semiconductor heterojunctions simulated in the context of the interface state continuum model with that simulated in the scope of the single-level state model was carried and possible misinterpretations were considered. The previously proposed approaches for the determination of the interface-state-related parameters and for the calculation of the actual barrier capacitance (the single-level state model) were modified in order to take into account the effect of interface state continuum. (paper)

  14. Electrostatics in Chemistry

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 4; Issue 7. Electrostatics in Chemistry - Molecular Electrostatic Potential: Visualization and Topography. Shridhar R Gadre Pravin K Bhadane. Series Article Volume 4 Issue 7 July 1999 pp 14-23 ...

  15. Cholesterol Promotes Protein Binding by Affecting Membrane Electrostatics and Solvation Properties.

    Science.gov (United States)

    Doktorova, Milka; Heberle, Frederick A; Kingston, Richard L; Khelashvili, George; Cuendet, Michel A; Wen, Yi; Katsaras, John; Feigenson, Gerald W; Vogt, Volker M; Dick, Robert A

    2017-11-07

    Binding of the retroviral structural protein Gag to the cellular plasma membrane is mediated by the protein's matrix (MA) domain. Prominent among MA-PM interactions is electrostatic attraction between the positively charged MA domain and the negatively charged plasma membrane inner leaflet. Previously, we reported that membrane association of HIV-1 Gag, as well as purified Rous sarcoma virus (RSV) MA and Gag, depends strongly on the presence of acidic lipids and is enhanced by cholesterol (Chol). The mechanism underlying this enhancement was unclear. Here, using a broad set of in vitro and in silico techniques we addressed molecular mechanisms of association between RSV MA and model membranes, and investigated how Chol enhances this association. In neutron scattering experiments with liposomes in the presence or absence of Chol, MA preferentially interacted with preexisting POPS-rich clusters formed by nonideal lipid mixing, binding peripherally to the lipid headgroups with minimal perturbation to the bilayer structure. Molecular dynamics simulations showed a stronger MA-bilayer interaction in the presence of Chol, and a large Chol-driven increase in lipid packing and membrane surface charge density. Although in vitro MA-liposome association is influenced by disparate variables, including ionic strength and concentrations of Chol and charged lipids, continuum electrostatic theory revealed an underlying dependence on membrane surface potential. Together, these results conclusively show that Chol affects RSV MA-membrane association by making the electrostatic potential at the membrane surface more negative, while decreasing the penalty for lipid headgroup desolvation. The presented approach can be applied to other viral and nonviral proteins. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  16. Control of density fluctuations in atomistic-continuum simulations of dense liquids

    DEFF Research Database (Denmark)

    Kotsalis, E.M.; Walther, Jens Honore; Koumoutsakos, P.

    2007-01-01

    with a continuum solver for the simulation of the Navier-Stokes equations. The lack of periodic boundary conditions in the molecular dynamics simulations hinders the proper accounting for the virial pressure leading to spurious density fluctuations at the continuum-atomistic interface. An ad hoc boundary force...... is usually employed to remedy this situation.We propose the calculation of this boundary force using a control algorithm that explicitly cancels the density fluctuations. The results demonstrate that the present approach outperforms state-of-the-art algorithms. The conceptual and algorithmic simplicity...

  17. Transfers of Colloidal Silica from Water into Organic Solvents of Intermediate Polarities

    Science.gov (United States)

    Kasseh; Keh

    1998-01-15

    Dispersions of discrete metal-oxide submicroparticles in organic solvents of medium polarities are uneasy to generate and weakly documented. We address this topic along two general methods focusing on silica. Successive transfers of colloidal particles from water into n-propanol and then into 1,2-dichloroethane by azeotropic distillation yield a stable organosol. The particles are found to be propanol-coated by surface esterification to the extent of 0.40 nm2 per molecule. Alternatively, centrifugation-redispersion cycles make it possible to obtain stable suspensions of unaltered silica in methanol and acetonitrile starting from an aqueous silicasol. Particles are characterized by various methods including nitrogen adsorption, transmission electron microscopy, dynamic light scattering, and electrophoresis. The stabilities of these suspensions in various organic solvents are investigated with special concern for the role of residual water. Stabilization of silica in methanol is inconspicuously related to solvent permittivity and prominently dependent on the presence of adsorbed water. In contrast, the acetonitrile silicasol, which is unaffected by residual water, displays electrophoretic behavior compatible with electrostatic stabilization. Copyright 1998 Academic Press. Copyright 1998Academic Press

  18. Electrostatics of spherical metallic particles in cylinder electrostatic separators/sizers

    International Nuclear Information System (INIS)

    Lu Hongzhou; Li Jia; Guo Jie; Xu Zhenming

    2006-01-01

    This paper presents a theoretical analysis of the dynamics of spherical metallic particles in electrostatic separators/sizers (ESSs). A computational algorithm is employed to depict the cylinder-type electrode arrangements applied in some electrostatic processes generating non-uniform electric fields. The ESS consists of a pair of conducting cylinders. The upper cylinder is energized by HVdc, while the lower one is grounded and mounted horizontally on a revolvable axis. The aim of this paper is to present a new electrode configuration and demonstrate the usefulness of numerical techniques for the evaluation of the particle's motion. A computer program was employed for analysing the behavior of spherical particles in a two-dimensional electrode arrangement that models the actual electric field configuration of cylinder-type electrostatic separators/sizers. The analysis is needed for the development of any new application of this cylinder-type electrode arrangement as an electrostatic separation method. The results reveal that the particle's motion depends on its radius and density and amplitude of the applied voltage. The actual granular mixtures with different specific mass and radius could be separated applying this cylinder-type electrostatic separation method; the lift voltage is an important parameter for separation. With a program for two-dimensional analysis of the electric field, the computational procedure presented in this paper could be employed for any particle shapes

  19. Theoretical study of solvent effects on the coil-globule transition

    Science.gov (United States)

    Polson, James M.; Opps, Sheldon B.; Abou Risk, Nicholas

    2009-06-01

    The coil-globule transition of a polymer in a solvent has been studied using Monte Carlo simulations of a single chain subject to intramolecular interactions as well as a solvent-mediated effective potential. This solvation potential was calculated using several different theoretical approaches for two simple polymer/solvent models, each employing hard-sphere chains and hard-sphere solvent particles as well as attractive square-well potentials between some interaction sites. For each model, collapse is driven by variation in a parameter which changes the energy mismatch between monomers and solvent particles. The solvation potentials were calculated using two fundamentally different methodologies, each designed to predict the conformational behavior of polymers in solution: (1) the polymer reference interaction site model (PRISM) theory and (2) a many-body solvation potential (MBSP) based on scaled particle theory introduced by Grayce [J. Chem. Phys. 106, 5171 (1997)]. For the PRISM calculations, two well-studied solvation monomer-monomer pair potentials were employed, each distinguished by the closure relation used in its derivation: (i) a hypernetted-chain (HNC)-type potential and (ii) a Percus-Yevick (PY)-type potential. The theoretical predictions were each compared to results obtained from explicit-solvent discontinuous molecular dynamics simulations on the same polymer/solvent model systems [J. Chem. Phys. 125, 194904 (2006)]. In each case, the variation in the coil-globule transition properties with solvent density is mostly qualitatively correct, though the quantitative agreement between the theory and prediction is typically poor. The HNC-type potential yields results that are more qualitatively consistent with simulation. The conformational behavior of the polymer upon collapse predicted by the MBSP approach is quantitatively correct for low and moderate solvent densities but is increasingly less accurate for higher densities. At high solvent densities

  20. Estimate of cryoscopic calculations accuracy from fusibility diagrams

    International Nuclear Information System (INIS)

    Viting, L.M.; Gorbovskaya, G.P.

    1975-01-01

    The melting points of some lead and zinc salts, that can be used as solvents for ferrites in systems: PbMoO 4 -MgFe 2 O 4 , Zn 2 V 2 O 7 -NiFe 2 O 4 , Pb 3 (VO 4 ) 2 -MgFe 2 O 4 , have been calculated in accordance with the hypotetical mechanism of the solvent dissociation. The accuracy of cryoscopic calculations based on melting point curves is evaluated. Cryoscopic calculations permit to determin the solvent activity with the accuracy of +-0.3% and the heat of its fusion, with the accuracy of +-3%. The comparison of the calculated and experimental values of the entropy of melting, as well as calculated and experimental values of the cryoscopic constant elucidates the mechanism of dissociation of both the dissolved compound and the solvent

  1. Solvent effect in implicit/explicit model on FT-IR, 1H, 13C and 19F NMR, UV-vis and fluorescence spectra, linear, second- and third-nonlinear optical parameters of 2-(trifluoromethyl)benzoic acid: Experimental and computational study

    Science.gov (United States)

    Avcı, Davut; Altürk, Sümeyye; Tamer, Ömer; Kuşbazoğlu, Mustafa; Atalay, Yusuf

    2017-09-01

    FT-IR, 1H, 13C and 19F NMR, UV-vis and fluorescence spectra for 2-(trifluoromethyl)benzoic acid (2-TFMBA) were recorded. DFT//B3LYP/6-31++G(d,p) calculations were used to determine the optimized molecular geometry, vibrational frequencies, 1H, 13C and 19F GIAO-NMR chemical shifts of 2-TFMBA. The detailed assignments of vibrational frequencies were carried out on the basis of potential energy distribution (PED) by using VEDA program. TD-DFT/B3LYP/6-31++G(d,p) calculations with the PCM (polarizable continuum model) in ethanol and DMSO solvents based on implicit/explicit model and gas phase in the excited state were employed to investigate UV-vis absorption and fluorescence emission wavelengths. The UV-vis and emission spectra were given in ethanol and DMSO solvents, and the major contributions to the electronic transitions were obtained. In addition, the NLO parameters (β, γ and χ(3)) and frontier molecular orbital energies of 2-TFMBA were calculated by using B3LYP/6-31++G(d,p) level. The NLO parameters of 2-TFMBA were compared with that of para-Nitroaniline (pNA) and urea which are the typical NLO materials. The refractive index (n) is calculated by using the Lorentz-Lorenz equation to observe polarization behavior of 2-TFMBA in DMSO and ethanol solvents. In order to investigate intramolecular and hydrogen bonding interactions, NBO calculations were also performed by the same level. To sum up, considering the well-known biological role, photochemical properties of 2-TFMBA were discussed.

  2. A computer code for calculation of solvent-extraction separation in a multicomponent system with reference to nuclear fuel reprocessing

    International Nuclear Information System (INIS)

    Carassiti, F.; Liuzzo, G.; Morelli, A.

    1982-01-01

    Nuclear technology development pointed out the need for a new assessment of the fuel cycle back-end. Treatment and disposal of radioactive wastes arising from nuclear fuel reprocessing is known as one of the problems not yet satisfactorily solved, together with separation process of uranium and plutonium from fission products in highly irradiated fuels. Aim of this work is to present an improvement of the computer code for solvent extraction process calculation previously designed by the authors. The modeling of the extraction system has been modified by introducing a new method for calculating the distribution coefficients. The new correlations were based on deriving empirical functions for not only the apparent equilibrium constants, but also the solvation number. The mathematical model derived for calculating separation performance has been then tested for up to ten components and twelve theoretical stages with minor modifications to the convergence criteria. Suitable correlations for the calculation of the distribution coefficients of Uranium, Plutonium, Nitric Acid and fission products were constructed and used to successfully simulate several experimental conditions. (Author)

  3. Computational scheme for pH-dependent binding free energy calculation with explicit solvent.

    Science.gov (United States)

    Lee, Juyong; Miller, Benjamin T; Brooks, Bernard R

    2016-01-01

    We present a computational scheme to compute the pH-dependence of binding free energy with explicit solvent. Despite the importance of pH, the effect of pH has been generally neglected in binding free energy calculations because of a lack of accurate methods to model it. To address this limitation, we use a constant-pH methodology to obtain a true ensemble of multiple protonation states of a titratable system at a given pH and analyze the ensemble using the Bennett acceptance ratio (BAR) method. The constant pH method is based on the combination of enveloping distribution sampling (EDS) with the Hamiltonian replica exchange method (HREM), which yields an accurate semi-grand canonical ensemble of a titratable system. By considering the free energy change of constraining multiple protonation states to a single state or releasing a single protonation state to multiple states, the pH dependent binding free energy profile can be obtained. We perform benchmark simulations of a host-guest system: cucurbit[7]uril (CB[7]) and benzimidazole (BZ). BZ experiences a large pKa shift upon complex formation. The pH-dependent binding free energy profiles of the benchmark system are obtained with three different long-range interaction calculation schemes: a cutoff, the particle mesh Ewald (PME), and the isotropic periodic sum (IPS) method. Our scheme captures the pH-dependent behavior of binding free energy successfully. Absolute binding free energy values obtained with the PME and IPS methods are consistent, while cutoff method results are off by 2 kcal mol(-1) . We also discuss the characteristics of three long-range interaction calculation methods for constant-pH simulations. © 2015 The Protein Society.

  4. Electrostatic septum, SPS

    CERN Multimedia

    CERN PhotoLab

    1978-01-01

    To minimize losses during slow extraction towards N- and W-Area, electrostatic septa in long straight sections 2 and 6 precede the magnetic septa. This picture shows such an electrostatic septum in its tank. See 7501120X, 7501199 and 7501201 for more detailed pictures.

  5. Spectral properties of minimal-basis-set orbitals: Implications for molecular electronic continuum states

    Science.gov (United States)

    Langhoff, P. W.; Winstead, C. L.

    Early studies of the electronically excited states of molecules by John A. Pople and coworkers employing ab initio single-excitation configuration interaction (SECI) calculations helped to simulate related applications of these methods to the partial-channel photoionization cross sections of polyatomic molecules. The Gaussian representations of molecular orbitals adopted by Pople and coworkers can describe SECI continuum states when sufficiently large basis sets are employed. Minimal-basis virtual Fock orbitals stabilized in the continuous portions of such SECI spectra are generally associated with strong photoionization resonances. The spectral attributes of these resonance orbitals are illustrated here by revisiting previously reported experimental and theoretical studies of molecular formaldehyde (H2CO) in combination with recently calculated continuum orbital amplitudes.

  6. Application of the finite-difference approximation to electrostatic problems in gaseous proportional counters

    International Nuclear Information System (INIS)

    Waligorski, M.P.R.; Urbanczyk, K.M.

    1975-01-01

    The basic principles of the finite-difference approximation applied to the solution of electrostatic field distributions in gaseous proportional counters are given. Using this method, complicated two-dimensional electrostatic problems may be solved, taking into account any number of anodes, each with its own radius, and any cathode shape. A general formula for introducing the anode radii into the calculations is derived and a method of obtaining extremely accurate (up to 0.1%) solutions is developed. Several examples of potential and absolute field distributions for single rectangular and multiwire proportional counters are calculated and compared with exact results according to Tomitani, in order to discuss in detail errors of the finite-difference approximation. (author)

  7. Effects of solvent and structure on the reactivity of 6-substituted nicotinic acids with diazodiphenylmethane in aprotic solvents

    Directory of Open Access Journals (Sweden)

    BRATISLAV Ž. JOVANOVIĆ

    2009-12-01

    Full Text Available The rate constants for the reactions of diazodiphenylmethane (DDM with 6-substituted nicotinic acids in aprotic solvents at 30 °C were determined. The obtained second order rate constants in aprotic solvents, together with literature data for benzoic and nicotinic acids in protic solvents, were used for the calculation of solvent effects, employing the Kamlet-Taft solvatochromic equation (linear solvation energy relationship – LSER in the form: log k = log k0 + s* + a + b. The correlations of the kinetic data were performed by means of multiple linear regression analysis taking appropriate solvent parameters. The sign of the equation coefficients (s, a and b were in agreement with the postulated reaction mechanism, and the mode of the solvent influences on the reaction rate is discussed based on the correlation results. A similar contribution of the non-specific solvent effect and electrophilic solvation was observed for all acids, while the highest contribution of nucleophilic solvation was influenced by their high acidity. Correlation analysis of the rate data with substituent p parameters in an appropriate solvent using the Hammett equation was also performed. The substituent effect on the acid reactivity was higher in aprotic solvents of higher dipolarity/polarizability. The mode of the transmission of the substituent effect is discussed in light of the contribution of solute–solvent interaction on the acid reactivity.

  8. The solvent effects on dimethyl phthalate investigated by FTIR characterization, solvent parameter correlation and DFT computation

    Science.gov (United States)

    Chen, Yi; Zhang, Hui; Zhou, Wenzhao; Deng, Chao; Liao, Jian

    2018-06-01

    This study set out with the aim of investigating the solvent effects on dimethyl phthalate (DMP) using FTIR characterization, solvent parameter correlation and DFT calculation. DMP exposed to 17 organic solvents manifested varying shift in the carbonyl stretching vibration frequency (νCdbnd O). Non-alkanols induced Band I and alkanols produced Band I and Band II. Through correlating the νCdbnd O with the empirical solvent scales including acceptor parameter (AN), Schleyer's linear free energy parameter (G), and linear free salvation energy relationships (LSER), Band I was mainly ascribed to non-specific effects from either non-alkanols or alkanol polymers ((alkanol)n). νCdbnd O of the latter indicated minor red shift and less variability compared to the former. An assumption was made and validated about the sequestering of hydroxyl group by the bulky hydrophobic chain in (alkanol)n, creating what we refer to as "screening effects". Ab initio calculation, on the other hand, provided insights for possible hydrogen binding between DMP and (ethanol)n or between ethanol monomers. The two components of Band I observed in inert solvents were assigned to the two Cdbnd O groups adopting differentiated conformations. This in turn prompted our consideration that hydrogen binding was highly selective in favor of lowly associated (alkanol)n and the particular Cdbnd O group having relatively less steric hindrance and stronger electron-donating capacity. Band II was therefore believed to derive from hydrogen-bond interactions mainly in manner of 1:1 and 1:2 DMP-(alkanol)n complexes.

  9. Multipolar electrostatics.

    Science.gov (United States)

    Cardamone, Salvatore; Hughes, Timothy J; Popelier, Paul L A

    2014-06-14

    Atomistic simulation of chemical systems is currently limited by the elementary description of electrostatics that atomic point-charges offer. Unfortunately, a model of one point-charge for each atom fails to capture the anisotropic nature of electronic features such as lone pairs or π-systems. Higher order electrostatic terms, such as those offered by a multipole moment expansion, naturally recover these important electronic features. The question remains as to why such a description has not yet been widely adopted by popular molecular mechanics force fields. There are two widely-held misconceptions about the more rigorous formalism of multipolar electrostatics: (1) Accuracy: the implementation of multipole moments, compared to point-charges, offers little to no advantage in terms of an accurate representation of a system's energetics, structure and dynamics. (2) Efficiency: atomistic simulation using multipole moments is computationally prohibitive compared to simulation using point-charges. Whilst the second of these may have found some basis when computational power was a limiting factor, the first has no theoretical grounding. In the current work, we disprove the two statements above and systematically demonstrate that multipole moments are not discredited by either. We hope that this perspective will help in catalysing the transition to more realistic electrostatic modelling, to be adopted by popular molecular simulation software.

  10. Collisionless electrostatic shocks

    DEFF Research Database (Denmark)

    Andersen, H.K.; Andersen, S.A.; Jensen, Vagn Orla

    1970-01-01

    An attempt was made in the laboratory to observe the standing collisionless electrostatic shocks in connection with the bow shock of the earth......An attempt was made in the laboratory to observe the standing collisionless electrostatic shocks in connection with the bow shock of the earth...

  11. Self-consistent field model for strong electrostatic correlations and inhomogeneous dielectric media.

    Science.gov (United States)

    Ma, Manman; Xu, Zhenli

    2014-12-28

    Electrostatic correlations and variable permittivity of electrolytes are essential for exploring many chemical and physical properties of interfaces in aqueous solutions. We propose a continuum electrostatic model for the treatment of these effects in the framework of the self-consistent field theory. The model incorporates a space- or field-dependent dielectric permittivity and an excluded ion-size effect for the correlation energy. This results in a self-energy modified Poisson-Nernst-Planck or Poisson-Boltzmann equation together with state equations for the self energy and the dielectric function. We show that the ionic size is of significant importance in predicting a finite self energy for an ion in an inhomogeneous medium. Asymptotic approximation is proposed for the solution of a generalized Debye-Hückel equation, which has been shown to capture the ionic correlation and dielectric self energy. Through simulating ionic distribution surrounding a macroion, the modified self-consistent field model is shown to agree with particle-based Monte Carlo simulations. Numerical results for symmetric and asymmetric electrolytes demonstrate that the model is able to predict the charge inversion at high correlation regime in the presence of multivalent interfacial ions which is beyond the mean-field theory and also show strong effect to double layer structure due to the space- or field-dependent dielectric permittivity.

  12. Self-consistent field model for strong electrostatic correlations and inhomogeneous dielectric media

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Manman, E-mail: mmm@sjtu.edu.cn; Xu, Zhenli, E-mail: xuzl@sjtu.edu.cn [Department of Mathematics, Institute of Natural Sciences, and MoE Key Laboratory of Scientific and Engineering Computing, Shanghai Jiao Tong University, Shanghai 200240 (China)

    2014-12-28

    Electrostatic correlations and variable permittivity of electrolytes are essential for exploring many chemical and physical properties of interfaces in aqueous solutions. We propose a continuum electrostatic model for the treatment of these effects in the framework of the self-consistent field theory. The model incorporates a space- or field-dependent dielectric permittivity and an excluded ion-size effect for the correlation energy. This results in a self-energy modified Poisson-Nernst-Planck or Poisson-Boltzmann equation together with state equations for the self energy and the dielectric function. We show that the ionic size is of significant importance in predicting a finite self energy for an ion in an inhomogeneous medium. Asymptotic approximation is proposed for the solution of a generalized Debye-Hückel equation, which has been shown to capture the ionic correlation and dielectric self energy. Through simulating ionic distribution surrounding a macroion, the modified self-consistent field model is shown to agree with particle-based Monte Carlo simulations. Numerical results for symmetric and asymmetric electrolytes demonstrate that the model is able to predict the charge inversion at high correlation regime in the presence of multivalent interfacial ions which is beyond the mean-field theory and also show strong effect to double layer structure due to the space- or field-dependent dielectric permittivity.

  13. Predicted continuum spectra of type II supernovae - LTE results

    Science.gov (United States)

    Shaviv, G.; Wehrse, R.; Wagoner, R. V.

    1985-01-01

    The continuum spectral energy distribution of the flux emerging from type II supernovae is calculated from quasi-static radiative transfer through a power-law density gradient, assuming radiative equilibrium and LTE. It is found that the Balmer jump disappears at high effective temperatures and low densities, while the spectrum resembles that of a dilute blackbody but is flatter with a sharper cutoff at the short-wavelength end. A significant UV excess is found in all models calculated. The calculation should be considered exploratory because of significant effects which are anticipated to arise from departure from LTE.

  14. Three-body continuum states on a Lagrange mesh

    International Nuclear Information System (INIS)

    Descouvemont, P.; Tursunov, E.; Baye, D.

    2006-01-01

    Three-body continuum states are investigated with the hyperspherical method on a Lagrange mesh. The R-matrix theory is used to treat the asymptotic behaviour of scattering wave functions. The formalism is developed for neutral as well as for charged systems. We point out some specificities of continuum states in the hyperspherical method. The collision matrix can be determined with a good accuracy by using propagation techniques. The method is applied to the 6 He (=α+n+n) and 6 Be (=α+p+p) systems, as well as to 14 Be (=Be12+n+n). For 6 He, we essentially recover results of the literature. Application to 14 Be suggests the existence of an excited 2 + state below threshold. The calculated B(E2) value should make this state observable with Coulomb excitation experiments

  15. Passing waves from atomistic to continuum

    Science.gov (United States)

    Chen, Xiang; Diaz, Adrian; Xiong, Liming; McDowell, David L.; Chen, Youping

    2018-02-01

    Progress in the development of coupled atomistic-continuum methods for simulations of critical dynamic material behavior has been hampered by a spurious wave reflection problem at the atomistic-continuum interface. This problem is mainly caused by the difference in material descriptions between the atomistic and continuum models, which results in a mismatch in phonon dispersion relations. In this work, we introduce a new method based on atomistic dynamics of lattice coupled with a concurrent atomistic-continuum method to enable a full phonon representation in the continuum description. This permits the passage of short-wavelength, high-frequency phonon waves from the atomistic to continuum regions. The benchmark examples presented in this work demonstrate that the new scheme enables the passage of all allowable phonons through the atomistic-continuum interface; it also preserves the wave coherency and energy conservation after phonons transport across multiple atomistic-continuum interfaces. This work is the first step towards developing a concurrent atomistic-continuum simulation tool for non-equilibrium phonon-mediated thermal transport in materials with microstructural complexity.

  16. Influence of molecular geometry, exchange-correlation functional, and solvent effects in the modeling of vertical excitation energies in phthalocyanines using time-dependent density functional theory (TDDFT) and polarized continuum model TDDFT methods: can modern computational chemistry methods explain experimental controversies?

    Science.gov (United States)

    Nemykin, Victor N; Hadt, Ryan G; Belosludov, Rodion V; Mizuseki, Hiroshi; Kawazoe, Yoshiyuki

    2007-12-20

    A time-dependent density functional theory (TDDFT) approach coupled with 14 different exchange-correlation functionals was used for the prediction of vertical excitation energies in zinc phthalocyanine (PcZn). In general, the TDDFT approach provides a more accurate description of both visible and ultraviolet regions of the UV-vis and magnetic circular dichroism (MCD) spectra of PcZn in comparison to the more popular semiempirical ZINDO/S and PM3 methods. It was found that the calculated vertical excitation energies of PcZn correlate with the amount of Hartree-Fock exchange involved in the exchange-correlation functional. The correlation was explained on the basis of the calculated difference in energy between occupied and unoccupied molecular orbitals. The influence of PcZn geometry, optimized using different exchange-correlation functionals, on the calculated vertical excitation energies in PcZn was found to be relatively small. The influence of solvents on the calculated vertical excitation energies in PcZn was considered for the first time using a polarized continuum model TDDFT (PCM-TDDFT) method and was found to be relatively small in excellent agreement with the experimental data. For all tested TDDFT and PCM-TDDFT cases, an assignment of the Q-band as an almost pure a1u (HOMO)-->eg (LUMO) transition, initially suggested by Gouterman, was confirmed. Pure exchange-correlation functionals indicate the presence of six 1Eu states in the B-band region of the UV-vis spectrum of PcZn, while hybrid exchange-correlation functionals predict only five 1Eu states for the same energy envelope. The first two symmetry-forbidden n-->pi* transitions were predicted in the Q0-2 region and in the low-energy tail of the B-band, while the first two symmetry-allowed n-->pi* transitions were found within the B-band energy envelope when pure exchange-correlation functionals were used for TDDFT calculations. The presence of a symmetry-forbidden but vibronically allowed n

  17. Exact evaluation of the rates of electrostatic decay and scattering off thermal ions for an unmagnetized Maxwellian plasma

    Energy Technology Data Exchange (ETDEWEB)

    Layden, B.; Cairns, Iver H.; Robinson, P. A. [School of Physics, University of Sydney, Sydney, NSW 2006 (Australia)

    2013-08-15

    Electrostatic decay of Langmuir waves into Langmuir and ion sound waves (L→L′+S) and scattering of Langmuir waves off thermal ions (L+i→L′+i′, also called “nonlinear Landau damping”) are important nonlinear weak-turbulence processes. The rates for these processes depend on the quadratic longitudinal response function α{sup (2)} (or, equivalently, the quadratic longitudinal susceptibility χ{sup (2)}), which describes the second-order response of a plasma to electrostatic wave fields. Previous calculations of these rates for an unmagnetized Maxwellian plasma have relied upon an approximate form for α{sup (2)} that is valid where two of the wave fields are fast (i.e., v{sub φ}=ω/k≫V{sub e} where ω is the angular frequency, k is the wavenumber, and V{sub e} is the electron thermal speed) and one is slow (v{sub φ}≪V{sub e}). Recently, an exact expression was derived for α{sup (2)} that is valid for any phase speeds of the three waves in an unmagnetized Maxwellian plasma. Here, this exact α{sup (2)} is applied to the calculation of the three-dimensional rates for electrostatic decay and scattering off thermal ions, and the resulting exact rates are compared with the approximate rates. The calculations are performed using previously derived three-dimensional rates for electrostatic decay given in terms of a general α{sup (2)}, and newly derived three-dimensional rates for scattering off thermal ions; the scattering rate is derived assuming a Maxwellian ion distribution, and both rates are derived assuming arc distributions for the wave spectra. For most space plasma conditions, the approximate rate is found to be accurate to better than 20%; however, for sufficiently low Langmuir phase speeds (v{sub φ}/V{sub e}≈3) appropriate to some spatial domains of the foreshock regions of planetary bow shocks and type II solar radio bursts, the use of the exact rate may be necessary for accurate calculations. The relative rates of electrostatic decay

  18. Edutainment Science: Electrostatics

    Science.gov (United States)

    Ahlers, Carl

    2009-01-01

    Electrostatics should find a special place in all primary school science curricula. It is a great learning area that reinforces the basics that underpin electricity and atomic structure. Furthermore, it has many well documented hands-on activities. Unfortunately, the "traditional" electrostatics equipment such as PVC rods, woollen cloths, rabbit…

  19. Permanganate oxidation of alkenes. Substituent and solvent effects. Difficulties with MP2 calculations

    Czech Academy of Sciences Publication Activity Database

    Wiberg, K. B.; Wang, Y.; Sklenák, Štěpán; Deutsch, C.; Trucks, G.

    2006-01-01

    Roč. 128, č. 35 (2006), s. 11537-11544 ISSN 0002-7863 Grant - others:National Science Foundation Grant(US) CHE-0445847 Institutional research plan: CEZ:AV0Z40400503 Keywords : density-functional theory * polarizable continuum model * fumaric acids Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 7.696, year: 2006

  20. Calculation of spectral shifts in UV-visible region and photoresponsive behaviour of fluorinated liquid crystals: Effect of solvent and substituent

    Energy Technology Data Exchange (ETDEWEB)

    Lakshmi Praveen, P. [Liquid Crystal Research Laboratory, Post-Graduate Department of Physics, Andhra Loyola College, Vijayawada 520 008, A.P. (India); Ojha, Durga P., E-mail: durga_ojha@hotmail.com [Liquid Crystal Research Laboratory, Post-Graduate Department of Physics, Andhra Loyola College, Vijayawada 520 008, A.P. (India)

    2012-08-15

    The photoresponsive behaviour of fluorinated liquid crystals p-phenylene-4-methoxy benzoate-4-trifluoromethylbenzoate (FLUORO1), and 4-propyloxyphenyl-4-(4-trifluoromethylbenzoyloxy) benzoate (FLUORO2) has been systematically investigated using the CNDO/S + CI and INDO/S + CI methods. These methods have been employed to calculate/analyze the spectral shifts, and absorbance measurements in UV-visible region of the systems. The electronic transitions, absorption wavelength, HOMO (highest occupied molecular orbital), and LUMO (lowest unoccupied molecular orbital) energies have been calculated. Further, ultraviolet (UV) stability of the molecules has been discussed in the light of absorption wavelength and electronic transition oscillator strength (f). The effect of different solvent media and substituents on transition energies, oscillator strength, and other absorption parameters have also been reported. The present article provides valuable information regarding enhancing the UV stability of molecules by marinating their conductivity. Highlights: Black-Right-Pointing-Pointer The strongest bands of FLUORO molecules can be assigned as {pi} {yields} {pi}{sup Asterisk-Operator} transitions. Black-Right-Pointing-Pointer A small red-shift indicates a weak exciton coupling of chromophores. Black-Right-Pointing-Pointer No n {yields} {pi}{sup Asterisk-Operator} transition occurs due to the rigidity of the ring system of the molecules. Black-Right-Pointing-Pointer The HOMO, LUMO, and E{sub g} values have been found to be independent of solvent effect.

  1. Continuum mechanics of anisotropic materials

    CERN Document Server

    Cowin, Stephen C

    2013-01-01

    Continuum Mechanics of Anisotropic Materials(CMAM) presents an entirely new and unique development of material anisotropy in the context of an appropriate selection and organization of continuum mechanics topics. These features will distinguish this continuum mechanics book from other books on this subject. Textbooks on continuum mechanics are widely employed in engineering education, however, none of them deal specifically with anisotropy in materials. For the audience of Biomedical, Chemical and Civil Engineering students, these materials will be dealt with more frequently and greater accuracy in their analysis will be desired. Continuum Mechanics of Anisotropic Materials' author has been a leader in the field of developing new approaches for the understanding of anisotropic materials.

  2. Glutathione reductase: solvent equilibrium and kinetic isotope effects

    International Nuclear Information System (INIS)

    Wong, K.K.; Vanoni, M.A.; Blanchard, J.S.

    1988-01-01

    Glutathione reductase catalyzes the NADPH-dependent reduction of oxidized glutathione (GSSG). The kinetic mechanism is ping-pong, and we have investigated the rate-limiting nature of proton-transfer steps in the reactions catalyzed by the spinach, yeast, and human erythrocyte glutathione reductases using a combination of alternate substrate and solvent kinetic isotope effects. With NADPH or GSSG as the variable substrate, at a fixed, saturating concentration of the other substrate, solvent kinetic isotope effects were observed on V but not V/K. Plots of Vm vs mole fraction of D 2 O (proton inventories) were linear in both cases for the yeast, spinach, and human erythrocyte enzymes. When solvent kinetic isotope effect studies were performed with DTNB instead of GSSG as an alternate substrate, a solvent kinetic isotope effect of 1.0 was observed. Solvent kinetic isotope effect measurements were also performed on the asymmetric disulfides GSSNB and GSSNP by using human erythrocyte glutathione reductase. The Km values for GSSNB and GSSNP were 70 microM and 13 microM, respectively, and V values were 62 and 57% of the one calculated for GSSG, respectively. Both of these substrates yield solvent kinetic isotope effects greater than 1.0 on both V and V/K and linear proton inventories, indicating that a single proton-transfer step is still rate limiting. These data are discussed in relationship to the chemical mechanism of GSSG reduction and the identity of the proton-transfer step whose rate is sensitive to solvent isotopic composition. Finally, the solvent equilibrium isotope effect measured with yeast glutathione reductase is 4.98, which allows us to calculate a fractionation factor for the thiol moiety of GSH of 0.456

  3. Ions kinematics in an electrostatic ion beam trap

    Energy Technology Data Exchange (ETDEWEB)

    Attia, D

    2004-06-01

    In this study, I have tried to provide a better understanding of the dynamics of ions inside an electrostatic ion beam trap. The electrostatic ion trap allows to store ions moving between two electrostatic mirrors. Although the trap has been developed already seven years ago, no direct measurement of the transversal velocity distribution of the ions has been performed. Such quantity is central for understanding the conditions under which a beam should be produced (mainly emittance) in order to be trapped by such a device. The data I have obtained during the course of this work are based on an experimental technique which relies on the direct imaging of the particles exiting the trap, as well as on numerical simulations of the ion trajectories inside the trap. I have personally been involved in the hardware development of the imaging system, the data acquisition and analysis of the data as well as il all numerical calculations presented here. These results allow us to obtain, for the first time, experimental information on the transverse phase space of the trap, and contribute to the overall understanding of the ion motion in this system. (author)

  4. Development of coaxial speaker-like non-contact electrostatic sensor for aviation engine exhaust electrostatic character research

    Directory of Open Access Journals (Sweden)

    Du Zhaoheng

    2015-01-01

    Full Text Available Electrostatic sensor is the most important equipment in aero-engine exhaust electrostatic character research. By comparing a variety of sensor test programs, the coaxial speaker-like noncontact electrostatic sensor program is proposed. Numerical simulation analysis indicates the electric field distribution of electrostatic sensor, the influence principle of gap width, outer diameter, center diameter, angle and other factors on the sensor capacitance values which identify the key indicators of electrostatic sensor. The experiment test shows that the simulation analysis is in good agreement with the experimental results.

  5. Effect of ionic strength on the kinetics of ionic and micellar reactions in aqueous solution

    International Nuclear Information System (INIS)

    Dung, M.H.; Kozak, J.J.

    1982-01-01

    The effect of electrostatic forces on the rate of reaction between ions in aqueous solutions of intermediate ionic strength is studied in this paper. We consider the kinetics of reactions involving simple ionic species (1--1 and 2--2 electrolyte systems) as well as kinetic processes mediated by the presence of micellar ions (or other charged organizates). In the regime of ionic strength considered, dielectric saturation of the solvent in the vicinity of the reacting ions must be taken into account and this is done by introducing several models to describe the recovery of the solvent from saturation to its continuum dielectric behavior. To explore the effects of ion size, charge number, and ionic strength on the overall rate constant for the process considered, we couple the traditional theory of ionic reactions in aqueous solution with calculations of the electrostatic potential obtained via solution of the nonlinear Poisson--Boltzmann equation. The great flexibility of the nonlinear Poisson--Boltzmann theory allows us to explore quantitatively the influence of each of these effects, and our simulations show that the short-range properties of the electrostatic potential affect primarily kinetically controlled processes (to varying degrees, depending on the ionic system considered) whereas the down-range properties of the potential play a (somewhat) greater role in influencing diffusion-controlled processes. A detailed examination is made of ionic strength effects over a broad range of ionic concentrations. In the regime of low ionic strength, the limiting slope and intercept of the curve describing the dependence of log k/sub D/ on I/sup 1/2//(1+I/sup 1/2/) may differ considerably from the usual Debye--Hueckel limiting relations, depending on the particular model chosen to describe local saturation effects

  6. Continuum robots and underactuated grasping

    Directory of Open Access Journals (Sweden)

    N. Giri

    2011-02-01

    Full Text Available We discuss the capabilities of continuum (continuous backbone robot structures in the performance of under-actuated grasping. Continuum robots offer the potential of robust grasps over a wide variety of object classes, due to their ability to adapt their shape to interact with the environment via non-local continuum contact conditions. Furthermore, this capability can be achieved with simple, low degree of freedom hardware. However, there are practical issues which currently limit the application of continuum robots to grasping. We discuss these issues and illustrate via an experimental continuum grasping case study.

    This paper was presented at the IFToMM/ASME International Workshop on Underactuated Grasping (UG2010, 19 August 2010, Montréal, Canada.

  7. A Study of Electrostatic Charge on Insulating Film by Electrostatic Force Microscopy

    International Nuclear Information System (INIS)

    Kikunaga, K; Toosaka, K; Kamohara, T; Sakai, K; Nonaka, K

    2011-01-01

    Electrostatic charge properties on polypropylene film have been characterized by atomic force microscopy and electrostatic force microscopy. The measurements have been carried out after the polypropylene film was electrified by contact and separation process in an atmosphere of controlled humidity. The negative and positive charge in concave surface has been observed. The correlation between concave surface and charge position suggests that the electrostatic charges could be caused by localized contact. On the other hand, positive charge on a flat surface has been observed. The absence of a relationship between surface profile and charge position suggests that the electrostatic charge should be caused by discharge during the separation process. The spatial migration of other positive charges through surface roughness has been observed. The results suggest that there could be some electron traps on the surface roughness and some potentials on the polypropylene film.

  8. Dirac gap-induced graphene quantum dot in an electrostatic potential

    Science.gov (United States)

    Giavaras, G.; Nori, Franco

    2011-04-01

    A spatially modulated Dirac gap in a graphene sheet leads to charge confinement, thus enabling a graphene quantum dot to be formed without the application of external electric and magnetic fields [G. Giavaras and F. Nori, Appl. Phys. Lett. 97, 243106 (2010)]. This can be achieved provided the Dirac gap has a local minimum in which the states become localized. In this work, the physics of such a gap-induced dot is investigated in the continuum limit by solving the Dirac equation. It is shown that gap-induced confined states couple to the states introduced by an electrostatic quantum well potential. Hence the region in which the resulting hybridized states are localized can be tuned with the potential strength, an effect which involves Klein tunneling. The proposed quantum dot may be used to probe quasirelativistic effects in graphene, while the induced confined states may be useful for graphene-based nanostructures.

  9. Electrostatic accelerators

    CERN Document Server

    Hinterberger, F

    2006-01-01

    The principle of electrostatic accelerators is presented. We consider Cockcroft– Walton, Van de Graaff and Tandem Van de Graaff accelerators. We resume high voltage generators such as cascade generators, Van de Graaff band generators, Pelletron generators, Laddertron generators and Dynamitron generators. The speci c features of accelerating tubes, ion optics and methods of voltage stabilization are described. We discuss the characteristic beam properties and the variety of possible beams. We sketch possible applications and the progress in the development of electrostatic accelerators.

  10. Permeability of commercial solvents through living human skin

    DEFF Research Database (Denmark)

    Ursin, C; Hansen, C M; Van Dyk, J W

    1995-01-01

    A procedure has been developed for measuring the steady state rate of permeation of commercial solvents through living human skin. To get the most consistent results, it was necessary with some solvents to normalize the solvent permeation rate of a given skin sample with its [3H]water permeation...... rate. For other solvents this was not necessary, so the un-normalized data were used. High [3H]water permeation rate also was used as a criterion for "defective" skin samples that gave erroneous permeability rates, especially for solvents having slow permeability. The linearity of the steady state data...... was characterized by calculation of the "percent error of the slope." The following permeability rates (g/m2h) of single solvents were measured: dimethyl sulfoxide (DMSO), 176; N-methyl-2-pyrrolidone, 171; dimethyl acetamide, 107; methyl ethyl ketone, 53; methylene chloride, 24; [3H]water, 14.8; ethanol, 11...

  11. NMR investigation and theoretical calculations of the solvent effect on the conformation of valsartan

    Science.gov (United States)

    Chashmniam, Saeed; Tafazzoli, Mohsen

    2017-11-01

    Structure and conformational properties of valsartan were studied by advanced NMR techniques and quantum calculation methods. Potential energy scanning using B3LYP/6-311++g** and B3LYP-D3/6-311++g** methods were performed and four conformers (V1-V4) at minimum points of PES diagram were observed. According to the NMR spectra in acetone-d6, there are two conformers (M and m) with m/M = 0.52 ratio simultaneously and energy barriers of the two conformers were predicted from chemical shifts and multiplicities. While, intramolecular hydrogen bond at tetrazole ring and carboxylic groups prevent the free rotation on N6sbnd C11 bond in M-conformer, this bond rotates freely in m-conformer. On the other hand, intramolecular hydrogen bond at carbonyl and carboxylic acid can be observed at m-conformer. So, different intramolecular hydrogen bond is the reason for the stability of both M and m structures. Quite interestingly, 1H NMR spectra in CDCl3 show two distinct conformers (N and n) with unequal ratio which are differ from M-m conformers. Also, intramolecular hydrogen bond seven-member ring involving five-membered tetrazole ring and carboxylic acid group observed in both N and n-conformers Solvent effect, by using a set of polar and non-polar solvents including DMSO-d6, methanol-d4, benzene-d6, THF-d8, nitromethane-d3, methylene chloride-d2 and acetonitrile-d3 were investigated. NMR parameters include chemical shifts and spin-spin coupling constants were obtained from a set of 2D NMR spectra (H-H COSY, HMQC and HMBC). For this purpose, several DFT functionals from LDA, GGA and hybrid categories were used which the hybrid method showed better agreement with experiment values.

  12. Electrostatics in Chemistry

    Indian Academy of Sciences (India)

    characteristics and applications of the electrostatic potential of many-electron atoms, ions and molecules are discussed. Electrostatic Potential of Atoms and Singly. Charged ..... [6] R K Pathak and S R Gadre,J. Chat. Phys., 93, 1770, 1990. [7] S R Gadre, S A Kalkarni and I H Shrivastava,J. Chern. Phys., 96,52;3,. 1992. ~ .1.

  13. Lunar electrostatic effects and protection

    International Nuclear Information System (INIS)

    Sun, Yongwei; Yuan, Qingyun; Xiong, Jiuliang

    2013-01-01

    The space environment and features on the moon surface are factors in strong electrostatic electrification. Static electricity will be produced in upon friction between lunar soil and detectors or astronauts on the lunar surface. Lunar electrostatic environment effects from lunar exploration equipment are very harmful. Lunar dust with electrostatic charge may enter the equipment or even cover the instruments. It can affect the normal performance of moon detectors. Owing to the huge environmental differences between the moon and the earth, the electrostatic protection technology on the earth can not be applied. In this paper, we review the electrostatic characteristics of lunar dust, its effects on aerospace equipment and moon static elimination technologies. It was concluded that the effect of charged lunar dust on detectors and astronauts should be completely researched as soon as possible.

  14. Analytical calculation of geometric and chromatic aberrations in a bi-potential electrostatic and bell-shaped magnetic combined lens

    International Nuclear Information System (INIS)

    Ximen Jiye; Liu Zhixiong

    2000-01-01

    In the present paper, Gaussian optical property in the bi-potential electrostatic and the bell-shaped magnetic combined lens - a new theoretical model first proposed in electron optics - has been thoroughly studied. Meanwhile, based on electron optical canonical aberration theory, analytical formulas of third-order geometrical and first-order chromatic aberration coefficients and their computational results have first been derived for this bi-potential electrostatic and bell-shaped magnetic combined lens. It is to emphasized that this theoretical study can be used to estimate third-order geometric and first-order chromatic aberrations and to provide a theoretical criterion for numerical computation in a rotationally symmetric electromagnetic lens

  15. Triple-probe method applied to the direct display of plasma parameters in a supersonic flowing continuum plasma

    International Nuclear Information System (INIS)

    Ogram, G.L.; Chang, J.; Hobson, R.M.

    1979-01-01

    The calibration of electrostatic triple-probe voltage and current response in a supersonic continuum plasma has been carried out using a low-pressure shock tube. The electron temperature T/sub e/ and charge number density N/sub e/ are compared to probe voltage and current response, respectively, for a useful range of plasma parameters (1 13 13 is the nondimensional probe voltage). The dependence of probe response on Debye ratio R/sub p//lambda/sub D/ and various flow parameters was investigated. The probe voltage response was found to depend significantly on the Debye ratio. Expressions for electron temperature determination by triple probe are presented

  16. Continuum mechanics

    CERN Document Server

    Spencer, A J M

    2004-01-01

    The mechanics of fluids and the mechanics of solids represent the two major areas of physics and applied mathematics that meet in continuum mechanics, a field that forms the foundation of civil and mechanical engineering. This unified approach to the teaching of fluid and solid mechanics focuses on the general mechanical principles that apply to all materials. Students who have familiarized themselves with the basic principles can go on to specialize in any of the different branches of continuum mechanics. This text opens with introductory chapters on matrix algebra, vectors and Cartesian ten

  17. Continuum shell-model study of 16O and 40Ca

    International Nuclear Information System (INIS)

    Heil, V.; Stock, W.

    1976-06-01

    Continuum shell-model calculations of the E1 and E2 strengths in 16 O and 40 Ca are presented. A consistent microscopic description of both the giant resonances and isospin forbidden E1- transitions between bound states can be achieved through 1) a careful choice of the single-particle potential, 2) the use of a finite-range residual interaction (including the Coulomb particle-hole force), and 3) the removal of spurious states. The results obtained within the separation expansion approximation of Birkholz are in reasonable agreement with measured photonucleon angular distributions and formfactors for electroexcitation. The influence of the continuum on the isospin mixing in bound states is found to be very strong. (orig.) [de

  18. Coupling effects of resonant and discretized non-resonant continuum states in 4He+6Li scattering at 10 MeV/A

    International Nuclear Information System (INIS)

    Sinha, T.; Kanungo, R.; Samanta, C.; Ghosh, S.; Basu, P.; Rebel, H.

    1996-01-01

    Alpha- particle scattering from the resonant (3 + 1 ) and non-resonant continuum states of 6 Li is studied at incident energy 10 MeV/A. The α+d breakup continuum part within the excitation energy E ex = 1.475-2.475 MeV is discretized in two energy bins. Unlike the results at higher incident energies, here the coupled-channel calculations show significant breakup continuum coupling effects on the elastic and inelastic scattering. It is shown that even when the continuum-continuum coupling effects are strong, the experimental data of the ground state and the resonant as well as discretized non-resonant continuum states impose stringent constraint on the coupling strengths of the non-resonant continuum states. (orig.). With 2 figs., 1 tab

  19. Experimental and Computational Approaches to the Molecular Structure of 3-(2-Mercaptopyridine)phthalonitrile

    International Nuclear Information System (INIS)

    Tanak, Hasan; Koysal, Yavuz; Isik, Samil; Yaman, Hanifi; Ahsen, Vefa

    2011-01-01

    The compound 3-(2-Mercaptopyridine)phthalonitrile has been synthesized and characterized by IR, UV-vis, and X-ray single-crystal determination. The molecular geometry from X-ray determination of the title compound in the ground state has been compared using the Hartree-Fock (HF) and density functional theory (DFT) with the 6-31G(d) basis set. The calculated results show that the DFT and HF can well reproduce the structure of the title compound. The energetic behavior of the title compound in solvent media was examined using the B3LYP method with the 6-31G(d) basis set by applying the Onsager and polarizable continuum model. Using the TD-DFT and TD-HF methods, electronic absorption spectra of the title compound have been predicted and good agreement with the TD-DFT method and the experimental determination was found. The predicted nonlinear optical properties of the title compound are much greater than those of urea. Besides, molecular electrostatic potential of the title compound were investigated by theoretical calculations. The thermodynamic properties of the compound at different temperatures have been calculated and corresponding relations between the properties and temperature have also been obtained

  20. Experimental and Computational Approaches to the Molecular Structure of 3-(2-Mercaptopyridine)phthalonitrile

    Energy Technology Data Exchange (ETDEWEB)

    Tanak, Hasan [Amasya University, Amasys (Turkmenistan); Koysal, Yavuz; Isik, Samil [Ondokuz Mayis University, Samsun (Turkmenistan); Yaman, Hanifi; Ahsen, Vefa [Gebze Institute of Technology Department of Chemistry, Gebze-Kocaeli (Turkmenistan)

    2011-02-15

    The compound 3-(2-Mercaptopyridine)phthalonitrile has been synthesized and characterized by IR, UV-vis, and X-ray single-crystal determination. The molecular geometry from X-ray determination of the title compound in the ground state has been compared using the Hartree-Fock (HF) and density functional theory (DFT) with the 6-31G(d) basis set. The calculated results show that the DFT and HF can well reproduce the structure of the title compound. The energetic behavior of the title compound in solvent media was examined using the B3LYP method with the 6-31G(d) basis set by applying the Onsager and polarizable continuum model. Using the TD-DFT and TD-HF methods, electronic absorption spectra of the title compound have been predicted and good agreement with the TD-DFT method and the experimental determination was found. The predicted nonlinear optical properties of the title compound are much greater than those of urea. Besides, molecular electrostatic potential of the title compound were investigated by theoretical calculations. The thermodynamic properties of the compound at different temperatures have been calculated and corresponding relations between the properties and temperature have also been obtained.

  1. Charged patchy particle models in explicit salt: Ion distributions, electrostatic potentials, and effective interactions.

    Science.gov (United States)

    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.

  2. Continuum limbed robots for locomotion

    Science.gov (United States)

    Mutlu, Alper

    This thesis focuses on continuum robots based on pneumatic muscle technology. We introduce a novel approach to use these muscles as limbs of lightweight legged robots. The flexibility of the continuum legs of these robots offers the potential to perform some duties that are not possible with classical rigid-link robots. Potential applications are as space robots in low gravity, and as cave explorer robots. The thesis covers the fabrication process of continuum pneumatic muscles and limbs. It also provides some new experimental data on this technology. Afterwards, the designs of two different novel continuum robots - one tripod, one quadruped - are introduced. Experimental data from tests using the robots is provided. The experimental results are the first published example of locomotion with tripod and quadruped continuum legged robots. Finally, discussion of the results and how far this technology can go forward is presented.

  3. A density functional and quantum Monte Carlo study of glutamic acid in vacuo and in a dielectric continuum medium

    NARCIS (Netherlands)

    Floris, F.; Filippi, Claudia; Amovilli, C.

    2012-01-01

    We present density functional theory (DFT) and quantum Monte Carlo (QMC) calculations of the glutamic acid and glutamate ion in vacuo and in various dielectric continuum media within the polarizable continuum model (PCM). In DFT, we employ the integral equation formalism variant of PCM while, in

  4. Molecular recognition in a diverse set of protein-ligand interactions studied with molecular dynamics simulations and end-point free energy calculations.

    Science.gov (United States)

    Wang, Bo; Li, Liwei; Hurley, Thomas D; Meroueh, Samy O

    2013-10-28

    End-point free energy calculations using MM-GBSA and MM-PBSA provide a detailed understanding of molecular recognition in protein-ligand interactions. The binding free energy can be used to rank-order protein-ligand structures in virtual screening for compound or target identification. Here, we carry out free energy calculations for a diverse set of 11 proteins bound to 14 small molecules using extensive explicit-solvent MD simulations. The structure of these complexes was previously solved by crystallography and their binding studied with isothermal titration calorimetry (ITC) data enabling direct comparison to the MM-GBSA and MM-PBSA calculations. Four MM-GBSA and three MM-PBSA calculations reproduced the ITC free energy within 1 kcal·mol(-1) highlighting the challenges in reproducing the absolute free energy from end-point free energy calculations. MM-GBSA exhibited better rank-ordering with a Spearman ρ of 0.68 compared to 0.40 for MM-PBSA with dielectric constant (ε = 1). An increase in ε resulted in significantly better rank-ordering for MM-PBSA (ρ = 0.91 for ε = 10), but larger ε significantly reduced the contributions of electrostatics, suggesting that the improvement is due to the nonpolar and entropy components, rather than a better representation of the electrostatics. The SVRKB scoring function applied to MD snapshots resulted in excellent rank-ordering (ρ = 0.81). Calculations of the configurational entropy using normal-mode analysis led to free energies that correlated significantly better to the ITC free energy than the MD-based quasi-harmonic approach, but the computed entropies showed no correlation with the ITC entropy. When the adaptation energy is taken into consideration by running separate simulations for complex, apo, and ligand (MM-PBSAADAPT), there is less agreement with the ITC data for the individual free energies, but remarkably good rank-ordering is observed (ρ = 0.89). Interestingly, filtering MD snapshots by prescoring

  5. Cesium Concentration in MCU Solvent

    International Nuclear Information System (INIS)

    Walker, D

    2006-01-01

    During Modular Caustic-Side Solvent Extraction (CSSX) Unit (MCU) operations, Cs-137 concentrations in product streams will vary depending on the location in the process and on the recent process conditions. Calculations of cesium concentrations under a variety of operating conditions reveal the following: (1) Under nominal operations with salt solution feed containing 1.1 Ci Cs-137 per gallon, the maximum Cs-137 concentration in the process will occur in the strip effluent (SE) and equal 15-16.5 Ci/gal. (2) Under these conditions, the majority of the solvent will contain 0.005 to 0.01 Ci/gal, with a limited portion of the solvent in the contactor stages containing ∼4 Ci/gal. (3) When operating conditions yield product near 0.1 Ci Cs-137/gal in the decontaminated salt solution (DSS), the SE cesium concentration will be the same or lower than in nominal operations, but majority of the stripped solvent will increase to ∼2-3 Ci/gal. (4) Deviations in strip and waste stream flow rates cause the largest variations in cesium content: (a) If strip flow rates deviate by -30% of nominal, the SE will contain ∼23 Ci/gal, although the cesium content of the solvent will increase to only 0.03 Ci/gal; (b) If strip flow rate deviates by -77% (i.e., 23% of nominal), the SE will contain 54 Ci/gal and solvent will contain 1.65 Ci/gal. At this point, the product DSS will just reach the limit of 0.1 Ci/gal, causing the DSS gamma monitors to alarm; and (c) Moderate (+10 to +30%) deviations in waste flow rate cause approximately proportional increases in the SE and solvent cesium concentrations. Recovery from a process failure due to poor cesium stripping can achieve any low cesium concentration required. Passing the solvent back through the contactors while recycling DSS product will produce a ∼70% reduction during one pass through the contactors (assuming the stripping D value is no worse than 0.36). If the solvent is returned to the solvent hold tank (containing additional

  6. Investigation of the sensitivity of visible continuum Zeff(0) to edge radiation

    International Nuclear Information System (INIS)

    Telesca, G.; Oost, G. Van; Ongena, J.; Leys, C.; Schoon, N.

    1992-01-01

    The determination of Z eff from visible continuum radiation is based on the assumption that the line-integrated continuum signal is mostly composed of bremsstrahlung radiation. In practice a wavelength window relatively free of spectral lines is selected, and the line-integrated continuum signal along different chords from the edge up to the central plasma is measured. The local emissivity ε(r) is then calculated using an Abel inversion procedure, and the Z eff profile can be obtained. Although theory and techniques are well established, in any experimental device there remains an uncertainty in the calculated value of Z eff due to the non-bremsstrahlung radiation from the cooler edge plasma (e.g. emission from recombination and molecular bands). As a consequence, the local bremsstrahlung emissivity in the outer region of the plasma cannot be determined and the signal measured along every chord through the plasma contains a spurious contribution. In this paper the error in the value of the central plasma emissivity (and Z eff ) due to edge radiation has been investigated. Qualitative analytical considerations have been complemented by a qualitative analysis, consisting of the comparison of test emissivity profiles with Abel-inverted profiles obtained from the integrals along central chords only. (author) 5 refs., 5 figs

  7. Investigation of an inventory calculation model for a solvent extraction system and the development of its computer programme - SEPHIS-J

    International Nuclear Information System (INIS)

    Ihara, Hitoshi; Nishimura, Hideo; Ikawa, Koji; Ido, Masaru.

    1986-11-01

    In order to improve the applicability of near-real-time materials accountancy (N.R.T.MA) to a reprocessing plant, it is necessary to develop an estimation method for the nuclear material inventory at a solvent extraction system under operation. For designing the solvent extraction system, such computer codes as SEPHIS, SOLVEX and TRANSIENTS had been used. Accuracy of these codes in tracing operations and predicting inventories in the extraction system had been discussed. Then, much better codes, e.g., SEPHIS Mod4 and PUBG, were developed. Unfortunately, SEPHIS Mod4 was not available in countries other than the USA and PUBG was not suitable for use with a mini-computer which would be practical as a field computer because of quite a lot of computing time needed. The authors investigated an inventory estimation model compatible with PUBG in functions and developed the corresponding computer programme, SEPHIS-J, based on the SEPHIS Mod3 code, resulting in a third of computing time compared with PUBG. They also validated the programme by calculating a static state as well as a dynamic one of the solvent extraction process and by comparing them among the programme, SEPHIS Mod3 and PUBG. Using the programme, it was shown that the inventory changes due to changes of feed flow and concentration were not so small that they might be neglected although the changes of feed flow and concentration were within measurement errors. (author)

  8. Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes

    Czech Academy of Sciences Publication Activity Database

    Gkionis, Konstantinos; Kruse, Holger; Šponer, Jiří

    2016-01-01

    Roč. 12, č. 4 (2016), s. 2000-2016 ISSN 1549-9618 R&D Projects: GA ČR(CZ) GAP208/11/1822 Institutional support: RVO:68081707 Keywords : molecular-dynamics simulations * quantum-chemical computations * continuum solvation models Subject RIV: BO - Biophysics Impact factor: 5.245, year: 2016

  9. Continuum limit of gl(M vertical stroke N) spin chains

    International Nuclear Information System (INIS)

    Candu, Constantin

    2011-03-01

    We study the spectrum of an integrable antiferromagnetic Hamiltonian of the gl(M vertical stroke N) spin chain of alternating fundamental and dual representations. After extensive numerical analysis, we identify the vacuum and low lying excitations and with this knowledge perform the continuum limit, while keeping a finite gap. All antiferromagnetic gl(n+N vertical stroke N) spin chains with n>0 and N≠0 are shown to possess in the continuum limit 2n-2 multiplets of massive particles which scatter with gl(n) Gross-Neveu like S-matrices, namely their eigenvalues do not depend on N. We argue that the continuum theory is the gl(M vertical stroke N) Gross-Neveu model, that is the massive deformation of the gl(M vertical stroke N) 1 Wess-Zumino-Witten model. As we can see ion the example of gl(2m vertical stroke 1) spin chains, the full particle spectrum is much richer. Our analysis suggests that for a complete characterization of the latter it is not enough to restrict to large volume calculations, as we do in this work. (orig.)

  10. Modification of equivalent charge method for the Roben three-dimensional problem in electrostatics

    International Nuclear Information System (INIS)

    Barsukov, A.B.; Surenskij, A.V.

    1989-01-01

    The approach of the Roben problem solution for the calculation of the potential of intermediate electrode of accelerating structure with HFQ focusing is considered. The solution is constructed on the basis of variational formulation of the equivalent charge method, where electrostatic problem is reduced to equations of root-mean-square residuals on the system conductors. The technique presented permits to solve efficiently the three-dimensional problems of electrostatics for rather complicated from geometrical viewpoint systems of electrodes. Processing time is comparable with methods of integral equations. 5 refs.; 2 figs

  11. Accurate pKa calculation of the conjugate acids of alkanolamines, alkaloids and nucleotide bases by quantum chemical methods.

    Science.gov (United States)

    Gangarapu, Satesh; Marcelis, Antonius T M; Zuilhof, Han

    2013-04-02

    The pKa of the conjugate acids of alkanolamines, neurotransmitters, alkaloid drugs and nucleotide bases are calculated with density functional methods (B3LYP, M08-HX and M11-L) and ab initio methods (SCS-MP2, G3). Implicit solvent effects are included with a conductor-like polarizable continuum model (CPCM) and universal solvation models (SMD, SM8). G3, SCS-MP2 and M11-L methods coupled with SMD and SM8 solvation models perform well for alkanolamines with mean unsigned errors below 0.20 pKa units, in all cases. Extending this method to the pKa calculation of 35 nitrogen-containing compounds spanning 12 pKa units showed an excellent correlation between experimental and computational pKa values of these 35 amines with the computationally low-cost SM8/M11-L density functional approach. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Electrostatic attraction between overall neutral surfaces.

    Science.gov (United States)

    Adar, Ram M; Andelman, David; Diamant, Haim

    2016-08-01

    Two overall neutral surfaces with positively and negatively charged domains ("patches") have been shown in recent experiments to exhibit long-range attraction when immersed in an ionic solution. Motivated by the experiments, we calculate analytically the osmotic pressure between such surfaces within the Poisson-Boltzmann framework, using a variational principle for the surface-averaged free energy. The electrostatic potential, calculated beyond the linear Debye-Hückel theory, yields an overall attraction at large intersurface separations, over a wide range of the system's controlled length scales. In particular, the attraction is stronger and occurs at smaller separations for surface patches of larger size and charge density. In this large patch limit, we find that the attraction-repulsion crossover separation is inversely proportional to the square of the patch-charge density and to the Debye screening length.

  13. Solvents effects on crystallinity and dissolution of β-artemether.

    Science.gov (United States)

    Xu, Jianghui; Singh, Vikramjeet; Yin, Xianzhen; Singh, Parbeen; Wu, Li; Xu, Xiaonan; Guo, Tao; Sun, Lixin; Gui, Shuangying; Zhang, Jiwen

    2017-03-01

    β-artemether (ARM) is a widely used anti-malarial drug isolated from the Chinese antimalarial plant, Artemisia annua. The solvent effects on crystal habits and dissolution of ARM were thoroughly investigated and discussed herein. The ARM was recrystallized in nine different solvents of varied polarity, namely, methanol, ethanol, isopropanol, tetrahydrofuran, dichloromethane, trichloromethane, ethyl acetate, acetone and hexane by solvent evaporation method. The obtained crystals were morphologically characterized using scanning electron microscope (SEM). The average sizes of crystals were 1.80-2.64 μm calculated from microscopic images using Image-Pro software. No significant change in chemical structure was noticed after recrystallization and the specific band at 875 cm -1 wavenumber (C-O-O-C) confirmed the presence of most sensitive functional group in the ARM chemical structure. The existence and production of two polymorphic forms, polymorph A and polymorph B, was confirmed by differential scanning calorimetry (DSC) and powder X-ray diffraction (PXRD). The data suggested that the fabrication of polymorph B can be simply obtained from the recrystallization of ARM in a specific solvent. Significant effects of solvent polarity, crystals shapes and sizes on drug dissolution were noticed during in vitro dissolution test. The release kinetics were calculated and well fitted by the Higuchi and Hixon-Crowell models. The ARM-methanol and ARM-hexane showed highest and slowest dissolution, respectively, due to the effects of solvent polarity and crystal morphologies. Overall, proper selection of the solvents for the final crystallization of ARM helps to optimize dissolution and bioavailability for a better delivery of anti-malarial drug.

  14. Polarizable atomistic calculation of site energy disorder in amorphous Alq3.

    Science.gov (United States)

    Nagata, Yuki

    2010-02-01

    A polarizable molecular dynamics simulation and calculation scheme for site energy disorder is presented in amorphous tris(8-hydroxyquinolinato)aluminum (Alq(3)) by means of the charge response kernel (CRK) method. The CRK fit to the electrostatic potential and the tight-binding approximation are introduced, which enables modeling of the polarizable electrostatic interaction for a large molecule systematically from an ab initio calculation. The site energy disorder for electron and hole transfers is calculated in amorphous Alq(3) and the effect of the polarization on the site energy disorder is discussed.

  15. The Virtuality Continuum Revisited

    NARCIS (Netherlands)

    Nijholt, Antinus; Traum, D.; Zhai, Sh.; Kellogg, W.

    2005-01-01

    We survey the themes and the aims of a workshop devoted to the state-of-the-art virtuality continuum. In this continuum, ranging from fully virtual to real physical environments, allowing for mixed, augmented and desktop virtual reality, several perspectives can be taken. Originally, the emphasis

  16. Properties of warm nuclei in the quasi-continuum

    Directory of Open Access Journals (Sweden)

    Voinov A.

    2010-03-01

    Full Text Available Nuclear thermodynamic quantities are extracted from nuclear level densities measured with the CACTUS detector array at the Oslo Cyclotron Laboratory. The experiments are performed with light-particle inelastic or transfer reactions. A simple combinatorial model is used to describe the underlying mechanisms responsible for the exponential increasing level density as function of excitation energy. The calculated number of broken Cooper pairs and the parity distribution in continuum are discussed.

  17. The first step in layer-by-layer deposition: Electrostatics and/or non-electrostatics?

    NARCIS (Netherlands)

    Lyklema, J.; Deschênes, L.

    2011-01-01

    A critical discussion is presented on the properties and prerequisites of adsorbed polyelectrolytes that have to function as substrates for further layer-by-layer deposition. The central theme is discriminating between the roles of electrostatic and non-electrostatic interactions. In order to

  18. Solid–liquid phase equilibrium and dissolution properties of ethyl vanillin in pure solvents

    International Nuclear Information System (INIS)

    Wu, Hao; Wang, Jingkang; Zhou, Yanan; Guo, Nannan; Liu, Qi; Zong, Shuyi; Bao, Ying; Hao, Hongxun

    2017-01-01

    Highlights: • Solubility of ethyl vanillin in eight pure solvents were determined by a static analytical method. • The experimental solubility data of ethyl vanillin were correlated and analyzed by four thermodynamic models. • Dissolution thermodynamic properties of ethyl vanillin were calculated and discussed. - Abstract: The solubility of ethyl vanillin (EVA) in eight pure solvents were determined in different temperature ranges from (273.15 to 318.15) K by a static analytical method. In the temperature ranges investigated, it was found that the solubility of EVA in all the selected solvents increased with the rising of temperature. Furthermore, four thermodynamic models were used to correlate the experimental solubility data and the calculation results showed that selected models can be used to correlate the solubility data with satisfactory accuracy. Finally, the dissolution thermodynamic properties, including dissolution Gibbs energy, dissolution enthalpy and dissolution entropy of EVA in the eight selected solvents were calculated.

  19. Is Water a Universal Solvent for Life?

    Science.gov (United States)

    Pohorill, Andrew

    2012-01-01

    There are strong reasons to believe that the laws, principles and constraints of physics and chemistry are universal. It is much less clear how this universality translates into our understanding of the origins of life. Conventionally, discussions of this topic focus on chemistry that must be sufficiently rich to seed life. Although this is clearly a prerequisite for the emergence of living systems, I propose to focus instead on self-organization of matter into functional structures capable of reproduction, evolution and responding to environmental changes. In biology, most essential functions are largely mediated by noncovalent interactions (interactions that do not involve making or breaking chemical bonds). Forming chemical bonds is only a small part of what living systems do. There are specific implications of this point of view for universality. I will concentrate on one of these implications. Strength of non-covalent interactions must be properly tuned. If they were too weak, the system would exhibit undesired, uncontrolled response to natural fluctuations of physical and chemical parameters. If they were too strong kinetics of biological processes would be slow and energetics costly. This balance, however, is not a natural property of complex chemical systems. Instead, it has to be achieved with the aid of an appropriate solvent for life. In particular, potential solvents for life must be characterized by a high dielectric constant to ensure solubility of polar species and sufficient flexibility of biological structures stabilized by electrostatic interactions. Among these solvents, water exhibits a remarkable trait that it also promotes solvophobic (hydrophobic) interactions between non-polar species, typically manifested by a tendency of these species to aggregate and minimize their contacts with the aqueous solvent. Hydrophobic interactions are responsible, at least in part, for many self-organization phenomena in biological systems, such as the formation

  20. Activity and conformation of lysozyme in molecular solvents, protic ionic liquids (PILs) and salt-water systems.

    Science.gov (United States)

    Wijaya, Emmy C; Separovic, Frances; Drummond, Calum J; Greaves, Tamar L

    2016-09-21

    Improving protein stabilisation is important for the further development of many applications in the pharmaceutical, specialty chemical, consumer product and agricultural sectors. However, protein stabilization is highly dependent on the solvent environment and, hence, it is very complex to tailor protein-solvent combinations for stable protein maintenance. Understanding solvent features that govern protein stabilization will enable selection or design of suitable media with favourable solution environments to retain protein native conformation. In this work the structural conformation and activity of lysozyme in 29 solvent systems were investigated to determine the role of various solvent features on the stability of the enzyme. The solvent systems consisted of 19 low molecular weight polar solvents and 4 protic ionic liquids (PILs), both at different water content levels, and 6 aqueous salt solutions. Small angle X-ray scattering, Fourier transform infrared spectroscopy and UV-vis spectroscopy were used to investigate the tertiary and secondary structure of lysozyme along with the corresponding activity in various solvation systems. At low non-aqueous solvent concentrations (high water content), the presence of solvents and salts generally maintained lysozyme in its native structure and enhanced its activity. Due to the presence of a net surface charge on lysozyme, electrostatic interactions in PIL-water systems and salt solutions enhanced lysozyme activity more than the specific hydrogen-bond interactions present in non-ionic molecular solvents. At higher solvent concentrations (lower water content), solvents with a propensity to exhibit the solvophobic effect, analogous to the hydrophobic effect in water, retained lysozyme native conformation and activity. This solvophobic effect was observed particularly for solvents which contained hydroxyl moieties. Preferential solvophobic effects along with bulky chemical structures were postulated to result in less

  1. Ion sources for electrostatic accelerators

    International Nuclear Information System (INIS)

    Hellborg, R.

    1998-01-01

    Maybe the most important part of an electrostatic accelerator system, and also often the most tricky part is the ion source. There has been a rapid growth in activity in ion-source research and development during the last two to three decades. Some of these developments have also been of benefit to electrostatic accelerator users. In this report some of the different types of ion sources used in electrostatic accelerators are described. The list is not complete but more an overview of some of the more commonly used sources. The description is divided into two groups; positive ion sources for single stage electrostatic accelerators and negative ion sources for two stages (i.e. tandem) accelerators

  2. Microencapsulation by solvent extraction/evaporation: reviewing the state of the art of microsphere preparation process technology.

    Science.gov (United States)

    Freitas, Sergio; Merkle, Hans P; Gander, Bruno

    2005-02-02

    The therapeutic benefit of microencapsulated drugs and vaccines brought forth the need to prepare such particles in larger quantities and in sufficient quality suitable for clinical trials and commercialisation. Very commonly, microencapsulation processes are based on the principle of so-called "solvent extraction/evaporation". While initial lab-scale experiments are frequently performed in simple beaker/stirrer setups, clinical trials and market introduction require more sophisticated technologies, allowing for economic, robust, well-controllable and aseptic production of microspheres. To this aim, various technologies have been examined for microsphere preparation, among them are static mixing, extrusion through needles, membranes and microfabricated microchannel devices, dripping using electrostatic forces and ultrasonic jet excitation. This article reviews the current state of the art in solvent extraction/evaporation-based microencapsulation technologies. Its focus is on process-related aspects, as described in the scientific and patent literature. Our findings will be outlined according to the four major substeps of microsphere preparation by solvent extraction/evaporation, namely, (i) incorporation of the bioactive compound, (ii) formation of the microdroplets, (iii) solvent removal and (iv) harvesting and drying the particles. Both, well-established and more advanced technologies will be reviewed.

  3. A strong focussing cylindrical electrostatic quadrupole

    International Nuclear Information System (INIS)

    Sheng Yaochang

    1986-01-01

    The construction and performance of small cylindrical electrostatic quadrupole, which is installed in JM-400 pulse electrostatic accelerator, are described. This electrostatic quadrupole is not only used in neutron generator, but also suitable for ion injector as well as for low energy electron accelerator

  4. CDW (continuum distorted wave) type approximation for electron capture at large angles

    International Nuclear Information System (INIS)

    Fojon, O.A.; Maidagan, J.M.

    1990-01-01

    A calculation is made for the probability of electron capture in shell K at great angles using a second order symmetrical model used related to the continuum distorted wave (CDW) approximation. The influence of Coulomb distortion of nuclei is studied and compared with OBK and CIS type calculations. Numerical results are compared with experimental results of the collision of H + on C at intermediate energies. (Author). 19 refs., 2 figs

  5. Electrostatic Detumble of Space Objects

    Data.gov (United States)

    National Aeronautics and Space Administration — Electrostatic Tractor Technology research explores the harmony of physics and engineering to develop and test electrostatic actuation methods for touchless detumble...

  6. Continuum photon spectrum from Z1Z1 annihilations in universal extra dimensions

    International Nuclear Information System (INIS)

    Melbéus, Henrik; Merle, Alexander; Ohlsson, Tommy

    2012-01-01

    We calculate the continuum photon spectrum from the pair annihilation of a Z 1 LKP in non-minimal universal extra dimensions. We find that, due to the preferred annihilation into W + W - pairs, the continuum flux of collinear photons is relatively small compared to the standard case of the B 1 as the LKP. This conclusion applies in particular to the spectral endpoint, where also the additional fermionic contributions are not large enough to increase the flux significantly. When searching for the line signal originating from Z 1 Z 1 annihilations, this is actually a perfect situation, since the continuum signal can be regarded as background to the smoking gun signature of a peak in the photon flux at an energy that is nearly equal to the mass of the dark matter particle. This signal, in combination with (probably) a non-observation of the continuum signal at lower photon energies, constitutes a perfect handle to probe the hypothesis of the Z 1 LKP being the dominant component of the dark matter observed in the Universe.

  7. A knowledge based advisory system for acid/base titrations in non-aqueous solvents

    NARCIS (Netherlands)

    Bos, M.; van der Linden, W.E.

    1996-01-01

    A computer program was developed that could advice on the choice of solvent and titrant for acid/base titrations in nonaqueous media. It is shown that the feasibility of a titration in a given solvent can be calculated from solvent properties and intrinsic acid/base properties of the sample

  8. Electrostatic Levitator Layout

    Science.gov (United States)

    1998-01-01

    Electrostatic Levitator (ESL) general layout with captions. The ESL uses static electricity to suspend an object (about 2-3 mm in diameter) inside a vacuum chamber while a laser heats the sample until it melts. This lets scientists record a wide range of physical properties without the sample contacting the container or any instruments, conditions that would alter the readings. The Electrostatic Levitator is one of several tools used in NASA's microgravity materials science program.

  9. The influence of actuator materials and nozzle designs on electrostatic charge of pressurised metered dose inhaler (pMDI) formulations.

    Science.gov (United States)

    Chen, Yang; Young, Paul M; Fletcher, David F; Chan, Hak Kim; Long, Edward; Lewis, David; Church, Tanya; Traini, Daniela

    2014-05-01

    To investigate the influence of different actuator materials and nozzle designs on the electrostatic charge properties of a series of solution metered dose inhaler (pMDI) aerosols. Actuators were manufactured with flat and cone nozzle designs using five different materials from the triboelectric series (Nylon, Polyethylene terephthalate, Polyethylene-High density, Polypropylene copolymer and Polytetrafluoroethylene). The electrostatic charge profiles of pMDI containing beclomethasone dipropionate (BDP) as model drug in HFA-134a propellant, with different concentrations of ethanol were studied. Electrostatic measurements were taken using a modified electrical low-pressure impactor (ELPI) and the deposited drug mass assayed chemically using HPLC. The charge profiles of HFA 134a alone have shown strong electronegativity with all actuator materials and nozzle designs, at an average of -1531.34 pC ± 377.34. The presence of co-solvent ethanol significantly reduced the negative charge magnitude. BDP reduced the suppressing effect of ethanol on the negative charging of the propellant. For all tested formulations, the flat nozzle design showed no significant differences in net charge between different actuator materials, whereas the charge profiles of cone designs followed the triboelectric series. The electrostatic charging profiles from a solution pMDI containing BDP and ethanol can be significantly influenced by the actuator material, nozzle design and formulation components. Ethanol concentration appears to have the most significant impact. Furthermore, BDP interactions with ethanol and HFA have an influence on the electrostatic charge of aerosols. By choosing different combinations of actuator materials and orifice design, the fine particle fractions of formulations can be altered.

  10. Shuffle motor: a high force, high precision linear electrostatic stepper motor

    NARCIS (Netherlands)

    Tas, Niels Roelof; Wissink, Jeroen; Sander, A.F.M.; Sander, Louis; Lammerink, Theodorus S.J.; Elwenspoek, Michael Curt

    1997-01-01

    The shuffle motor is a electrostatic stepper motor that employs a mechanical transformation to obtain high forces and small steps. A model has been made to calculate the driving voltage, step size and maximum load to pull as well as the optimal geometry. Tests results are an effective step size of

  11. Solvent extraction for spent nuclear fuel reprocessing plant

    International Nuclear Information System (INIS)

    Masui, Jinichi

    1986-01-01

    The purex process provides a solvent extraction method widely used for separating uranium and plutonium from nitric acid solution containing spent fuel. The Tokai Works has adopted the purex process with TPB-n dodecane as the extraction agent and a mixer settler as the solvent extraction device. The present article outlines the solvent extraction process and discuss the features of various extraction devices. The chemical principle of the process is described and a procedure for calculating the number of steps for countercurrent equilibrium extraction is proposed. Discussion is also made on extraction processes for separating and purifying uranium and plutonium from fission products and on procedures for managing these processes. A small-sized high-performance high-reliability device is required for carrying out solvent extraction in reprocessing plants. Currently, mixer settler, pulse column and centrifugal contactor are mainly used in these plants. Here, mixer settler is comparted with pulse column with respect to their past achievements, design, radiation damage to solvent, operation halt, controllability and maintenance. Processes for co-extraction, partition, purification and solvent recycling are described. (Nogami, K.)

  12. Thermal quasiparticle correlations and continuum coupling in nuclei far from stability

    International Nuclear Information System (INIS)

    Dang, Nguyen Dinh; Arima, Akito

    2003-01-01

    The contributions of quasiparticle correlations and continuum coupling upon the superfluid properties of neutron-rich Ni isotopes are studied within the modified BCS approximation at finite temperature. The effect of quasiparticle correlations is included using a secondary Bogoliubov transformation explicitly involving the quasiparticle occupation numbers at temperature T. The effect of continuum coupling is taken in to account via the finite widths of the single-particle resonant states. It is shown that the combination of these effects washes out the sharp superfluid-normal phase transition given by the standard finite-temperature BCS calculations. It is also found that the two-neutron separation energy for 84 Ni drops to zero at T congruent with 0.8 MeV

  13. Analytic perturbation theory for screened Coulomb potential: full continuum wave function

    International Nuclear Information System (INIS)

    Bechler, A.; Ennan, Mc J.; Pratt, R.H.

    1979-01-01

    An analytic perturbation theory developed previously is used to find a continuum screened-Coulomb wave function characterized by definite asymptotic momentum. This wave function satisfies an inhomogeneous partial differential equation which is solved in parabolic coordinates; the solution depends on both parabolic variables. We calculate partial wave projections of this solution and show that we can choose to add a solution of the homogeneous equation such that the partial wave projections become equal to the normalized continuum radial function found previously. However, finding the unique solution with given asymptotic linear momentum will require either using boundary conditions to determine the unique needed solution of the homogeneous equation or equivalently specifying the screened-Coulomb phase-shifts. (author)

  14. The solvation reaction field for a hydrogen atom in a dielectric continuum

    International Nuclear Information System (INIS)

    Chipman, D.M.

    1996-01-01

    A reaction field exists even for a nonpolar solute embedded in a spherical cavity within a surrounding homogeneous dielectric continuum. This arises from the tail of the electronic wave function that penetrates beyond the cavity boundary into the dielectric region. This effect, which is neglected or treated only in cursory fashion in most reaction field implementations, is examined in detail for the simple case of a ground state hydrogen atom, where very accurate solutions of the relevant equations can be obtained. Properties considered include the penetration of the electron outside the cavity, the electronic density at the nucleus, the electron binding energy, the electrostatic free energy of solvation, the polarizability, and the vertical 1s→2p excitation energy. Also, the effect of the common approximation of neglecting the volume polarization and treating only the surface polarization contribution to the reaction field is critically evaluated. copyright 1996 American Institute of Physics

  15. Limiting assumptions in molecular modeling: electrostatics.

    Science.gov (United States)

    Marshall, Garland R

    2013-02-01

    Molecular mechanics attempts to represent intermolecular interactions in terms of classical physics. Initial efforts assumed a point charge located at the atom center and coulombic interactions. It is been recognized over multiple decades that simply representing electrostatics with a charge on each atom failed to reproduce the electrostatic potential surrounding a molecule as estimated by quantum mechanics. Molecular orbitals are not spherically symmetrical, an implicit assumption of monopole electrostatics. This perspective reviews recent evidence that requires use of multipole electrostatics and polarizability in molecular modeling.

  16. Multiple Temperature Model for Near Continuum Flows

    International Nuclear Information System (INIS)

    XU, Kun; Liu, Hongwei; Jiang, Jianzheng

    2007-01-01

    In the near continuum flow regime, the flow may have different translational temperatures in different directions. It is well known that for increasingly rarefied flow fields, the predictions from continuum formulation, such as the Navier-Stokes equations, lose accuracy. These inaccuracies may be partially due to the single temperature assumption in the Navier-Stokes equations. Here, based on the gas-kinetic Bhatnagar-Gross-Krook (BGK) equation, a multitranslational temperature model is proposed and used in the flow calculations. In order to fix all three translational temperatures, two constraints are additionally proposed to model the energy exchange in different directions. Based on the multiple temperature assumption, the Navier-Stokes relation between the stress and strain is replaced by the temperature relaxation term, and the Navier-Stokes assumption is recovered only in the limiting case when the flow is close to the equilibrium with the same temperature in different directions. In order to validate the current model, both the Couette and Poiseuille flows are studied in the transition flow regime

  17. Spectroscopic and DFT study of solvent effects on the electronic absorption spectra of sulfamethoxazole in neat and binary solvent mixtures

    Science.gov (United States)

    Almandoz, M. C.; Sancho, M. I.; Blanco, S. E.

    2014-01-01

    The solvatochromic behavior of sulfamethoxazole (SMX) was investigated using UV-vis spectroscopy and DFT methods in neat and binary solvent mixtures. The spectral shifts of this solute were correlated with the Kamlet and Taft parameters (α, β and π*). Multiple lineal regression analysis indicates that both specific hydrogen-bond interaction and non specific dipolar interaction play an important role in the position of the absorption maxima in neat solvents. The simulated absorption spectra using TD-DFT methods were in good agreement with the experimental ones. Binary mixtures consist of cyclohexane (Cy)-ethanol (EtOH), acetonitrile (ACN)-dimethylsulfoxide (DMSO), ACN-dimethylformamide (DMF), and aqueous mixtures containing as co-solvents DMSO, ACN, EtOH and MeOH. Index of preferential solvation was calculated as a function of solvent composition and non-ideal characteristics are observed in all binary mixtures. In ACN-DMSO and ACN-DMF mixtures, the results show that the solvents with higher polarity and hydrogen bond donor ability interact preferentially with the solute. In binary mixtures containing water, the SMX molecules are solvated by the organic co-solvent (DMSO or EtOH) over the whole composition range. Synergistic effect is observed in the case of ACN-H2O and MeOH-H2O, indicating that at certain concentrations solvents interact to form association complexes, which should be more polar than the individual solvents of the mixture.

  18. Investigations on geometrical features in induced ordering of ...

    Indian Academy of Sciences (India)

    Unknown

    molecular volumes can be calculated from the solvent inaccessible surface areas and ... protein–DNA interactions has been examined.13–15 On similar lines, ... Through the electrostatic topography of a polyphenol molecule, possible ...

  19. Chromatic aberrations of electrostatic axisymmetric lenses produced by circular cylinders

    International Nuclear Information System (INIS)

    Baranova, L.A.; Ul'yanova, N.S.; Yavor, S.Ya.

    1989-01-01

    Ion beams both to test material and for technological processes have being used lately in science and technology more and more. Electrostatic lenses are used, as a rule, for such beam production. Coefficients of chromatic aberrration for a wide range of changes in lense parameters are calculated on the basis of analytical expressions to determine the potential in immerse and isolated lenses. The chromatic aberration coefficient is presented as a polynomial according to the degrees of reverse increase, that permits to calculate a circle of blurring of subject arbitrary position

  20. Notes on continuum mechanics

    CERN Document Server

    Chaves, Eduardo W V

    2013-01-01

    This publication is aimed at students, teachers, and researchers of Continuum Mechanics and focused extensively on stating and developing Initial Boundary Value equations used to solve physical problems. With respect to notation, the tensorial, indicial and Voigt notations have been used indiscriminately.   The book is divided into twelve chapters with the following topics: Tensors, Continuum Kinematics, Stress, The Objectivity of Tensors, The Fundamental Equations of Continuum Mechanics, An Introduction to Constitutive Equations, Linear Elasticity, Hyperelasticity, Plasticity (small and large deformations), Thermoelasticity (small and large deformations), Damage Mechanics (small and large deformations), and An Introduction to Fluids. Moreover, the text is supplemented with over 280 figures, over 100 solved problems, and 130 references.

  1. Plastic dislocation motion via nonequilibrium molecular and continuum dynamics

    International Nuclear Information System (INIS)

    Hoover, W.G.; Ladd, A.J.C.; Hoover, N.E.

    1980-01-01

    The classical two-dimensional close-packed triangular lattice, with nearest-neighbor spring forces, is a convenient standard material for the investigation of dislocation motion and plastic flow. Two kinds of calculations, based on this standard material, are described here: (1) Molecular Dynamics simulations, incorporating adiabatic strains described with the help of Doll's Tensor, and (2) Continuum Dynamics simulations, incorporating periodic boundaries and dislocation interaction through stress-field superposition

  2. Angle-correlated cross sections in the framework of the continuum shell model

    International Nuclear Information System (INIS)

    Moerschel, K.P.

    1984-01-01

    In the present thesis in the framework of the continuum shell modell a concept for the treatment of angle-correlated cross sections was developed by which coincidence experiments on electron scattering on nuclei are described. For this the existing Darmstadt continuum-shell-model code had to be extended to the calculation of the correlation coefficients in which nuclear dynamics enter and which determine completely the angle-correlated cross sections. Under inclusion of the kinematics a method for the integration over the scattered electron was presented and used for the comparison with corresponding experiments. As application correlation coefficients for the proton channel in 12 C with 1 - and 2 + excitations were studied. By means of these coefficients finally cross sections for the reaction 12 C (e,p) 11 B could be calculated and compared with the experiment whereby the developed methods were proved as suitable to predict correctly both the slope and the quantity of the experimental cross sections. (orig.) [de

  3. Changing public stigma with continuum beliefs.

    Science.gov (United States)

    Corrigan, Patrick W; Schmidt, Annie; Bink, Andrea B; Nieweglowski, Katherine; Al-Khouja, Maya A; Qin, Sang; Discont, Steve

    2017-10-01

    Given the egregious effect of public stigma on the lives of people with mental illness, researchers have sought to unpack and identify effective components of anti-stigma programs. We expect to show that continuum messages have more positive effect on stigma and affirming attitudes (beliefs that people with mental illness recover and should be personally empowered) than categorical perspectives. The effect of continuum beliefs will interact with contact strategies. A total of 598 research participants were randomly assigned to online presentations representing one of the six conditions: three messages (continuum, categorical, or neutral control) by two processes (education or contact). Participants completed measures of continuum beliefs (as a manipulation check), stigma and affirming attitudes after viewing the condition. Continuum messages had significantly better effect on views that people with mental illness are "different," a finding that interacted with contact. Continuum messages also had better effects on recovery beliefs, once again an effect that interacted significantly with contact. Implications of these findings for improving anti-stigma programs are discussed.

  4. Study of talcum charging status in parallel plate electrostatic separator based on particle trajectory analysis

    Science.gov (United States)

    Yunxiao, CAO; Zhiqiang, WANG; Jinjun, WANG; Guofeng, LI

    2018-05-01

    Electrostatic separation has been extensively used in mineral processing, and has the potential to separate gangue minerals from raw talcum ore. As for electrostatic separation, the particle charging status is one of important influence factors. To describe the talcum particle charging status in a parallel plate electrostatic separator accurately, this paper proposes a modern images processing method. Based on the actual trajectories obtained from sequence images of particle movement and the analysis of physical forces applied on a charged particle, a numerical model is built, which could calculate the charge-to-mass ratios represented as the charging status of particle and simulate the particle trajectories. The simulated trajectories agree well with the experimental results obtained by images processing. In addition, chemical composition analysis is employed to reveal the relationship between ferrum gangue mineral content and charge-to-mass ratios. Research results show that the proposed method is effective for describing the particle charging status in electrostatic separation.

  5. Advances in electrostatic accelerators

    International Nuclear Information System (INIS)

    Wegner, H.E.

    1975-01-01

    Advances in the design and performance of electrostatic accelerators since 1969 are reviewed with special emphasis on the ''forefront'' accelerators that are currently leading in voltage capability. A comparison of the acceleration tube design offered by the National Electrostatics Corporation and the High Voltage Engineering Corporation is also made. Other methods of increasing heavy ion energy by means of dual foil stripping are discussed as well as the performance of a newly developed sputter ion source for the production of negative heavy ions with reliability and flexibility that greatly exceeds all other present systems. Finally, new developments in terms of both booster systems and very high voltage electrostatic accelerators (25 to 60 MV) are discussed. (U.S.)

  6. Electrostatic Phenomena on Planetary Surfaces

    Science.gov (United States)

    Calle, Carlos I.

    2017-02-01

    The diverse planetary environments in the solar system react in somewhat different ways to the encompassing influence of the Sun. These different interactions define the electrostatic phenomena that take place on and near planetary surfaces. The desire to understand the electrostatic environments of planetary surfaces goes beyond scientific inquiry. These environments have enormous implications for both human and robotic exploration of the solar system. This book describes in some detail what is known about the electrostatic environment of the solar system from early and current experiments on Earth as well as what is being learned from the instrumentation on the space exploration missions (NASA, European Space Agency, and the Japanese Space Agency) of the last few decades. It begins with a brief review of the basic principles of electrostatics.

  7. Electro-osmosis over inhomogeneously charged surfaces in presence of non-electrostatic ion-ion interactions

    Science.gov (United States)

    Ghosh, Uddipta; Chakraborty, Suman

    2016-06-01

    In this study, we attempt to bring out a generalized formulation for electro-osmotic flows over inhomogeneously charged surfaces in presence of non-electrostatic ion-ion interactions. To this end, we start with modified electro-chemical potential of the individual species and subsequently use it to derive modified Nernst-Planck equation accounting for the ionic fluxes generated because of the presence of non-electrostatic potential. We establish what we refer to as the Poisson-Helmholtz-Nernst-Planck equations, coupled with the Navier-Stokes equations, to describe the complete transport process. Our analysis shows that the presence of non-electrostatic interactions between the ions results in an excess body force on the fluid, and modifies the osmotic pressure as well, which has hitherto remained unexplored. We further apply our analysis to a simple geometry, in an effort to work out the Smoluchowski slip velocity for thin electrical double layer limits. To this end, we employ singular perturbation and develop a general framework for the asymptotic analysis. Our calculations reveal that the final expression for slip velocity remains the same as that without accounting for non-electrostatic interactions. However, the presence of non-electrostatic interactions along with ion specificity can significantly change the quantitative behavior of Smoluchowski slip velocity. We subsequently demonstrate that the presence of non-electrostatic interactions may significantly alter the effective interfacial potential, also termed as the "Zeta potential." Our analysis can potentially act as a guide towards the prediction and possibly quantitative determination of the implications associated with the existence of non-electrostatic potential, in an electrokinetic transport process.

  8. Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level.

    Science.gov (United States)

    Wang, Meiting; Li, Pengfei; Jia, Xiangyu; Liu, Wei; Shao, Yihan; Hu, Wenxin; Zheng, Jun; Brooks, Bernard R; Mei, Ye

    2017-10-23

    The partitioning of solute molecules between immiscible solvents with significantly different polarities is of great importance. The polarization between the solute and solvent molecules plays an essential role in determining the solubility of the solute, which makes computational studies utilizing molecular mechanics (MM) rather difficult. In contrast, quantum mechanics (QM) can provide more reliable predictions. In this work, the partition coefficients of the side chain analogs of some amino acids between water and chloroform were computed. The QM solvation free energies were calculated indirectly via a series of MM states using the multistate Bennett acceptance ratio (MBAR) and the MM-to-QM corrections were applied at the two endpoints using thermodynamic perturbation (TP). Previously, it has been shown (Jia et al. J. Chem. Theory Comput. 2016, 12, 499-511) that this method provides the minimal variance in the results without running QM simulations. However, if there is insufficient overlap in phase space between the MM and QM Hamiltonians, this method fails. In this work, we propose, for the first time, a quantity termed the reweighting entropy that serves as a metric for the reliability of the TP calculations. If the reweighting entropy is below a certain threshold (0.65 for the solvation free energy calculations in this work), this MM-to-QM correction should be avoided and two alternative methods can be employed by either introducing a semiempirical state or conducting nonequilibrium simulations. However, the results show that the QM methods are not guaranteed to yield better results than the MM methods. Further improvement of the QM methods are imperative, especially the treatment of the van der Waals and the electrostatic interactions between the QM region and the MM region in the first shell. We also propose a scheme for the calculation of the van der Waals parameters for the solute molecules in nonaqueous solvent, which improves the quality of the

  9. Quantum Monte Carlo calculations of light nuclei

    International Nuclear Information System (INIS)

    Pandharipande, V. R.

    1999-01-01

    Quantum Monte Carlo methods provide an essentially exact way to calculate various properties of nuclear bound, and low energy continuum states, from realistic models of nuclear interactions and currents. After a brief description of the methods and modern models of nuclear forces, we review the results obtained for all the bound, and some continuum states of up to eight nucleons. Various other applications of the methods are reviewed along with future prospects

  10. MCCE analysis of the pKas of introduced buried acids and bases in staphylococcal nuclease.

    Science.gov (United States)

    Gunner, M R; Zhu, Xuyu; Klein, Max C

    2011-12-01

    The pK(a)s of 96 acids and bases introduced into buried sites in the staphylococcal nuclease protein (SNase) were calculated using the multiconformation continuum electrostatics (MCCE) program and the results compared with experimental values. The pK(a)s are obtained by Monte Carlo sampling of coupled side chain protonation and position as a function of pH. The dependence of the results on the protein dielectric constant (ε(prot)) in the continuum electrostatics analysis and on the Lennard-Jones non-electrostatics parameters was evaluated. The pK(a)s of the introduced residues have a clear dependence on ε(prot,) whereas native ionizable residues do not. The native residues have electrostatic interactions with other residues in the protein favoring ionization, which are larger than the desolvation penalty favoring the neutral state. Increasing ε(prot) scales both terms, which for these residues leads to small changes in pK(a). The introduced residues have a larger desolvation penalty and negligible interactions with residues in the protein. For these residues, changing ε(prot) has a large influence on the calculated pK(a). An ε(prot) of 8-10 and a Lennard-Jones scaling of 0.25 is best here. The X-ray crystal structures of the mutated proteins are found to provide somewhat better results than calculations carried out on mutations made in silico. Initial relaxation of the in silico mutations by Gromacs and extensive side chain rotamer sampling within MCCE can significantly improve the match with experiment. Copyright © 2011 Wiley-Liss, Inc.

  11. Driving electrostatic transducers

    DEFF Research Database (Denmark)

    Nielsen, Dennis; Knott, Arnold; Andersen, Michael A. E.

    2013-01-01

    Electrostatic transducers represent a very interesting alternative to the traditional inefficient electrodynamic transducers. In order to establish the full potential of these transducers, power amplifiers which fulfill the strict requirements imposed by such loads (high impedance, frequency...... depended, nonlinear and high bias voltage for linearization) must be developed. This paper analyzes power stages and bias configurations suitable for driving an electrostatic transducer. Measurement results of a 300 V prototype amplifier are shown. Measuring THD across a high impedance source is discussed...

  12. Measurement and correlation of solubility of ciclesonide in seven pure organic solvents

    International Nuclear Information System (INIS)

    Zhou, Lina; Yin, Qiuxiang; Guo, Zhiqiang; Lu, Haijiao; Liu, Mingyan; Chen, Wei; Hou, Baohong

    2017-01-01

    Highlights: • The solubility of ciclesonide in seven pure organic solvents was determined by gravimetric method. • The solubility order was interpreted by virtue of density function theory (DFT). • The experimental solubility of ciclesonide was correlated by four thermodynamic models. • Mixing thermodynamic properties of ciclesonide were calculated and discussed. - Abstract: The solubility of ciclesonide in seven organic solvents (ethanol, 2-propanol, 1-propanol, 1-butanol, acetonitrile, toluene and ethyl acetate) in the temperature range from 278.15 K to 313.15 K was measured by gravimetrical method under atmospheric pressure. The results indicate that the solubility of ciclesonide increases with elevating temperature in all investigated solvents. The solubility order in different solvents was interpreted through comparing interaction force between solute and solvent molecules by virtue of density function theory (DFT). Thermodynamic equations including the modified Apelblat equation, λh equation, Wilson equation and NRTL equation are all suitable to correlate the solubility results. Based on the Wilson equation, the thermodynamic parameters from the mixing process are calculated, and the results indicate the mixing process of ciclesonide in the selected pure solvents is spontaneous and entropy-driven.

  13. Extension versus Bending for Continuum Robots

    Directory of Open Access Journals (Sweden)

    George Grimes

    2008-11-01

    Full Text Available In this paper, we analyze the capabilities of a novel class of continuous-backbone ("continuum" robots. These robots are inspired by biological "trunks, and tentacles". However, the capabilities of established continuum robot designs, which feature controlled bending but not extension, fall short of those of their biological counterparts. In this paper, we argue that the addition of controlled extension provides dual and complementary functionality, and correspondingly enhanced performance, in continuum robots. We present an interval-based analysis to show how the inclusion of controllable extension significantly enhances the workspace and capabilities of continuum robots.

  14. Continuum limit of gl(M vertical stroke N) spin chains

    Energy Technology Data Exchange (ETDEWEB)

    Candu, Constantin [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany). Gruppe Theorie

    2011-03-15

    We study the spectrum of an integrable antiferromagnetic Hamiltonian of the gl(M vertical stroke N) spin chain of alternating fundamental and dual representations. After extensive numerical analysis, we identify the vacuum and low lying excitations and with this knowledge perform the continuum limit, while keeping a finite gap. All antiferromagnetic gl(n+N vertical stroke N) spin chains with n>0 and N{ne}0 are shown to possess in the continuum limit 2n-2 multiplets of massive particles which scatter with gl(n) Gross-Neveu like S-matrices, namely their eigenvalues do not depend on N. We argue that the continuum theory is the gl(M vertical stroke N) Gross-Neveu model, that is the massive deformation of the gl(M vertical stroke N){sub 1} Wess-Zumino-Witten model. As we can see ion the example of gl(2m vertical stroke 1) spin chains, the full particle spectrum is much richer. Our analysis suggests that for a complete characterization of the latter it is not enough to restrict to large volume calculations, as we do in this work. (orig.)

  15. Effect of solvent polarity and temperature on the spectral and thermodynamic properties of exciplexes of 1-cyanonaphthalene with hexamethylbenzene in organic solvents

    International Nuclear Information System (INIS)

    Asim, Sadia; Mansha, Asim; Grampp, Günter; Landgraf, Stephan; Zahid, Muhammad; Bhatti, Ijaz Ahmad

    2014-01-01

    Study of the effect of solvent polarity and temperature is done on the exciplex emission spectra of 1-cyanonaphthalene with hexamethylbenzene. Exciplex system is studied in the range of partially polar solvents and in solvent mixture of propyl acetate and butyronitrile. The unique feature of this solvent mixture is that only the solvent polarity changes (6.0≤ε s ≤24.7) with the change in the mole fraction of solvents whereas the solvent viscosity and refractive index remains unaffected. Thermodynamic properties are calculated according to the models developed by Weller and Kuzmin. Fluorescence lifetimes for both the fluorophore as well as the exciplex are evaluated in all used solvents. Exciplex energetics as a function of solvent polarity and temperature are also discussed. Kuzmin model of self-consistent polarization is used for the explanation of the exciplex emission spectra. The effects of solvent polarity and temperature on energy of zero–zero transitions (hv 0 / ), Huang–Rhys factor (S), Gauss broadening of vibronic level (σ) and the dominant high-frequency vibration (hν ν ) are investigated. The strong dependence of exciplex stability and energetics upon the solvent polarity and temperature are observed. Full charge transfer exciplexes were observed in solvents of all polarities and stronger exciplex with large emission intensities were found in solvents of low polarities but with the increase in solvent polarity the exciplex becomes weak and they dissociate fastly into radical ion pairs. The kinetic model of Kuzmin was observed to reduce into the Weller kinetic model for this exciplex system with ∆G ET = −0.22 eV and the spectral shift, h∆ν>0.2 eV. - Highlights: • Exciplex formed as a result of mixing of charge transfer and locally excited states. • Effect of solvents polarity and temperature on the exciplex stability and thermodynamics. • Solvent polarity will decide the formation of contact radical ion pair or solvent separated

  16. Electrical operation of electrostatic precipitators

    CERN Document Server

    Parker, Ken

    2003-01-01

    The electrostatic precipitator remains on of the most cost effective means of controlling the emission of particulates from most industrial processes. This book will be of interest to both users and suppliers of electrostatic precipitators as well as advanced students on environmental based courses. The author identifies the physical and engineering basis for the development of electrical equipment for electrostatic precipitators and thoroughly explores the technological factors which optimize the efficiency of the precipitator and hence minimize emissions, as well as future developments in th

  17. Development of a tandem-electrostatic-quadrupole accelerator facility for BNCT

    International Nuclear Information System (INIS)

    Kreiner, A.J.; Thatar Vento, V.; Levinas, P.; Bergueiro, J.; Di Paolo, H.; Burlon, A.A.; Kesque, J.M.; Valda, A.A.; Debray, M.E.; Somacal, H.R.; Minsky, D.M.

    2009-01-01

    In this work we describe the present status of an ongoing project to develop a tandem-electrostatic-quadrupole (TESQ) accelerator facility for accelerator-based (AB) BNCT at the Atomic Energy Commission of Argentina in Buenos Aires. The project final goal is a machine capable of delivering 30 mA of 2.4 MeV protons to be used in conjunction with a neutron production target based on the 7 Li(p,n) 7 Be reaction slightly beyond its resonance at 2.25 MeV. These are the specifications needed to produce sufficiently intense and clean epithermal neutron beams, based on the 7 Li(p,n) 7 Be reaction, to perform BNCT treatment for deep-seated tumors in less than an hour. An electrostatic machine is the technologically simplest and cheapest solution for optimized AB-BNCT. The machine being designed and constructed is a folded TESQ with a high-voltage terminal at 1.2 MV intended to work in air. Such a machine is conceptually shown to be capable of transporting and accelerating a 30 mA proton beam to 2.4 MeV. The general geometric layout, its associated electrostatic fields, and the acceleration tube are simulated using a 3D finite element procedure. The design and construction of the ESQ modules is discussed and their electrostatic fields are investigated. Beam transport calculations through the accelerator are briefly mentioned. Likewise, work related to neutron production targets, strippers, beam shaping assembly and patient treatment room is briefly described.

  18. Development of a tandem-electrostatic-quadrupole accelerator facility for BNCT.

    Science.gov (United States)

    Kreiner, A J; Thatar Vento, V; Levinas, P; Bergueiro, J; Di Paolo, H; Burlon, A A; Kesque, J M; Valda, A A; Debray, M E; Somacal, H R; Minsky, D M; Estrada, L; Hazarabedian, A; Johann, F; Suarez Sandin, J C; Castell, W; Davidson, J; Davidson, M; Giboudot, Y; Repetto, M; Obligado, M; Nery, J P; Huck, H; Igarzabal, M; Fernandez Salares, A

    2009-07-01

    In this work we describe the present status of an ongoing project to develop a tandem-electrostatic-quadrupole (TESQ) accelerator facility for accelerator-based (AB) BNCT at the Atomic Energy Commission of Argentina in Buenos Aires. The project final goal is a machine capable of delivering 30 mA of 2.4 MeV protons to be used in conjunction with a neutron production target based on the (7)Li(p,n)(7)Be reaction slightly beyond its resonance at 2.25 MeV. These are the specifications needed to produce sufficiently intense and clean epithermal neutron beams, based on the (7)Li(p,n)(7)Be reaction, to perform BNCT treatment for deep-seated tumors in less than an hour. An electrostatic machine is the technologically simplest and cheapest solution for optimized AB-BNCT. The machine being designed and constructed is a folded TESQ with a high-voltage terminal at 1.2 MV intended to work in air. Such a machine is conceptually shown to be capable of transporting and accelerating a 30 mA proton beam to 2.4 MeV. The general geometric layout, its associated electrostatic fields, and the acceleration tube are simulated using a 3D finite element procedure. The design and construction of the ESQ modules is discussed and their electrostatic fields are investigated. Beam transport calculations through the accelerator are briefly mentioned. Likewise, work related to neutron production targets, strippers, beam shaping assembly and patient treatment room is briefly described.

  19. Image reconstruction in electrostatic tomography using a priori knowledge from ECT

    International Nuclear Information System (INIS)

    Zhou Bin; Zhang Jianyong; Xu Chuanlong; Wang Shimin

    2011-01-01

    Research highlights: → A dual-mode sensor technique based on ECT and EST is proposed. → The interference of the charged particles to ECT can be eliminated. → A priori knowledge from ECT improves the inversion accuracy. - Abstract: In gas-solid two-phase flow, the charge distribution is a very important process parameter which is useful to the study of electrostatic adhesion. Electrostatic tomography (EST) is a relatively new non-intrusive technique which can be used to acquire charge distribution. However, due to limited measurements, the quality of image reconstruction is poor. In this paper, a dual-mode sensor technique based on electrical capacitance tomography (ECT) and EST is proposed. The theoretical analysis and the numerical simulation results reveal that the permittivity distribution obtained from ECT can provide a priori knowledge for the inversion calculation of EST, so that the accuracy of spatial sensitivity calculation in EST can be improved. This proposed technique is expected to be prospective in industrial applications and will also be beneficial to the research on the fluid dynamics of gas-solid two-phase flow.

  20. Convenient solvatochromic probes for the determination of solvent properties: {beta}-carotene and 2-chloro-7-nitro-9H-fluorene

    Energy Technology Data Exchange (ETDEWEB)

    Seoud, Omar A. El; Pires, Paulo A.R.; Loffredo, Carina; Imran, Muhammad; Pulcini, Paolo D.; Correa, Michelle F.; Mustafa, Rizwana, E-mail: elseoud@iq.usp.br [Universidade de Sao Paulo (USP), SP (Brazil). Instituto de Quimica

    2013-07-15

    Solvent dipolarity/polarizability (SDP) has been previously calculated from the UV-Vis spectra of 2-(N,N-dimethylamino)-7-nitro-9H-fluorene and 2-fluoro-7-nitro-9H- fluorene. Based on theoretical calculations (23 solvents) and experimental data (56 solvents), it is shown that 2-chloro-7-nitro-9H-fluorene (commercially available) can be conveniently employed for the calculation of this property, instead of its 2-fluoro-7-nitro counterpart. The splitting of SDP into its components (solvent dipolarity (SD) and polarizability (SP)) requires the use of a synthetic polyene compound whose synthesis is laborious, involving 15 steps. Our research group has recently shown that the natural dye {beta}-carotene can be conveniently employed for the determination of SP, allowing the calculation of SD. Using these solvatochromic probes, SDP, SP and SD for a series of 1-bromo alkanes were calculated. For several homologous series, the dependence of solvent SDP (SD and SP for one series) on the number of carbon atoms in the 1-alkyl- or acyl-group was calculated and discussed. (author)

  1. Electrostatic septum, SPS

    CERN Multimedia

    1975-01-01

    To minimize losses during slow extraction towards N- and W-Areas, electrostatic septa in long straight sections 2 an 6 precede the magnetic septa. The 2 electrode plates, visible at the entrance to the septum, provide a vertical electric field to remove the ions created by the circulating beam in the residual gas. Here we see one of the electrostatic septa being assembled by Faustin Emery (left) and Jacques Soubeyran (right), in the clean room of building 867. See also 7501199, 7501201, 7801286 and further explanations there.

  2. Explosion safety in industrial electrostatics

    Science.gov (United States)

    Szabó, S. V.; Kiss, I.; Berta, I.

    2011-01-01

    Complicated industrial systems are often endangered by electrostatic hazards, both from atmospheric (lightning phenomenon, primary and secondary lightning protection) and industrial (technological problems caused by static charging and fire and explosion hazards.) According to the classical approach protective methods have to be used in order to remove electrostatic charging and to avoid damages, however no attempt to compute the risk before and after applying the protective method is made, relying instead on well-educated and practiced expertise. The Budapest School of Electrostatics - in close cooperation with industrial partners - develops new suitable solutions for probability based decision support (Static Control Up-to-date Technology, SCOUT) using soft computing methods. This new approach can be used to assess and audit existing systems and - using the predictive power of the models - to design and plan activities in industrial electrostatics.

  3. Computational Methods for Biomolecular Electrostatics

    Science.gov (United States)

    Dong, Feng; Olsen, Brett; Baker, Nathan A.

    2008-01-01

    An understanding of intermolecular interactions is essential for insight into how cells develop, operate, communicate and control their activities. Such interactions include several components: contributions from linear, angular, and torsional forces in covalent bonds, van der Waals forces, as well as electrostatics. Among the various components of molecular interactions, electrostatics are of special importance because of their long range and their influence on polar or charged molecules, including water, aqueous ions, and amino or nucleic acids, which are some of the primary components of living systems. Electrostatics, therefore, play important roles in determining the structure, motion and function of a wide range of biological molecules. This chapter presents a brief overview of electrostatic interactions in cellular systems with a particular focus on how computational tools can be used to investigate these types of interactions. PMID:17964951

  4. Experimental study of a variable-capacitance micromotor with electrostatic suspension

    Science.gov (United States)

    Han, F. T.; Wu, Q. P.; Wang, L.

    2010-11-01

    A variable-capacitance micromotor where the rotor is supported electrostatically in five degrees of freedom was designed, fabricated and tested in order to study the behavior of this electrostatic motor. The micromachined device is based on a glass/silicon/glass stack bonding structure, fabricated by bulk micromachining and initially operated in atmospheric environment. The analytical torque model is obtained by calculating the capacitances between different stator electrodes and the rotor. Capacitance values in the order of 10-13 pF and torque values in the order of 10-10 N m have been calculated from the motor geometry and attainable drive voltage. A dynamic model of the motor is proposed by further estimating the air-film damping effect in an effort to explain the experimental rotation measurements. Experimental results of starting voltage, continuous operation, switching response and electric bearing of the micromotor are presented and discussed. Preliminary measurements indicate that a rotor rotating speed of 73.3 r min-1 can be achieved at a drive voltage of 28.3 V, equivalent to a theoretical motive torque of 517 pN m. Starting voltage results obtained from experimental measurement are in agreement with the developed dynamic model.

  5. SMPBS: Web server for computing biomolecular electrostatics using finite element solvers of size modified Poisson-Boltzmann equation.

    Science.gov (United States)

    Xie, Yang; Ying, Jinyong; Xie, Dexuan

    2017-03-30

    SMPBS (Size Modified Poisson-Boltzmann Solvers) is a web server for computing biomolecular electrostatics using finite element solvers of the size modified Poisson-Boltzmann equation (SMPBE). SMPBE not only reflects ionic size effects but also includes the classic Poisson-Boltzmann equation (PBE) as a special case. Thus, its web server is expected to have a broader range of applications than a PBE web server. SMPBS is designed with a dynamic, mobile-friendly user interface, and features easily accessible help text, asynchronous data submission, and an interactive, hardware-accelerated molecular visualization viewer based on the 3Dmol.js library. In particular, the viewer allows computed electrostatics to be directly mapped onto an irregular triangular mesh of a molecular surface. Due to this functionality and the fast SMPBE finite element solvers, the web server is very efficient in the calculation and visualization of electrostatics. In addition, SMPBE is reconstructed using a new objective electrostatic free energy, clearly showing that the electrostatics and ionic concentrations predicted by SMPBE are optimal in the sense of minimizing the objective electrostatic free energy. SMPBS is available at the URL: smpbs.math.uwm.edu © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  6. HYBRID CONTINUUM-DISCONTINUUM MODELLING OF ROCK FRACUTRE PROCESS IN BRAZILIAN TENSILE STRENGTH TEST

    Directory of Open Access Journals (Sweden)

    Huaming An

    2017-10-01

    Full Text Available A hybrid continuum-discontinuum method is introduced to model the rock failure process in Brazilian tensile strength (BTS test. The key component of the hybrid continuum-discontinuum method, i.e. transition from continuum to discontinuum through fracture and fragmentation, is introduced in detail. A laboratory test is conducted first to capture the rock fracture pattern in the BTS test while the tensile strength is calculated according to the peak value of the loading forces. Then the proposed method is used to model the rock behaviour during BTS test. The stress propagation is modelled and compared with those modelled by finite element method in literatures. In addition, the crack initiation and propagation are captured and compared with the facture patter in laboratory test. Moreover, the force-loading displacement curve is obtained which represents a typical brittle material failure process. Furthermore, the stress distributions along the vertical direction are compared with the theoretical solution. It is concluded that the hybrid continuum-discontinuum method can model the stress propagation process and the entire rock failure process in BTS test. The proposed method is a valuable numerical tool for studying the rock behaviour involving the fracture and fragmentation processes.

  7. Convergent j-matrix calculation of electron-helium resonances

    International Nuclear Information System (INIS)

    Konovalov, D.A.; McCarthy, I.E.

    1994-12-01

    Resonance structures in n=2 and n=3 electron-helium excitation cross sections are calculated using the J-matrix method. The number of close-coupled helium bound and continuum states is taken to convergence, e.g. about 100 channels are coupled for each total spin and angular momentum. It is found that the present J-matrix results are in good shape agreement with recent 29-state R-matrix calculations. However the J-matrix absolute cross sections are slightly lower due to the influence of continuum channels included in the present method. Experiment and theory agree on the positions of n=2 and n=3 resonances. 22 refs., 1 tab.; 3 figs

  8. Preconceptual design for the electrostatic enclosure

    International Nuclear Information System (INIS)

    Meyer, L.C.

    1992-09-01

    This report presents a preconceptual design (design criteria and assumptions) for electrostatic enclosures to be used during buried transuranic waste recovery operations. These electrostatic enclosures (along with the application of dust control products) will provide an in-depth contamination control strategy. As part of this preconceptual design, options for electrostatic curtain design are given including both hardwall and fabric enclosures. Ventilation systems, doors, air locks, electrostatic curtains, and supporting systems also are discussed. In addition to the conceptual design, engineering scale tests are proposed to be run at the Test Reactor Area. The planned engineering scale tests will give final material specifications for full-scale retrieval demonstrations

  9. Progress toward bridging from atomistic to continuum modeling to predict nuclear waste glass dissolution.

    Energy Technology Data Exchange (ETDEWEB)

    Zapol, Peter (Argonne National Laboratory, Argonne, IL); Bourg, Ian (Lawrence Berkeley National Laboratories, Berkeley, CA); Criscenti, Louise Jacqueline; Steefel, Carl I. (Lawrence Berkeley National Laboratories, Berkeley, CA); Schultz, Peter Andrew

    2011-10-01

    This report summarizes research performed for the Nuclear Energy Advanced Modeling and Simulation (NEAMS) Subcontinuum and Upscaling Task. The work conducted focused on developing a roadmap to include molecular scale, mechanistic information in continuum-scale models of nuclear waste glass dissolution. This information is derived from molecular-scale modeling efforts that are validated through comparison with experimental data. In addition to developing a master plan to incorporate a subcontinuum mechanistic understanding of glass dissolution into continuum models, methods were developed to generate constitutive dissolution rate expressions from quantum calculations, force field models were selected to generate multicomponent glass structures and gel layers, classical molecular modeling was used to study diffusion through nanopores analogous to those in the interfacial gel layer, and a micro-continuum model (K{mu}C) was developed to study coupled diffusion and reaction at the glass-gel-solution interface.

  10. Solvent selection methodology for pharmaceutical processes: Solvent swap

    DEFF Research Database (Denmark)

    Papadakis, Emmanouil; Kumar Tula, Anjan; Gani, Rafiqul

    2016-01-01

    A method for the selection of appropriate solvents for the solvent swap task in pharmaceutical processes has been developed. This solvent swap method is based on the solvent selection method of Gani et al. (2006) and considers additional selection criteria such as boiling point difference...... in pharmaceutical processes as well as new solvent swap alternatives. The method takes into account process considerations such as batch distillation and crystallization to achieve the swap task. Rigorous model based simulations of the swap operation are performed to evaluate and compare the performance...

  11. Electrostatic settling of catalyst particles in hydrogenation of methyl benzoate. Denkai chinkoho ni yoru ansokukosan mechiru suisoka hannoeki kara no shokubai ryushi bunri

    Energy Technology Data Exchange (ETDEWEB)

    Kato, K. (Japan Energy Corp., Tokyo (Japan). Central Research Lab.)

    1994-03-01

    As benzyl alcohol (BA), which is one of the simplest alcohol having aromatic ring, has been used widely for the fields related to soap, perfume and chemicals industry, its usage has not always been so much because of its expensiveness. Authors developed previously a new process technique to produce cheaper and higher purity BA not through chlorination process using toluene as its raw materials. The BA can be obtained by hydrogenating methyl benzoate (MB) at a dispersion babble tower using cupper-chromium type powder catalyst in mixed solvent of methanol and toluene. The catalyst becomes much fine particles after the reaction. In this study, it is examined to separate MB hydrogenation reaction solution obtained by electrostatic settling into solid and liquid phases as an aim to improve the BA production process. Rate of electrostatic settling does not depend upon solid concentration, slurry forming conditions, electrode materials, specific resistance of slurry layer and others, but is in proportion to electric field intensity. Furthermore, process of the electrostatic settling is expressed by an equation. 9 refs., 9 figs., 3 tabs.

  12. Loop electrostatics modulates the intersubunit interactions in ferritin.

    Science.gov (United States)

    Bernacchioni, Caterina; Ghini, Veronica; Pozzi, Cecilia; Di Pisa, Flavio; Theil, Elizabeth C; Turano, Paola

    2014-11-21

    Functional ferritins are 24-mer nanocages that self-assemble with extended contacts between pairs of 4-helix bundle subunits coupled in an antiparallel fashion along the C2 axes. The largest intersubunit interaction surface in the ferritin nanocage involves helices, but contacts also occur between groups of three residues midway in the long, solvent-exposed L-loops of facing subunits. The anchor points between intersubunit L-loop pairs are the salt bridges between the symmetry-related, conserved residues Asp80 and Lys82. The resulting quaternary structure of the cage is highly soluble and thermostable. Substitution of negatively charged Asp80 with a positively charged Lys in homopolymeric M ferritin introduces electrostatic repulsions that inhibit the oligomerization of the ferritin subunits. D80K ferritin was present in inclusion bodies under standard overexpressing conditions in E. coli, contrasting with the wild type protein. Small amounts of fully functional D80K nanocages formed when expression was slowed. The more positively charged surface results in a different solubility profile and D80K crystallized in a crystal form with a low density packing. The 3D structure of D80K variant is the same as wild type except for the side chain orientations of Lys80 and facing Lys82. When three contiguous Lys groups are introduced in D80KI81K ferritin variant the nanocage assembly is further inhibited leading to lower solubility and reduced thermal stability. Here, we demonstrate that the electrostatic pairing at the center of the L-loops has a specific kinetic role in the self-assembly of ferritin nanocages.

  13. Ions, solutes and solvents, oh my!

    Energy Technology Data Exchange (ETDEWEB)

    Kemp, Daniel David [Iowa State Univ., Ames, IA (United States)

    2009-08-01

    Modern methods in ab initio quantum mechanics have become efficient and accurate enough to study many gas-phase systems. However, chemists often work in the solution phase. The presence of solvent molecules has been shown to affect reaction mechanisms1, lower reaction energy barriers2, participate in energy transfer with the solute3 and change the physical properties of the solute4. These effects would be overlooked in simple gas phase calculations. Careful study of specific solvents and solutes must be done in order to fully understand the chemistry of the solution phase. Water is a key solvent in chemical and biological applications. The properties of an individual water molecule (a monomer) and the behavior of thousands of molecules (bulk solution) are well known for many solvents. Much is also understood about aqueous microsolvation (small clusters containing ten water molecules or fewer) and the solvation characteristics when bulk water is chosen to solvate a solute. However, much less is known about how these properties behave as the cluster size transitions from the microsolvated cluster size to the bulk. This thesis will focus on species solvated with water clusters that are large enough to exhibit the properties of the bulk but small enough to consist of fewer than one hundred solvent molecules. New methods to study such systems will also be presented.

  14. 9Be scattering with microscopic wave functions and the continuum-discretized coupled-channel method

    Science.gov (United States)

    Descouvemont, P.; Itagaki, N.

    2018-01-01

    We use microscopic 9Be wave functions defined in a α +α +n multicluster model to compute 9Be+target scattering cross sections. The parameter sets describing 9Be are generated in the spirit of the stochastic variational method, and the optimal solution is obtained by superposing Slater determinants and by diagonalizing the Hamiltonian. The 9Be three-body continuum is approximated by square-integral wave functions. The 9Be microscopic wave functions are then used in a continuum-discretized coupled-channel (CDCC) calculation of 9Be+208Pb and of 9Be+27Al elastic scattering. Without any parameter fitting, we obtain a fair agreement with experiment. For a heavy target, the influence of 9Be breakup is important, while it is weaker for light targets. This result confirms previous nonmicroscopic CDCC calculations. One of the main advantages of the microscopic CDCC is that it is based on nucleon-target interactions only; there is no adjustable parameter. The present work represents a first step towards more ambitious calculations involving heavier Be isotopes.

  15. Gyrokinetic continuum simulations of turbulence in the Texas Helimak

    Science.gov (United States)

    Bernard, T. N.; Shi, E. L.; Hammett, G. W.; Hakim, A.; Taylor, E. I.

    2017-10-01

    We have used the Gkeyll code to perform 3x-2v full-f gyrokinetic continuum simulations of electrostatic plasma turbulence in the Texas Helimak. The Helimak is an open field-line experiment with magnetic curvature and shear. It is useful for validating numerical codes due to its extensive diagnostics and simple, helical geometry, which is similar to the scrape-off layer region of tokamaks. Interchange and drift-wave modes are the main turbulence mechanisms in the device, and potential biasing is applied to study the effect of velocity shear on turbulence reduction. With Gkeyll, we varied field-line pitch angle and simulated biased and unbiased cases to study different turbulent regimes and turbulence reduction. These are the first kinetic simulations of the Helimak and resulting plasma profiles agree fairly well with experimental data. This research demonstrates Gkeyll's progress towards 5D simulations of the SOL region of fusion devices. Supported by the U.S. DOE SCGSR program under contract DE-SC0014664, the Max-Planck/Princeton Center for Plasma Physics, the SciDAC Center for the Study of Plasma Microturbulence, and DOE contract DE-AC02-09CH11466.

  16. Electrostatic fluctuations in soap films

    International Nuclear Information System (INIS)

    Dean, D.S.; Horgan, R.R.

    2002-01-01

    A field theory to describe electrostatic interactions in soap films, described by electric multilayers with a generalized thermodynamic surface-charging mechanism, is studied. In the limit where the electrostatic interactions are weak, this theory is exactly soluble. The theory incorporates in a consistent way, the surface-charging mechanism and the fluctuations in the electrostatic field that correspond to the zero-frequency component of the van der Waals force. It is shown that these terms lead to a Casimir-like attraction that can be sufficiently large to explain the transition between the common black film to a Newton black film

  17. Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography

    Science.gov (United States)

    Wan, Qun; Parks, Jerry M.; Hanson, B. Leif; Fisher, Suzanne Zoe; Ostermann, Andreas; Schrader, Tobias E.; Graham, David E.; Coates, Leighton; Langan, Paul; Kovalevsky, Andrey

    2015-01-01

    Glycoside hydrolase (GH) enzymes apply acid/base chemistry to catalyze the decomposition of complex carbohydrates. These ubiquitous enzymes accept protons from solvent and donate them to substrates at close to neutral pH by modulating the pKa values of key side chains during catalysis. However, it is not known how the catalytic acid residue acquires a proton and transfers it efficiently to the substrate. To better understand GH chemistry, we used macromolecular neutron crystallography to directly determine protonation and ionization states of the active site residues of a family 11 GH at multiple pD (pD = pH + 0.4) values. The general acid glutamate (Glu) cycles between two conformations, upward and downward, but is protonated only in the downward orientation. We performed continuum electrostatics calculations to estimate the pKa values of the catalytic Glu residues in both the apo- and substrate-bound states of the enzyme. The calculated pKa of the Glu increases substantially when the side chain moves down. The energy barrier required to rotate the catalytic Glu residue back to the upward conformation, where it can protonate the glycosidic oxygen of the substrate, is 4.3 kcal/mol according to free energy simulations. These findings shed light on the initial stage of the glycoside hydrolysis reaction in which molecular motion enables the general acid catalyst to obtain a proton from the bulk solvent and deliver it to the glycosidic oxygen. PMID:26392527

  18. The structure of the interface in the solvent mediated interaction of dipolar surfaces

    International Nuclear Information System (INIS)

    Dzhavakhidze, P.G.; Levadny, V.G.

    1987-08-01

    Interaction of two dipolar surfaces separated by a polar medium is considered within the framework of nonlocal electrostatics. The dipolar surface layers are modelled as regular lattices with fixed orientation of dipoles which are immersed into the solvent; solvent response is characterized by nonlocal dielectric function. The model is elaborated in order to reveal the role of the dipolar layer discreteness in the electric field produced by one surface and the interaction between two surfaces (which gives rise to the so called ''hydration'' or ''structural'' force acting between mineral surfaces and phospholipid bilayers). The discreteness effects are present only for commensurate lattices. Their special mutual arrangement then may lead to considerable reduction of structural forces, viz. the usual repulsion regime may change at short distances to attraction. Conditions are considered when repulsion is entirely replaced by attraction, i.e. the ''hydration barrier'' disappears. In appended note we discuss the role of solvation of surface dipolar groups. We propose an explanation of why two modes of decay (one with oscillative fine structure) may be present in the dependence of the force upon distance if the surface dipolar groups are immersed deep enough in the solvent and how the long-range oscillative mode disappears when the surface is but weakly solvated. (author). 35 refs, 5 figs

  19. The structure of the interface in the solvent-mediated interaction of dipolar surfaces

    International Nuclear Information System (INIS)

    Dzhavakhidze, P.G.; Kornyshev, A.A.; Levadny, V.G.

    1988-01-01

    Interaction of two dipolar surfaces separated by a polar medium is considered within the framework of nonlocal electrostatics. The dipolar-surface layers are modelled as regular lattices with fixed orientation of dipoles which are immersed into the solvent; solvent response is characterized by nonlocal dielectric function. The model is elaborated in order to reveal the role of the dypolar-layer discreteness in the electric field produced by one surface and the interaction between two surfaces (which gives rise to the so-called ''hydration'' or ''structural'' force acting between mineral surfaces and phospholipid bilayers). The discreteness effects are present only for commensurate lattices. Their special mutual arrangement then may lead to considerable reduction of structural forces, viz. the usual repulsion regime may change at short distances to attraction. Conditions are considered when repulsion is entirely replaced by attraction, i.e. the ''hydration barrier'' disappears. In appended note it is discussed the role of solvation of surface dipolar groups. It is proposed an explanation of why two modes of decay (one with oscillative fine structure) may be present in the dependence of the force upon distance, if the surface dipolar groups are immersed deep enough in the solvent, and how the long-range oscillative mode disappears when the surface is but weakly solvated

  20. Conformation Analysis of T1 Lipase on Alcohols Solvent using Molecular Dynamics Simulation

    Science.gov (United States)

    Putri, A. M.; Sumaryada, T.; Wahyudi, S. T.

    2017-07-01

    Biodiesel usually is produced commercially via a transesterification reaction of vegetable oil with alcohol and alkali catalyst. The alkali catalyst has some drawbacks, such as the soap formation during the reaction. T1 Lipase enzyme had been known as a thermostable biocatalyst which is able to produce biodiesel through a cleaner process. In this paper the performance of T1 lipase enzyme as catalyst for transesterification reaction in pure ethanol, methanol, and water solvents were studied using a Molecular Dynamics (MD) Simulation at temperature of 300 K for 10 nanoseconds. The results have shown that in general the conformation of T1 lipase enzyme in methanol is more dynamics as shown by the value of root mean square deviation (RMSD), root mean squared fluctuation (RMSF), and radius of gyration. The highest solvent accessible surface area (SASA) total was also found in methanol due to the contribution of non-polar amino acid in the interior of the protein. Analysis of MD simulation has also revealed that the enzyme structure tend to be more rigid in ethanol environment. The analysis of electrostatic interactions have shown that Glu359-Arg270 salt-bridge pair might hold the key of thermostability of T1 lipase enzyme as shown by its strong and stable binding in all three solvents.

  1. Electrostatic correlations: from plasma to biology

    International Nuclear Information System (INIS)

    Levin, Yan

    2002-01-01

    Electrostatic correlations play an important role in physics, chemistry and biology. In plasmas they result in thermodynamic instability similar to the liquid-gas phase transition of simple molecular fluids. For charged colloidal suspensions the electrostatic correlations are responsible for screening and colloidal charge renormalization. In aqueous solutions containing multivalent counterions they can lead to charge inversion and flocculation. In biological systems the correlations account for the organization of cytoskeleton and the compaction of genetic material. In spite of their ubiquity, the true importance of electrostatic correlations has come to be fully appreciated only quite recently. In this paper, we will review the thermodynamic consequences of electrostatic correlations in a variety of systems ranging from classical plasmas to molecular biology

  2. Global spiral structure of M81 - radio continuum maps

    International Nuclear Information System (INIS)

    Bash, F.N.; Kaufman, M.; Ohio State Univ., Columbus)

    1986-01-01

    VLA observations of the radio continuum emission from M81 at 6 and 20 cm are presented and used to check the predictions of density-wave theories. Both thermal and nonthermal radiation from the spiral arms are detected. Most of the bright knots along the radio arms are giant radio H II regions. The nonthermal emission defines spiral arms that are patchy and well-resolved, with a width of 1-2 kpc. The observed nonthermal arms are too broad to agree with the continuum gasdynamical calculations of Roberts (1969), Shu et al. (1972), and Visser (1978, 1980) for a classical density wave model. The observed arm widths appear consistent with the predictions of density-wave models that emphasize the clumpy nature of the ISM. The 20 cm arms appear to spiral outward from a faint inner H I ring, suggesting that the ring is produced by the inner Lindblad resonance. 36 references

  3. Effect of solvent polarity and temperature on the spectral and thermodynamic properties of exciplexes of 1-cyanonaphthalene with hexamethylbenzene in organic solvents

    Energy Technology Data Exchange (ETDEWEB)

    Asim, Sadia [Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremaryrgasse 9, A-8010 Graz (Austria); Department of Chemistry and Biochemistry, University of Agriculture, Faisalabad (Pakistan); Mansha, Asim [Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremaryrgasse 9, A-8010 Graz (Austria); Department of Chemistry, Government College University, Faisalabad (Pakistan); Grampp, Günter, E-mail: grampp@tugraz.at [Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremaryrgasse 9, A-8010 Graz (Austria); Landgraf, Stephan [Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremaryrgasse 9, A-8010 Graz (Austria); Zahid, Muhammad [Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremaryrgasse 9, A-8010 Graz (Austria); Department of Chemistry and Biochemistry, University of Agriculture, Faisalabad (Pakistan); Bhatti, Ijaz Ahmad [Department of Chemistry and Biochemistry, University of Agriculture, Faisalabad (Pakistan)

    2014-09-15

    Study of the effect of solvent polarity and temperature is done on the exciplex emission spectra of 1-cyanonaphthalene with hexamethylbenzene. Exciplex system is studied in the range of partially polar solvents and in solvent mixture of propyl acetate and butyronitrile. The unique feature of this solvent mixture is that only the solvent polarity changes (6.0≤ε{sub s}≤24.7) with the change in the mole fraction of solvents whereas the solvent viscosity and refractive index remains unaffected. Thermodynamic properties are calculated according to the models developed by Weller and Kuzmin. Fluorescence lifetimes for both the fluorophore as well as the exciplex are evaluated in all used solvents. Exciplex energetics as a function of solvent polarity and temperature are also discussed. Kuzmin model of self-consistent polarization is used for the explanation of the exciplex emission spectra. The effects of solvent polarity and temperature on energy of zero–zero transitions (hv{sub 0}{sup /}), Huang–Rhys factor (S), Gauss broadening of vibronic level (σ) and the dominant high-frequency vibration (hν{sub ν}) are investigated. The strong dependence of exciplex stability and energetics upon the solvent polarity and temperature are observed. Full charge transfer exciplexes were observed in solvents of all polarities and stronger exciplex with large emission intensities were found in solvents of low polarities but with the increase in solvent polarity the exciplex becomes weak and they dissociate fastly into radical ion pairs. The kinetic model of Kuzmin was observed to reduce into the Weller kinetic model for this exciplex system with ∆G{sub ET} = −0.22 eV and the spectral shift, h∆ν>0.2 eV. - Highlights: • Exciplex formed as a result of mixing of charge transfer and locally excited states. • Effect of solvents polarity and temperature on the exciplex stability and thermodynamics. • Solvent polarity will decide the formation of contact radical ion pair

  4. Analytical model spectrum for electrostatic turbulence in tokamaks

    International Nuclear Information System (INIS)

    Fiedler-Ferrari, N.; Misguich, J.H.

    1990-04-01

    In this work we present an analytical model spectrum, for three-dimensional electrostatic turbulence (homogeneous, stationary and locally isotropic in the plane perpendicular to the magnetic field), constructed by using experimental results from TFR and TEXT Tokamaks, and satisfying basic symmetry and parity conditions. The proposed spectrum seems to be tractable for explicit analytical calculations of transport processes, and consistent with experimental data. Additional experimental measurements in the bulk plasma remain however necessary in order to determine some unknown spectral properties of parallel propagation

  5. Research on electrostatic electrification during jet kerosene spraying

    International Nuclear Information System (INIS)

    Liu, Quanzhen; Li, Yipeng; Zhang, Wentian; Sun, Keping

    2013-01-01

    Multiple electrostatic electrifications during aircraft fuelling process may cause a fire disaster or explosion, so study on the protection measure for electrostatic electrification is very important for the security of aircraft fuelling. This paper investigated the electrostatic voltage and charge of the fuel nozzle and metal parts during the fuel spraying by self-designed jet kerosene spraying electrostatic electrification test system. The experimental results indicate that the voltage on the fuel nozzle and metal parts is very dangerous for electrostatic safety if they are not reliably grounded.

  6. Charging and absorption characteristics of small particulates under alternative and electrostatic voltages in an electrostatic precipitator

    International Nuclear Information System (INIS)

    Jiang Xue-Dong; Xu He; Wang Xin

    2014-01-01

    The charge quantity of small particulates such as PM2.5 plays a key role in the collection efficiency of an electrostatic precipitator (ESP). Under a single electrostatic voltage, it is difficult to charge and absorb small particulates. A new method of superimposing an alternative voltage on the electrostatic voltage is provided in this paper. Characteristics of small particulates are analyzed under alternative and electrostatic voltages. It is demonstrated that an alternative voltage can significantly improve the collection efficiency in three aspects: preventing anti-corona, increasing the charge quantity of small particulates, and increasing the median particulate size by electric agglomeration. In addition, practical usage with the superposition of alternative voltage is provided, and the results are in agreement with the theoretical analysis. (physics of gases, plasmas, and electric discharges)

  7. Electrostatics in pharmaceutical aerosols for inhalation.

    Science.gov (United States)

    Wong, Jennifer; Chan, Hak-Kim; Kwok, Philip Chi Lip

    2013-08-01

    Electrostatics continues to play an important role in pharmaceutical aerosols for inhalation. Despite its ubiquitous nature, the charging process is complex and not well understood. Nonetheless, significant advances in the past few years continue to improve understanding and lead to better control of electrostatics. The purpose of this critical review is to present an overview of the literature, with an emphasis on how electrostatic charge can be useful in improving pulmonary drug delivery.

  8. Continuum emission in the 1980 July 1 solar flare

    International Nuclear Information System (INIS)

    Zirin, H.; Neidig, D.F.

    1981-01-01

    Comparison of continuum measurements of the 1980 July 1 flare at Big Bear Solar Observatory and Sacramento Peak Observatory show strong blue emission kernels with the ratio of Balmer continuum (Bac):lambda3862 continuum:continuum above 4275 A to be about 10:5:1. The blue continuum at 3862 A is too strong to be explained by unresolved lines. The Bac intensity was 2.5 times the photosphere and the strongest lambda3862 continuum was 2 times the photosphere. The brightest continuum kernel occurred late in the flare, after the hard X-ray peak and related in time to an isolated peak in the 2.2 MeV line, suggesting that the continuum was excited by protons above 20 MeV

  9. Atom-partitioned multipole expansions for electrostatic potential boundary conditions

    Energy Technology Data Exchange (ETDEWEB)

    Lee, M., E-mail: michael.s.lee131.civ@mail.mil [Simulation Sciences Branch, U.S. Army Research Laboratory, Aberdeen Proving Ground, MD 21005 (United States); Leiter, K. [Simulation Sciences Branch, U.S. Army Research Laboratory, Aberdeen Proving Ground, MD 21005 (United States); Eisner, C. [Secure Mission Solutions, a Parsons Company (United States); Simulation Sciences Branch, U.S. Army Research Laboratory, Aberdeen Proving Ground, MD 21005 (United States); Knap, J. [Simulation Sciences Branch, U.S. Army Research Laboratory, Aberdeen Proving Ground, MD 21005 (United States)

    2017-01-01

    Applications such as grid-based real-space density functional theory (DFT) use the Poisson equation to compute electrostatics. However, the expected long tail of the electrostatic potential requires either the use of a large and costly outer domain or Dirichlet boundary conditions estimated via multipole expansion. We find that the oft-used single-center spherical multipole expansion is only appropriate for isotropic mesh domains such as spheres and cubes. In this work, we introduce a method suitable for high aspect ratio meshes whereby the charge density is partitioned into atomic domains and multipoles are computed for each domain. While this approach is moderately more expensive than a single-center expansion, it is numerically stable and still a small fraction of the overall cost of a DFT calculation. The net result is that when high aspect ratio systems are being studied, form-fitted meshes can now be used in lieu of cubic meshes to gain computational speedup.

  10. New numerical methods for quantum field theories on the continuum

    Energy Technology Data Exchange (ETDEWEB)

    Emirdag, P.; Easter, R.; Guralnik, G.S.; Hahn, S.C

    2000-03-01

    The Source Galerkin Method is a new numerical technique that is being developed to solve Quantum Field Theories on the continuum. It is not based on Monte Carlo techniques and has a measure to evaluate relative errors. It promises to increase the accuracy and speed of calculations, and takes full advantage of symmetries of the theory. The application of this method to the non-linear {sigma} model is outlined.

  11. Mode structure and continuum damping of high-n toroidal Alfven eigenmodes

    International Nuclear Information System (INIS)

    Rosenbluth, M.N.; Berk, H.L.; Van Dam, J.W.; Lindberg, D.M.

    1992-02-01

    An asymptotic theory is described for calculating the mode structure and continuum damping of short wave-length toroidal Alfven eigenmodes (TAE). The formalism somewhat resembles the treatment used for describing low-frequency toroidal modes with singular structure at a rational surface, where an inner solution, which for the TAE mode has toroidal coupling, is matched to an outer toroidally uncoupled solution. A three-term recursion relation among coupled poloidal harmonic amplitudes is obtained, whose solution gives the structure of the global wavefunction and the complex eigenfrequency, including continuum damping. Both analytic and numerical solutions are presented. The magnitude of the damping is essential for determining the thresholds for instability driven by the spatial gradients of energetic particles (e.g., neutral beam-injected ions or fusion-product alpha particles) contained in a tokamak plasma

  12. Coupled channel calculations of K-shell ionization in asymmetric collision systems

    International Nuclear Information System (INIS)

    Mehler, G.; Greiner, W.; Soff, G.

    1986-07-01

    We report theoretical results on K-shell ionization for a variety of asymmetric collision systems. The calculated ionization rates are compared with experimental data. The coupled channel formalism underlying these calculations is presented. It is based on a set of relativistic target centred states, taking a screened potential of Dirac-Fock-Slater type into account. We discuss the effects of different matrix elements, e.g. continuum-continuum couplings. The binding effect is inherently contained in our approach and described in a dynamical way. (orig.)

  13. The continuum of behavior guidance.

    Science.gov (United States)

    Nelson, Travis

    2013-01-01

    Behavior guidance is a continuum of techniques, basic and advanced, fundamental to the provision of quality dental care for pediatric patients. This practice must be individualized, pairing the correct method of behavior guidance with each child. To select the appropriate technique, the clinician must have a thorough understanding of each aspect of the continuum and anticipate parental expectations, child temperament, and the technical procedures necessary to complete care. By effectively using techniques within the continuum of behavior guidance, a healing relationship with the family is maintained while addressing dental disease and empowering the child to receive dental treatment throughout their lifetime. Copyright © 2013 Elsevier Inc. All rights reserved.

  14. On the Relativistic Correction of Particles Trajectory in Tandem Type Electrostatic Accelerator

    Science.gov (United States)

    Minárik, Stanislav

    2015-08-01

    A constant potential is applied to the acceleration of the ion-beam in the tandem type electrostatic accelerator. However, not just one voltage is applied, but instead a number of applications can be made in succession by means of the tandem arrangement of high voltage tubes. This number of voltage applications, which is the number of so-called "stages" of a tandem accelerator, may be two, three, or four, depending on the chosen design. Electrostatic field with approximately constant intensity acts on ions in any stage. In general, non-relativistic dynamics is used for the description of the ion transport in tandem accelerator. Energies of accelerated ions are too low and relativistic effects cannot be commonly observed by standard experimental technique. Estimation of possible relativistic correction of ion trajectories is therefore only a matter of calculation. In this note, we briefly present such calculation. Our aim is to show how using the relativistic dynamics modifies the particles trajectory in tandem type accelerator and what parameters determine this modification.

  15. Stability studies of colloidal silica dispersions in binary solvent mixtures

    International Nuclear Information System (INIS)

    Bean, Keith Howard

    1997-01-01

    A series of monodispersed colloidal silica dispersions, of varying radii, has been prepared. These particles are hydrophilic in nature due to the presence of surface silanol groups. Some of the particles have been rendered hydrophobic by terminally grafting n-alkyl (C 18 ) chains to the surface. The stability of dispersions of these various particles has been studied in binary mixtures of liquids, namely (i) ethanol and cyclohexane, and (ii) benzene and n-heptane. The ethanol - cyclohexane systems have been studied using a variety of techniques. Adsorption excess isotherms have been established and electrophoretic mobility measurements have been made. The predicted stability of the dispersions from D.V.L.O. calculations is compared to the observed stability. The hydrophilic silica particles behave as predicted by the calculations, with the zeta potential decreasing and the van der Waals attraction increasing with increasing cyclohexane concentration. The hydrophobic particles behave differently than expected, and the stability as a function of solvent mixture composition does not show a uniform trend. The effect of varying the coverage of C 18 chains on the surface and the effect of trace water in the systems has also been investigated. Organophilic silica dispersions in benzene - n-heptane solvent mixtures show weak aggregation and phase separation into a diffuse 'gas-like' phase and a more concentrated 'liquid-like' phase, analogous to molecular condensation processes. Calculations of the van der Waals potential as a function of solvent mixture composition show good agreement with the observed stability. Determination of the number of particles in each phase at equilibrium allows the energy of flocculation to be determined using a simple thermodynamic relationship. Finally, the addition of an AB block copolymer to organophilic silica particles in benzene n-heptane solvent mixtures has been shown to have a marked effect on the dispersion stability. This stability

  16. Solvent extraction

    Energy Technology Data Exchange (ETDEWEB)

    Coombs, D.M.; Latimer, E.G.

    1988-01-05

    It is an object of this invention to provide for the demetallization and general upgrading of heavy oil via a solvent extracton process, and to improve the efficiency of solvent extraction operations. The yield and demetallization of product oil form heavy high-metal content oil is maximized by solvent extractions which employ either or all of the following techniques: premixing of a minor amount of the solvent with feed and using countercurrent flow for the remaining solvent; use of certain solvent/free ratios; use of segmental baffle tray extraction column internals and the proper extraction column residence time. The solvent premix/countercurrent flow feature of the invention substantially improves extractions where temperatures and pressures above the critical point of the solvent are used. By using this technique, a greater yield of extract oil can be obtained at the same metals content or a lower metals-containing extract oil product can be obtained at the same yield. Furthermore, the premixing of part of the solvent with the feed before countercurrent extraction gives high extract oil yields and high quality demetallization. The solvent/feed ratio features of the invention substanially lower the captial and operating costs for such processes while not suffering a loss in selectivity for metals rejection. The column internals and rsidence time features of the invention further improve the extractor metals rejection at a constant yield or allow for an increase in extract oil yield at a constant extract oil metals content. 13 figs., 3 tabs.

  17. Performance-based shape optimization of continuum structures

    International Nuclear Information System (INIS)

    Liang Qingquan

    2010-01-01

    This paper presents a performance-based optimization (PBO) method for optimal shape design of continuum structures with stiffness constraints. Performance-based design concepts are incorporated in the shape optimization theory to achieve optimal designs. In the PBO method, the traditional shape optimization problem of minimizing the weight of a continuum structure with displacement or mean compliance constraints is transformed to the problem of maximizing the performance of the structure. The optimal shape of a continuum structure is obtained by gradually eliminating inefficient finite elements from the structure until its performance is maximized. Performance indices are employed to monitor the performance of optimized shapes in an optimization process. Performance-based optimality criteria are incorporated in the PBO method to identify the optimum from the optimization process. The PBO method is used to produce optimal shapes of plane stress continuum structures and plates in bending. Benchmark numerical results are provided to demonstrate the effectiveness of the PBO method for generating the maximum stiffness shape design of continuum structures. It is shown that the PBO method developed overcomes the limitations of traditional shape optimization methods in optimal design of continuum structures. Performance-based optimality criteria presented can be incorporated in any shape and topology optimization methods to obtain optimal designs of continuum structures.

  18. Electrostatic effect for the collisionless tearing mode

    International Nuclear Information System (INIS)

    Hoshino, M.

    1987-01-01

    Electron dynamics has not been self-consistently considered in collisionless tearing mode theories to date because of the mathematical complexity of the Vlasov-Maxwell equations. We have found using computer simulations that electrostatic fields play an important role in the tearing mode. Vlasov theory, including the electrostatic field, is investigated for topologies with both antiparallel and nonantiparallel magnetic field lines. The electrostatic field influences the resonant current in the neutral sheet which is a non-MHD effect, and modifies the linear growth rate. At the magnetopause, where the field lines are not antiparallel, the electrostatic effect acts to raise the linear growth rate of the tearing mode. On the other hand, in the magnetotail, where magnetic field lines are antiparallel, the electrostatic effect reduces the tearing mode growth rate. copyright American Geophysical Union 1987

  19. Calculation of photoionization differential cross sections using complex Gauss-type orbitals.

    Science.gov (United States)

    Matsuzaki, Rei; Yabushita, Satoshi

    2017-09-05

    Accurate theoretical calculation of photoelectron angular distributions for general molecules is becoming an important tool to image various chemical reactions in real time. We show in this article that not only photoionization total cross sections but also photoelectron angular distributions can be accurately calculated using complex Gauss-type orbital (cGTO) basis functions. Our method can be easily combined with existing quantum chemistry techniques including electron correlation effects, and applied to various molecules. The so-called two-potential formula is applied to represent the transition dipole moment from an initial bound state to a final continuum state in the molecular coordinate frame. The two required continuum functions, the zeroth-order final continuum state and the first-order wave function induced by the photon field, have been variationally obtained using the complex basis function method with a mixture of appropriate cGTOs and conventional real Gauss-type orbitals (GTOs) to represent the continuum orbitals as well as the remaining bound orbitals. The complex orbital exponents of the cGTOs are optimized by fitting to the outgoing Coulomb functions. The efficiency of the current method is demonstrated through the calculations of the asymmetry parameters and molecular-frame photoelectron angular distributions of H2+ and H2 . In the calculations of H2 , the static exchange and random phase approximations are employed, and the dependence of the results on the basis functions is discussed. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  20. The electrostatic atomization of hydrocarbons

    Energy Technology Data Exchange (ETDEWEB)

    Kelly, A J

    1984-06-01

    Exploitation of the unique and potentially beneficial characteristics of electrostatic atomization in combustion systems has foundered upon the inability of two element, diode devices to operate at flow rates that are larger than a fraction of a millilitre per second. This restriction has been attributed to the high innate electrical resistivity of hydrocarbon fuels. A discussion of proposed electrostatic fuel atomizers and their limitations is presented from the vantage of a recently developed theory of electrostatic spraying. Comparison of theory and experiment reveals the existence of a 'constant of spraying' and the presence of an operational regime in which low charge density droplet development is possible. Operation with hydrocarbons in this regime occurs when the mean droplet size is greater than or equal to 10 ..mu..m and fluid viscosity is below about 250 cp. The resulting spray has a mean droplet size that is functionally dependent only upon the free charge density level of the fluid. Consequently there is no theoretical impediment to the attainment of high flow rate electrostatic atomization with fluids of arbitrary conductivity. Implementation is achieved by a general class of electrostatic spray devices which employ direct charge injection. The Spray Triode, a submerged field-emission electron gun, represents a particularly simple member of this new class of atomizer. Among the Spray Triode operational characteristics to be discussed is insensitivity to spray fluid properties and flow rate.

  1. Area Regge calculus and continuum limit

    International Nuclear Information System (INIS)

    Khatsymovsky, V.M.

    2002-01-01

    Encountered in the literature generalisations of general relativity to independent area variables are considered, the discrete (generalised Regge calculus) and continuum ones. The generalised Regge calculus can be either with purely area variables or, as we suggest, with area tensor-connection variables. Just for the latter, in particular, we prove that in analogy with corresponding statement in ordinary Regge calculus (by Feinberg, Friedberg, Lee and Ren), passing to the (appropriately defined) continuum limit yields the generalised continuum area tensor-connection general relativity

  2. catalysed ortho-carboxylation of acetanilide with CO

    Indian Academy of Sciences (India)

    Abstract. The mechanism of palladium(II)-catalysed carboxylation of acetanilide with CO has been investi- gated using density functional theory calculation done at the B3LYP/6-31G(d, p)(SDD for Pd) level of theory. Solvent effects on these reactions have been explored by calculation that included a polarizable continuum.

  3. Electrostatic turbulence with finite parallel correlation length and radial electric field generation

    International Nuclear Information System (INIS)

    Vlad, M.; Spineanu, F.; Misguich, J.H.; Balescu, R.

    2001-01-01

    Particle diffusion in a given electrostatic turbulence with a finite correlation length along the confining magnetic field is studied in the test particle approach. An anomalous diffusion regime of amplified diffusion coefficients is found in the conditions when particle trapping in the structure of the stochastic potential is effective. The auto-generated radial electric field is calculated. (author)

  4. Experimental study of a variable-capacitance micromotor with electrostatic suspension

    International Nuclear Information System (INIS)

    Han, F T; Wu, Q P; Wang, L

    2010-01-01

    A variable-capacitance micromotor where the rotor is supported electrostatically in five degrees of freedom was designed, fabricated and tested in order to study the behavior of this electrostatic motor. The micromachined device is based on a glass/silicon/glass stack bonding structure, fabricated by bulk micromachining and initially operated in atmospheric environment. The analytical torque model is obtained by calculating the capacitances between different stator electrodes and the rotor. Capacitance values in the order of 10 −13 pF and torque values in the order of 10 −10 N m have been calculated from the motor geometry and attainable drive voltage. A dynamic model of the motor is proposed by further estimating the air-film damping effect in an effort to explain the experimental rotation measurements. Experimental results of starting voltage, continuous operation, switching response and electric bearing of the micromotor are presented and discussed. Preliminary measurements indicate that a rotor rotating speed of 73.3 r min −1 can be achieved at a drive voltage of 28.3 V, equivalent to a theoretical motive torque of 517 pN m. Starting voltage results obtained from experimental measurement are in agreement with the developed dynamic model

  5. PREFACE: Electrostatics 2015

    Science.gov (United States)

    Matthews, James

    2015-10-01

    Electrostatics 2015, supported by the Institute of Physics, was held in the Sir James Matthews building at Southampton Solent University, UK between 12th and 16th April 2015. Southampton is a historic city on the South Coast of England with a strong military and maritime history. Southampton is home to two Universities: Solent University, which hosted the conference, and the University of Southampton, where much work is undertaken related to electrostatics. 37 oral and 44 poster presentations were accepted for the conference, and 60 papers were submitted and accepted for the proceedings. The Bill Bright Memorial Lecture was delivered this year by Professor Mark Horenstein from Boston University who was, until recently, Editor-in-Chief of the Journal of Electrostatics. He spoke on The contribution of surface potential to diverse problems in electrostatics and his thorough knowledge of the subject of electrostatics was evident in the presentation. The first session was chaired by the Conference Chair, Dr Keith Davies, whose experience in the field showed through his frequent contributions to the discussions throughout the conference. Hazards and Electrostatic Discharge have formed a strong core to Electrostatics conferences for many years, and this conference contained sessions on both Hazards and on ESD, including an invited talk from Dr Jeremy Smallwood on ESD in Industry - Present and Future. Another strong theme to emerge from this year's programme was Non-Thermal Plasmas, which was covered in two sessions. There were two invited talks on this subject: Professor Masaaki Okubo gave a talk on Development of super-clean diesel engine and combustor using nonthermal plasma hybrid after treatment and Dr David Go presented a talk on Atmospheric-pressure ionization processes: New approaches and applications for plasmas in contact with liquids. A new innovation to the conference this year was the opportunity for conference sponsors to present to the delegates a technical

  6. Two-dimensional hydrodynamics of uniform ion plasma in electrostatic field

    International Nuclear Information System (INIS)

    Mahdieh, M. H.; Gavili, A.

    2005-01-01

    Two-dimensional hydrodynamics of ion extraction from uniform quasi-neutral plasma, in electrostatic field has been simulated numerically. Experimentally, tunable pulsed lasers produce non-uniform plasma through stepwise photo-excitation and photo-ionization or multi-photo-ionization processes. Poisson's equation was solved simultaneously with the equations of mass, and momentum, assuming the Maxwell-Boltzmann distribution for electrons. In the calculation, the initial density profile at the boundaries has been assumed to be very steep for the ion plasma. In these calculations dynamics of electric potential and the ions density were assessed. The ion extraction time was also estimated from the calculation. The knowledge of spatial distribution of the ions across the cathode is very important for the practical purposes. In this simulation, the spatial distribution of the ion current density across the cathode as well as its temporal distribution was calculated

  7. Electrostatic curtain studies

    International Nuclear Information System (INIS)

    Meyer, L.C.

    1992-05-01

    This report presents the results of experiments using electrostatic curtains (ESCS) as a transuranic (TRU) contamination control technique. The TRU contaminants included small (micrometer to sub micrometer) particles of plutonium and americium compounds associated with defense-related waste. Three series of experiments were conducted. The first was with uncontaminated Idaho National Engineering Laboratory (INEL) soil, the second used contaminated soil containing plutonium-239 (from a mixture of Rocky Flats Plant contaminated soil and INEL uncontaminated soil), and the third was uncontaminated INEL soil spiked with plutonium-239. All experiments with contaminated soil were conducted inside a glove box containing a dust generator, low volume cascade impactor (LVCI), electrostatic separator, and electrostatic materials. The data for these experiments consisted of the mass of dust collected on the various material coupons, plates, and filters; radiochemical analysis of selected samples; and photographs, as well as computer printouts giving particle size distributions and dimensions from the scanning electron microscope (SEM). The following results were found: (a) plutonium content (pCi/g) was found to increase with smaller soil particle sizes and (b) the electrostatic field had a stronger influence on smaller particle sizes compared to larger particle sizes. The SEM analysis indicated that the particle size of the tracer Pu239 used in the spiked soil experiments was below the detectable size limit (0.5 μm) of the SEM and, thus, may not be representative of plutonium particles found in defense-related waste. The use of radiochemical analysis indicated that plutonium could be found on separator plates of both polarities, as well as passing through the electric field and collecting on LVCI filters

  8. Electrostatic Levitator Electrode Layout

    Science.gov (United States)

    1998-01-01

    Schematic of Electrostatic Levitator (ESL) electrodes and controls system. The ESL uses static electricity to suspend an object (about 2-3 mm in diameter) inside a vacuum chamber while a laser heats the sample until it melts. This lets scientists record a wide range of physical properties without the sample contacting the container or any instruments, conditions that would alter the readings. The Electrostatic Levitator is one of several tools used in NASA's microgravity materials science program.

  9. Calculation of the settling zone of a mixing-settling extractor

    International Nuclear Information System (INIS)

    Karpacheva, S.M.

    1987-01-01

    An attempt is made to construct a parameter-sensitive model for the optimal dimensional configuration of a mixer-settler for the extraction of uranyl and other nitrates with various solutions of tributylphosphate as the solvent. The model accounts for the emulsion and hydraulic behavior of the phases of the starting solutions as well as electrostatic and surface tension considerations and is shown to be capable of incorporating and assessing the separation rate and time dependence accurately for a wide range of dimensions. Nitrates of sodium, aluminium, and ammonium are used as the test extractants

  10. The electrostatic interaction of two point charges in equilibrium plasmas within the Debye approximation

    International Nuclear Information System (INIS)

    Filippov, A V

    2015-01-01

    This paper is devoted to a careful study of two charge interaction in an equilibrium plasma within the Debye approximation. The effect of external boundary conditions for the electric field strength and potential on the electrostatic force is studied. The problem is solved by the method of potential decomposition into Legendre polynomials up to the fifth multipole term included. It is shown that the effect of attraction of identically charged macroparticles is explained by the influence of the external boundary. When the size of a calculation cell is increased the attraction effect disappears and the electrostatic force is well described by the screened Debye-Hückel potential. (paper)

  11. Continuous electrodeionization through electrostatic shielding

    International Nuclear Information System (INIS)

    Dermentzis, Konstantinos

    2008-01-01

    We report a new continuous electrodeionization cell with electrostatically shielded concentrate compartments or electrochemical Faraday cages formed by porous electronically and ionically conductive media, instead of permselective ion exchange membranes. Due to local elimination of the applied electric field within the compartments, they electrostatically retain the incoming ions and act as 'electrostatic ion pumps' or 'ion traps' and therefore concentrate compartments. The porous media are chemically and thermally stable. Electrodeionization or electrodialysis cells containing such concentrate compartments in place of ion exchange membranes can be used to regenerate ion exchange resins and produce deionized water, to purify industrial effluents and desalinate brackish or seawater. The cells can work by polarity reversal without any negative impact to the deionization process. Because the electronically and ionically active media constituting the electrostatically shielded concentrate compartments are not permselective and coions are not repelled but can be swept by the migrating counterions, the cells are not affected by the known membrane associated limitations, such as concentration polarization or scaling and show an increased current efficiency

  12. Continuum mechanics of single-substance bodies

    CERN Document Server

    Eringen, A Cemal

    1975-01-01

    Continuum Physics, Volume II: Continuum Mechanics of Single-Substance Bodies discusses the continuum mechanics of bodies constituted by a single substance, providing a thorough and precise presentation of exact theories that have evolved during the past years. This book consists of three parts-basic principles, constitutive equations for simple materials, and methods of solution. Part I of this publication is devoted to a discussion of basic principles irrespective of material geometry and constitution that are valid for all kinds of substances, including composites. The geometrical notions, k

  13. Structural and vibrational properties of oxcarbazepine, an anticonvulsant substance by using DFT and SCRF calculations

    Science.gov (United States)

    Ladetto, María F.; Márquez, María B.; Brandán, Silvia A.

    2014-10-01

    In this work, we have presented a structural and vibrational study on the properties in gas and aqueous solution phases of oxcarbazepine, a polymorphic anticonvulsant substance, combining the available IR and Raman spectra with Density Functional Theory (DFT) calculations. Two stable C1 and C2 forms for the title molecule were theoretically determined by using the hybrid B3LYP/6-31G* method. The integral equation formalism variant polarised continuum model (IEFPCM) was employed to study the solvent effects by means of the self-consistent reaction field (SCRF) method. The vibrational spectra for the two forms of oxcarbazepine were completely assigned together with two dimeric species also observed in the solid phase. The presences of the two C1 and C2 forms together with the two dimeric species are supported by the IR and Raman bands between 1424 and 125 cm-1. Here, the properties for both forms of oxcarbazepine are compared and discussed.

  14. Progresses in Ab Initio QM/MM Free Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pKa, Redox Reactions and Solvation Free Energies

    Energy Technology Data Exchange (ETDEWEB)

    Kamerlin, Shina C. L.; Haranczyk, Maciej; Warshel, Arieh

    2009-03-01

    Hybrid quantum mechanical / molecular mechanical (QM/MM) approaches have been used to provide a general scheme for chemical reactions in proteins. However, such approaches still present a major challenge to computational chemists, not only because of the need for very large computer time in order to evaluate the QM energy but also because of the need for propercomputational sampling. This review focuses on the sampling issue in QM/MM evaluations of electrostatic energies in proteins. We chose this example since electrostatic energies play a major role in controlling the function of proteins and are key to the structure-function correlation of biological molecules. Thus, the correct treatment of electrostatics is essential for the accurate simulation of biological systems. Although we will be presenting here different types of QM/MM calculations of electrostatic energies (and related properties), our focus will be on pKa calculations. This reflects the fact that pKa of ionizable groups in proteins provide one of the most direct benchmarks for the accuracy of electrostatic models of macromolecules. While pKa calculations by semimacroscopic models have given reasonable results in many cases, existing attempts to perform pKa calculations using QM/MM-FEP have led to large discrepancies between calculated and experimental values. In this work, we accelerate our QM/MM calculations using an updated mean charge distribution and a classical reference potential. We examine both a surface residue (Asp3) of the bovine pancreatic trypsin inhibitor, as well as a residue buried in a hydrophobic pocket (Lys102) of the T4-lysozyme mutant. We demonstrate that by using this approach, we are able to reproduce the relevant sidechain pKas with an accuracy of 3 kcal/mol. This is well within the 7 kcal/mol energy difference observed in studies of enzymatic catalysis, and is thus sufficient accuracy to determine the main contributions to the catalytic energies of enzymes. We also provide an

  15. Surface electrostatics: theory and computations

    KAUST Repository

    Chatzigeorgiou, G.

    2014-02-05

    The objective of this work is to study the electrostatic response of materials accounting for boundary surfaces with their own (electrostatic) constitutive behaviour. The electric response of materials with (electrostatic) energetic boundary surfaces (surfaces that possess material properties and constitutive structures different from those of the bulk) is formulated in a consistent manner using a variational framework. The forces and moments that appear due to bulk and surface electric fields are also expressed in a consistent manner. The theory is accompanied by numerical examples on porous materials using the finite-element method, where the influence of the surface electric permittivity on the electric displacement, the polarization stress and the Maxwell stress is examined.

  16. Canyon solvent cleaning

    International Nuclear Information System (INIS)

    Reif, D.J.

    1986-01-01

    The HM Process at the Savannah River Plant (SRP) uses 7.5% tributylphosphate in n-paraffin as an extraction solvent. During use, the solvent is altered due to hydrolysis and radiolysis, forming materials that influence product losses, produce decontamination, and separation efficiencies. Laboratory studies to improve online solvent cleaning have shown the carbonate washing, although removing residual solvent activity does not remove binding ligands that hold fission products in the solvent. Treatment of solvent by an alumina adsorption process removes binding ligands and significantly improves recycle solvent performance. Both laboratory work defining a full-scale alumina adsorption process and the use of the process to clean HM Process first cycle solvent are presented

  17. Distribution of multi-component solvents in solvent vapor extraction chamber

    Energy Technology Data Exchange (ETDEWEB)

    Das, S. [Society of Petroleum Engineers, Richardson, TX (United States)]|[Marathon Oil Corp., Houston, TX (United States)

    2008-10-15

    Vapex process performance is sensitive to operating pressures, temperatures and the types of solvent used. The hydrocarbon solvents used in Vapex processes typically have between 5 and 10 per cent hydrocarbon impurities, and the accumulation of dense phases inside the vapor chamber reduces gravity drainage potential. This study investigated the partitioning of solvent compounds inside the vapor chamber during in situ Vapex processes.The aim of the study was to examine how the different components of the mixed solvent partitioned inside the extracted chamber during the oil and vapor phase. A 2-D homogenous reservoir model was used to simulate the Vapex process with a solvent mixture comprised of propane and methane at various percentages. The effect of injecting a hot solvent vapor was also investigated. The study showed that injected methane accumulated at both the top and the extraction interface. Accumulations near the top had a positive impact on solvent confinement in thin reservoirs. Diffusion of the solvent component was controlled by gas phase molecular diffusion, and was much faster than the diffusion of solvent molecules in the liquid phase. The use of hot solvent mixtures slowed the extraction process due to lower solvent solubility in the oil phase. It was concluded that the negative impact on viscosity reduction by dilution was not compensated by rises in temperature. 6 refs., 11 figs.

  18. Theoretical calculation of reorganization energy for electron self-exchange reaction by constrained density functional theory and constrained equilibrium thermodynamics.

    Science.gov (United States)

    Ren, Hai-Sheng; Ming, Mei-Jun; Ma, Jian-Yi; Li, Xiang-Yuan

    2013-08-22

    Within the framework of constrained density functional theory (CDFT), the diabatic or charge localized states of electron transfer (ET) have been constructed. Based on the diabatic states, inner reorganization energy λin has been directly calculated. For solvent reorganization energy λs, a novel and reasonable nonequilibrium solvation model is established by introducing a constrained equilibrium manipulation, and a new expression of λs has been formulated. It is found that λs is actually the cost of maintaining the residual polarization, which equilibrates with the extra electric field. On the basis of diabatic states constructed by CDFT, a numerical algorithm using the new formulations with the dielectric polarizable continuum model (D-PCM) has been implemented. As typical test cases, self-exchange ET reactions between tetracyanoethylene (TCNE) and tetrathiafulvalene (TTF) and their corresponding ionic radicals in acetonitrile are investigated. The calculated reorganization energies λ are 7293 cm(-1) for TCNE/TCNE(-) and 5939 cm(-1) for TTF/TTF(+) reactions, agreeing well with available experimental results of 7250 cm(-1) and 5810 cm(-1), respectively.

  19. Introduction to numerical electrostatics using MATLAB

    CERN Document Server

    Dworsky, Lawrence N

    2014-01-01

    The first of its kind uniquely devoted to the field of computational electrostatics, this book dives headfirst into the actual problems that engineers are expected to solve using method of moment (MoM), finite difference, and finite element techniques. Readers are guided step by step through specific problems and challenges, covering all aspects of electrostatics with an emphasis on numerical procedures. Focusing on practical examples, mathematical equations, and common issues with algorithms, this is an ideal text for students in engineering, physics, and electrostatics-and working engineers

  20. Specific Electrostatic Molecular Recognition in Water

    DEFF Research Database (Denmark)

    Li, Ming; Hoeck, Casper; Schoffelen, Sanne

    2016-01-01

    The identification of pairs of small peptides that recognize each other in water exclusively through electrostatic interactions is reported. The target peptide and a structure-biased combinatorial ligand library consisting of ≈78 125 compounds were synthesized on different sized beads. Peptide......-bead binding assay and by 2D NMR spectroscopy. Molecular dynamics (MD) studies revealed a putative mode of interaction for this unusual electrostatic binding event. High binding specificity occurred through a combination of topological matching and electrostatic and hydrogen-bond complementarities. From MD...