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Sample records for continuum electrostatic calculations

  1. Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins.

    PubMed Central

    Georgescu, Roxana E; Alexov, Emil G; Gunner, Marilyn R

    2002-01-01

    Protein stability and function relies on residues being in their appropriate ionization states at physiological pH. In situ residue pK(a)s also provides a sensitive measure of the local protein environment. Multiconformation continuum electrostatics (MCCE) combines continuum electrostatics and molecular mechanics force fields in Monte Carlo sampling to simultaneously calculate side chain ionization and conformation. The response of protein to charges is incorporated both in the protein dielectric constant (epsilon(prot)) of four and by explicit conformational changes. The pK(a) of 166 residues in 12 proteins was determined. The root mean square error is 0.83 pH units, and >90% have errors of <1 pH units whereas only 3% have errors >2 pH units. Similar results are found with crystal and solution structures, showing that the method's explicit conformational sampling reduces sensitivity to the initial structure. The outcome also changes little with protein dielectric constant (epsilon(prot) 4-20). Multiconformation continuum electrostatics titrations show coupling of conformational flexibility and changes in ionization state. Examples are provided where ionizable side chain position (protein G), Asn orientation (lysozyme), His tautomer distribution (RNase A), and phosphate ion binding (RNase A and H) change with pH. Disallowing these motions changes the calculated pK(a). PMID:12324397

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

    SciTech Connect

    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.

  3. Structural Determinants of Improved Fluorescence in a Family of Bacteriophytochrome-Based Infrared Fluorescent Proteins: Insights from Continuum Electrostatic Calculations and Molecular Dynamics Simulations.

    PubMed

    Feliks, Mikolaj; Lafaye, Céline; Shu, Xiaokun; Royant, Antoine; Field, Martin

    2016-08-09

    Using X-ray crystallography, continuum electrostatic calculations, and molecular dynamics simulations, we have studied the structure, protonation behavior, and dynamics of the biliverdin chromophore and its molecular environment in a series of genetically engineered infrared fluorescent proteins (IFPs) based on the chromophore-binding domain of the Deinococcus radiodurans bacteriophytochrome. Our study suggests that the experimentally observed enhancement of fluorescent properties results from the improved rigidity and planarity of the biliverdin chromophore, in particular of the first two pyrrole rings neighboring the covalent linkage to the protein. We propose that the increases in the levels of both motion and bending of the chromophore out of planarity favor the decrease in fluorescence. The chromophore-binding pocket in some of the studied proteins, in particular the weakly fluorescent parent protein, is shown to be readily accessible to water molecules from the solvent. These waters entering the chromophore region form hydrogen bond networks that affect the otherwise planar conformation of the first three rings of the chromophore. On the basis of our simulations, the enhancement of fluorescence in IFPs can be achieved either by reducing the mobility of water molecules in the vicinity of the chromophore or by limiting the interactions of the nearby protein residues with the chromophore. Finally, simulations performed at both low and neutral pH values highlight differences in the dynamics of the chromophore and shed light on the mechanism of fluorescence loss at low pH.

  4. Continuum electrostatic calculations of the pKa of ionizable residues in an ion channel: dynamic vs. static input structure.

    PubMed

    Aguilella-Arzo, M; Aguilella, V M

    2010-04-01

    We have computed the pK(a)'s of the ionizable residues of a protein ion channel, the Staphylococcus aureus toxin alpha-hemolysin, by using two types of input structures, namely the crystal structure of the heptameric alpha-hemolysin and a set of over four hundred snapshots from a 4.38 ns Molecular Dynamics simulation of the protein inserted in a phospholipid planar bilayer. The comparison of the dynamic picture provided by the Molecular Simulation with the static one based on the X-ray crystal structure of the protein embedded in a lipid membrane allows analyzing the influence of the fluctuations in the protein structure on its ionization properties. We find that the use of the dynamic structure provides interesting information about the sensitivity of the computed pK(a) of a given residue to small changes in the local structure. The calculated pK(a) are consistent with previous indirect estimations obtained from single-channel conductance and selectivity measurements.

  5. Using Programmable Calculators to Solve Electrostatics Problems.

    ERIC Educational Resources Information Center

    Yerian, Stephen C.; Denker, Dennis A.

    1985-01-01

    Provides a simple routine which allows first-year physics students to use programmable calculators to solve otherwise complex electrostatic problems. These problems involve finding electrostatic potential and electric field on the axis of a uniformly charged ring. Modest programing skills are required of students. (DH)

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

    NASA Astrophysics Data System (ADS)

    Bardhan, Jaydeep P.

    2011-09-01

    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 pKa shifts and find that using standard protein parameters (ɛprotein = 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.

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

    PubMed

    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.

  8. The Calculation of the Electrostatic Potential of Infinite Charge Distributions

    ERIC Educational Resources Information Center

    Redzic, Dragan V.

    2012-01-01

    We discuss some interesting aspects in the calculation of the electrostatic potential of charge distributions extending to infinity. The presentation is suitable for the advanced undergraduate level. (Contains 3 footnotes.)

  9. Fast Calculations of Electrostatic Solvation Free Energy from Reconstructed Solvent Density Using Proximal Radial Distribution Functions

    SciTech Connect

    Lin, Bin; Wong, Ka-Yiu; Hu, Char Y.; Kokubo, Hironori; Pettitt, Bernard M.

    2011-07-07

    Although detailed atomic models may be applied for a full description of solvation, simpler phenomenologicalmodels are particularly useful to interpret the results for scanning many large, complex systems, where a full atomic model is too computationally expensive to use. Among the most costly are solvation free-energy evaluations by simulation. Here we develop a fast way to calculate electrostatic solvation free energy while retaining much of the accuracy of explicit solvent free-energy simulation. The basis of our method is to treat the solvent not as a structureless dielectric continuum but as a structured medium by making use of universal proximal radial distribution functions. Using a deca-alanine peptide as a test case, we compare the use of our theory with free-energy simulations and traditional continuum estimates of the electrostatic solvation free energy.

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

    NASA Technical Reports Server (NTRS)

    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 multispectral 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/sq m, which compared to the 4 W/sq m magnitude of the greenhouse gas forcing and the 1-2 W/sq 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

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

    NASA Technical Reports Server (NTRS)

    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

  12. Membrane protein properties revealed through data-rich electrostatics calculations

    PubMed Central

    Guerriero, Christopher J.; Brodsky, Jeffrey L.; Grabe, Michael

    2015-01-01

    SUMMARY 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. PMID:26118532

  13. A structural model for K2P potassium channels based on 23 pairs of interacting sites and continuum electrostatics

    PubMed Central

    Kollewe, Astrid; Lau, Albert Y.; Sullivan, Ashley; Benoît Roux

    2009-01-01

    K2PØ, the two-pore domain potassium background channel that determines cardiac rhythm in Drosophila melanogaster, and its homologues that establish excitable membrane activity in mammals are of unknown structure. K2P subunits have two pore domains flanked by transmembrane (TM) spans: TM1-P1-TM2-TM3-P2-TM4. To establish spatial relationships in K2PØ, we identified pairs of sites that display electrostatic compensation. Channels silenced by the addition of a charge in pore loop 1 (P1) or P2 were restored to function by countercharges at specific second sites. A three-dimensional homology model was determined using the crystal structure of KV1.2, effects of K2PØ mutations to establish alignment, and compensatory charge–charge pairs. The model was refined and validated by continuum electrostatic free energy calculations and covalent linkage of introduced cysteines. K2P channels use two subunits arranged so that the P1 and P2 loops contribute to one pore, identical P loops face each other diagonally across the pore, and the channel complex has bilateral symmetry with a fourfold symmetric selectivity filter. PMID:19564427

  14. Electrostatic calculations of amino acid titration and electron transfer, Q-AQB-->QAQ-B, in the reaction center.

    PubMed Central

    Beroza, P; Fredkin, D R; Okamura, M Y; Feher, G

    1995-01-01

    The titration of amino acids and the energetics of electron transfer from the primary electron acceptor (QA) to the secondary electron acceptor (QB) in the photosynthetic reaction center of Rhodobacter sphaeroides are calculated using a continuum electrostatic model. Strong electrostatic interactions between titrating sites give rise to complex titration curves. Glu L212 is calculated to have an anomalously broad titration curve, which explains the seemingly contradictory experimental results concerning its pKa. The electrostatic field following electron transfer shifts the average protonation of amino acids near the quinones. The pH dependence of the free energy between Q-AQB and QAQ-B calculated from these shifts is in good agreement with experiment. However, the calculated absolute free energy difference is in severe disagreement (by approximately 230 meV) with the observed experimental value, i.e., electron transfer from Q-A to QB is calculated to be unfavorable. The large stabilization energy of the Q-A state arises from the predominantly positively charged residues in the vicinity of QA in contrast to the predominantly negatively charged residues near QB. The discrepancy between calculated and experimental values for delta G(Q-AQB-->QAQ-B) points to limitations of the continuum electrostatic model. Inclusion of other contributions to the energetics (e.g., protein motion following quinone reduction) that may improve the agreement between theory and experiment are discussed. PMID:7647231

  15. Robust Identification of Binding Hot Spots Using Continuum Electrostatics: Application to Hen Egg-White Lysozyme

    PubMed Central

    2011-01-01

    Binding hot spots, protein regions with high binding affinity, can be identified by using X-ray crystallography or NMR spectroscopy to screen libraries of small organic molecules that tend to cluster at such hot spots. FTMap, a direct computational analogue of the experimental screening approaches, uses 16 different probe molecules for global sampling of the surface of a target protein on a dense grid and evaluates the energy of interaction using an empirical energy function that includes a continuum electrostatic term. Energy evaluation is based on the fast Fourier transform correlation approach, which allows for the sampling of billions of probe positions. The grid sampling is followed by off-grid minimization that uses a more detailed energy expression with a continuum electrostatics term. FTMap identifies the hot spots as consensus clusters formed by overlapping clusters of several probes. The hot spots are ranked on the basis of the number of probe clusters, which predicts their binding propensity. We applied FTMap to nine structures of hen egg-white lysozyme (HEWL), whose hot spots have been extensively studied by both experimental and computational methods. FTMap found the primary hot spot in site C of all nine structures, in spite of conformational differences. In addition, secondary hot spots in sites B and D that are known to be important for the binding of polysaccharide substrates were found. The predicted probe–protein interactions agree well with those seen in the complexes of HEWL with various ligands and also agree with an NMR-based study of HEWL in aqueous solutions of eight organic solvents. We argue that FTMap provides more complete information on the HEWL binding site than previous computational methods and yields fewer false-positive binding locations than the X-ray structures of HEWL from crystals soaked in organic solvents. PMID:22092261

  16. Calculation of electrostatic fields in periodic structures of complex shape

    NASA Technical Reports Server (NTRS)

    Kravchenko, V. F.

    1978-01-01

    A universal algorithm is presented for calculating electrostatic fields in an infinite periodic structure consisting of electrodes of arbitrary shape which are located in mirror-symmetrical manner along the axis of electron-beam propagation. The method is based on the theory of R-functions, and the differential operators which are derived on the basis of the functions. Numerical results are presented and the accuracy of the results is examined.

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

    PubMed

    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.

  18. MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations

    NASA Astrophysics Data System (ADS)

    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.

  19. Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility.

    PubMed

    You, T J; Bashford, D

    1995-11-01

    A new method for including local conformational flexibility in calculations of the hydrogen ion titration of proteins using macroscopic electrostatic models is presented. Intrinsic pKa values and electrostatic interactions between titrating sites are calculated from an ensemble of conformers in which the positions of titrating side chains are systematically varied. The method is applied to the Asp, Glu, and Tyr residues of hen lysozyme. The effects of different minimization and/or sampling protocols for both single-conformer and multi-conformer calculations are studied. For single-conformer calculations it is found that the results are sensitive to the choice of all-hydrogen versus polar-hydrogen-only atomic models and to the minimization protocol chosen. The best overall agreement of single-conformer calculations with experiment is obtained with an all-hydrogen model and either a two-step minimization process or minimization using a high dielectric constant. Multi-conformational calculations give significantly improved agreement with experiment, slightly smaller shifts between model compound pKa values and calculated intrinsic pKa values, and reduced sensitivity of the intrinsic pKa calculations to the initial details of the structure compared to single-conformer calculations. The extent of these improvements depends on the type of minimization used during the generation of conformers, with more extensive minimization giving greater improvements. The ordering of the titrations of the active-site residues, Glu-35 and Asp-52, is particularly sensitive to the minimization and sampling protocols used. The balance of strong site-site interactions in the active site suggests a need for including site-site conformational correlations.

  20. Calculating Free Energy Changes in Continuum Solvation Models

    SciTech Connect

    Ho, Junming; Ertem, Mehmed Z.

    2016-02-27

    We recently showed for a large dataset of pKas and reduction potentials that free energies calculated directly within the SMD continuum model compares very well with corresponding thermodynamic cycle calculations in both aqueous and organic solvents (Phys. Chem. Chem. Phys. 2015, 17, 2859). In this paper, we significantly expand the scope of our study to examine the suitability of this approach for the calculation of general solution phase kinetics and thermodynamics, in conjunction with several commonly used solvation models (SMDM062X, SMD-HF, CPCM-UAKS, and CPCM-UAHF) for a broad range of systems and reaction types. This includes cluster-continuum schemes for pKa calculations, as well as various neutral, radical and ionic reactions such as enolization, cycloaddition, hydrogen and chlorine atom transfer, and bimolecular SN2 and E2 reactions. On the basis of this benchmarking study, we conclude that the accuracies of both approaches are generally very similar – the mean errors for Gibbs free energy changes of neutral and ionic reactions are approximately 5 kJ mol-1 and 25 kJ mol-1 respectively. In systems where there are significant structural changes due to solvation, as is the case for certain ionic transition states and amino acids, the direct approach generally afford free energy changes that are in better agreement with experiment. The results indicate that when appropriate combinations of electronic structure methods are employed, the direct approach provides a reliable alternative to the thermodynamic cycle calculations of solution phase kinetics and thermodynamics across a broad range of organic reactions.

  1. Calculating Free Energy Changes in Continuum Solvation Models

    DOE PAGES

    Ho, Junming; Ertem, Mehmed Z.

    2016-02-27

    We recently showed for a large dataset of pKas and reduction potentials that free energies calculated directly within the SMD continuum model compares very well with corresponding thermodynamic cycle calculations in both aqueous and organic solvents (Phys. Chem. Chem. Phys. 2015, 17, 2859). In this paper, we significantly expand the scope of our study to examine the suitability of this approach for the calculation of general solution phase kinetics and thermodynamics, in conjunction with several commonly used solvation models (SMDM062X, SMD-HF, CPCM-UAKS, and CPCM-UAHF) for a broad range of systems and reaction types. This includes cluster-continuum schemes for pKa calculations,more » as well as various neutral, radical and ionic reactions such as enolization, cycloaddition, hydrogen and chlorine atom transfer, and bimolecular SN2 and E2 reactions. On the basis of this benchmarking study, we conclude that the accuracies of both approaches are generally very similar – the mean errors for Gibbs free energy changes of neutral and ionic reactions are approximately 5 kJ mol-1 and 25 kJ mol-1 respectively. In systems where there are significant structural changes due to solvation, as is the case for certain ionic transition states and amino acids, the direct approach generally afford free energy changes that are in better agreement with experiment. The results indicate that when appropriate combinations of electronic structure methods are employed, the direct approach provides a reliable alternative to the thermodynamic cycle calculations of solution phase kinetics and thermodynamics across a broad range of organic reactions.« less

  2. Continuum solvent model calculations of alamethicin-membrane interactions: thermodynamic aspects.

    PubMed Central

    Kessel, A; Cafiso, D S; Ben-Tal, N

    2000-01-01

    Alamethicin is a 20-amino acid antibiotic peptide that forms voltage-gated ion channels in lipid bilayers. Here we report calculations of its association free energy with membranes. The calculations take into account the various free-energy terms that contribute to the transfer of the peptide from the aqueous phase into bilayers of different widths. The electrostatic and nonpolar contributions to the solvation free energy are calculated using continuum solvent models. The contributions from the lipid perturbation and membrane deformation effects and the entropy loss associated with peptide immobilization in the bilayer are estimated from a statistical thermodynamic model. The calculations were carried out using two classes of experimentally observed conformations, both of which are helical: the NMR and the x-ray crystal structures. Our calculations show that alamethicin is unlikely to partition into bilayers in any of the NMR conformations because they have uncompensated backbone hydrogen bonds and their association with the membrane involves a large electrostatic solvation free energy penalty. In contrast, the x-ray conformations provide enough backbone hydrogen bonds for the peptide to associate with bilayers. We tested numerous transmembrane and surface orientations of the peptide in bilayers, and our calculations indicate that the most favorable orientation is transmembrane, where the peptide protrudes approximately 4 A into the water-membrane interface, in very good agreement with electron paramagnetic resonance and oriented circular dichroism measurements. The calculations were carried out using two alamethicin isoforms: one with glutamine and the other with glutamate in the 18th position. The calculations indicate that the two isoforms have similar membrane orientations and that their insertion into the membrane is likely to involve a 2-A deformation of the bilayer, again, in good agreement with experimental data. The implications of the results for the

  3. Simulation of electron-proton coupling with a Monte Carlo method: application to cytochrome c3 using continuum electrostatics.

    PubMed Central

    Baptista, A M; Martel, P J; Soares, C M

    1999-01-01

    A new method is presented for simulating the simultaneous binding equilibrium of electrons and protons on protein molecules, which makes it possible to study the full equilibrium thermodynamics of redox and protonation processes, including electron-proton coupling. The simulations using this method reflect directly the pH and electrostatic potential of the environment, thus providing a much closer and realistic connection with experimental parameters than do usual methods. By ignoring the full binding equilibrium, calculations usually overlook the twofold effect that binding fluctuations have on the behavior of redox proteins: first, they affect the energy of the system by creating partially occupied sites; second, they affect its entropy by introducing an additional empty/occupied site disorder (here named occupational entropy). The proposed method is applied to cytochrome c3 of Desulfovibrio vulgaris Hildenborough to study its redox properties and electron-proton coupling (redox-Bohr effect), using a continuum electrostatic method based on the linear Poisson-Boltzmann equation. Unlike previous studies using other methods, the full reduction order of the four hemes at physiological pH is successfully predicted. The sites more strongly involved in the redox-Bohr effect are identified by analysis of their titration curves/surfaces and the shifts of their midpoint redox potentials and pKa values. Site-site couplings are analyzed using statistical correlations, a method much more realistic than the usual analysis based on direct interactions. The site found to be more strongly involved in the redox-Bohr effect is propionate D of heme I, in agreement with previous studies; other likely candidates are His67, the N-terminus, and propionate D of heme IV. Even though the present study is limited to equilibrium conditions, the possible role of binding fluctuations in the concerted transfer of protons and electrons under nonequilibrium conditions is also discussed. The

  4. New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics

    NASA Astrophysics Data System (ADS)

    Xie, Dexuan

    2014-10-01

    The Poisson-Boltzmann equation (PBE) is one widely-used implicit solvent continuum model in the calculation of electrostatic potential energy for biomolecules in ionic solvent, but its numerical solution remains a challenge due to its strong singularity and nonlinearity caused by its singular distribution source terms and exponential nonlinear terms. To effectively deal with such a challenge, in this paper, new solution decomposition and minimization schemes are proposed, together with a new PBE analysis on solution existence and uniqueness. Moreover, a PBE finite element program package is developed in Python based on the FEniCS program library and GAMer, a molecular surface and volumetric mesh generation program package. Numerical tests on proteins and a nonlinear Born ball model with an analytical solution validate the new solution decomposition and minimization schemes, and demonstrate the effectiveness and efficiency of the new PBE finite element program package.

  5. Calculation of far wing of allowed spectra: The water continuum

    NASA Technical Reports Server (NTRS)

    Tipping, R. H.; Ma, Q.

    1995-01-01

    A far-wing line shape theory based on the binary collision and quasistatic approximations that is applicable for both the low- and high-frequency wings of allowed vibrational-rotational lines has been developed. This theory has been applied in order to calculate the frequency and temperature dependence of the continuous absorption coefficient for frequencies up to 10,000 cm(exp -1) for pure H2O and for H2O-N2 mixtures. The calculations are made assuming an interaction potential consisting of an isotropic Lennard-Jones part and the leading long-range anisotropic part, and utilizing the measured line strengths and transition frequencies. The results compare well with existing data, both in magnitude and in temperature dependence. This leads us to the conclusion that although dimer and collision-induced absorptions are present, the primary mechanism responsible for the observed water continuum is the far-wing absorption of allowed lines. Recent progress on near-wing corrections to the theory and validations with recent laboratory measurements are discussed briefly.

  6. Four-body continuum-discretized coupled-channels calculations

    SciTech Connect

    Rodriguez-Gallardo, M.; Arias, J. M.; Moro, A. M.; Gomez-Camacho, J.; Thompson, I. J.; Tostevin, J. A.

    2009-11-15

    The development of a continuum-bin scheme of discretization for three-body projectiles is necessary for studies of reactions of Borromean nuclei such as {sup 6}He within the continuum-discretized coupled-channels approach. Such a procedure, for constructing bin states on selected continuum energy intervals, is formulated and applied for the first time to reactions of a three-body projectile. The continuum representation uses the eigenchannel expansion of the three-body S matrix. The method is applied to the challenging case of the {sup 6}He+{sup 208}Pb reaction at 22 MeV, where an accurate treatment of both the Coulomb and the nuclear interactions with the target is necessary.

  7. Footprinting molecular electrostatic potential surfaces for calculation of solvation energies.

    PubMed

    Calero, Christian Solis; Farwer, Jochen; Gardiner, Eleanor J; Hunter, Christopher A; Mackey, Mark; Scuderi, Serena; Thompson, Stuart; Vinter, Jeremy G

    2013-11-07

    A liquid is composed of an ensemble of molecules that populate a large number of different states, so calculation of the solvation energy of a molecule in solution requires a method for summing the interactions with the environment over all of these states. The surface site interaction model for the properties of liquids at equilibrium (SSIMPLE) simplifies the surface of a molecule to a discrete number of specific interaction sites (SSIPs). The thermodynamic properties of these interaction sites can be characterised experimentally, for example, through measurement of association constants for the formation of simple complexes that feature a single H-bonding interaction. Correlation of experimentally determined solution phase H-bond parameters with gas phase ab initio calculations of maxima and minima on molecular electrostatic potential surfaces (MEPS) provides a method for converting gas phase calculations on isolated molecules to parameters that can be used to estimate solution phase interaction free energies. This approach has been generalised using a footprinting technique that converts an MEPS into a discrete set of SSIPs (each described by a polar interaction parameter, εi). These SSIPs represent the molecular recognition properties of the entire surface of the molecule. For example, water is described by four SSIPs, two H-bond donor sites and two H-bond acceptor sites. A liquid mixture is described as an ensemble of SSIPs that represent the components of the mixture at appropriate concentrations. Individual SSIPs are assumed to be independent, so speciation of SSIP contacts can be calculated based on properties of the individual SSIP interactions, which are given by the sum of a polar (εiεj) and a non-polar (E(vdW)) interaction term. Results are presented for calculation the free energies of transfer of a range of organic molecules from the pure liquid into water, from the pure liquid into n-hexadecane, from n-hexadecane into water, from n-octanol into

  8. Multiconformation Continuum Electrostatics Analysis of the Effects of a Buried Asp Introduced Near Heme a in Rb. sphaeroides Cytochrome c Oxidase

    PubMed Central

    Zhang, Jun; Gunner, M.R.

    2013-01-01

    Cytochrome c oxidase (CcO) reduces O2 to water via a series of proton coupled electron transfers generating a transmembrane electrochemical gradient. Coupling electron and proton transfer requires changing buried residues pKas at each stage in the reaction cycle. Heme a is a key cofactor in the CcO electron transfer chain. Mutation of Ser44 to Asp has been reported (Mills et al Biochemistry (2008) 47, 11499-11509), changing the hydrogen bond acceptor from His102, the Heme a axial ligand in Rhodobactor sphaeroides CcO. This adds an acidic residue to the CcO interior. The electrochemical behavior of Heme a in wild type and S44D CcO is compared using the continuum electrostatics program MCCE. The introduced, deeply buried Asp remains ionized at physiological pH only when the nearby heme is oxidized. Heme a reduction is now calculated to be strongly coupled to Asp proton binding, while with Ser44 it is weakly coupled to small protonation shifts at multiple sites, increasing the pH dependence in the mutant. At pH 7, the partially ionized Asp44 is calculated to lower the Heme redox potential by 50 mV as expected given the thermodynamics of coupled electron and proton transfers. This highlights an inconsistency in the experimental results where a low Asp pKa is found together with a stabilized reduced Heme. The stabilization of a model complex heme oxidation by a hydrogen bond to the axial His ligand calculated with Continuum Electrostatics and with Density Functional Theory was in good agreement. PMID:20701325

  9. On the origin and the calculation of the force in electrostatic actuators

    NASA Astrophysics Data System (ADS)

    Jakoby, Bernhard

    2016-07-01

    This paper reviews fundamental ways to calculate the forces between charged electrodes as they appear, e.g., in electrostatic drives. In particular the consideration of the force acting on the surface charge layers on the electrodes, the principle of virtual displacement, and the Maxwell stress tensor are considered for two examples: a parallel plate capacitor and an electrostatic comb drive featuring interdigitated electrodes.

  10. Polarization energy gradients in combined quantum mechanics, effective fragment potential, and polarizable continuum model calculations

    NASA Astrophysics Data System (ADS)

    Li, Hui; Gordon, Mark S.

    2007-03-01

    A method that combines quantum mechanics (QM), typically a solute, the effective fragment potential (EFP) discrete solvent model, and the polarizable continuum model is described. The EFP induced dipoles and polarizable continuum model (PCM) induced surface charges are determined in a self-consistent fashion. The gradients of these two energies with respect to molecular coordinate changes are derived and implemented. In general, the gradients can be formulated as simple electrostatic forces and torques among the QM nuclei, electrons, EFP static multipoles, induced dipoles, and PCM induced charges. Molecular geometry optimizations can be performed efficiently with these gradients. The formulas derived for EFP/PCM can be generally applied to other combined molecular mechanics and continuum methods that employ induced dipoles and charges.

  11. On the ability of molecular dynamics simulation and continuum electrostatics to treat interfacial water molecules in protein-protein complexes

    PubMed Central

    Copie, Guillaume; Cleri, Fabrizio; Blossey, Ralf; Lensink, Marc F.

    2016-01-01

    Interfacial waters are increasingly appreciated as playing a key role in protein-protein interactions. We report on a study of the prediction of interfacial water positions by both Molecular Dynamics and explicit solvent-continuum electrostatics based on the Dipolar Poisson-Boltzmann Langevin (DPBL) model, for three test cases: (i) the barnase/barstar complex (ii) the complex between the DNase domain of colicin E2 and its cognate Im2 immunity protein and (iii) the highly unusual anti-freeze protein Maxi which contains a large number of waters in its interior. We characterize the waters at the interface and in the core of the Maxi protein by the statistics of correctly predicted positions with respect to crystallographic water positions in the PDB files as well as the dynamic measures of diffusion constants and position lifetimes. Our approach provides a methodology for the evaluation of predicted interfacial water positions through an investigation of water-mediated inter-chain contacts. While our results show satisfactory behaviour for molecular dynamics simulation, they also highlight the need for improvement of continuum methods. PMID:27905545

  12. A singular finite element technique for calculating continuum damping of Alfvén eigenmodes

    SciTech Connect

    Bowden, G. W.; Hole, M. J.

    2015-02-15

    Damping due to continuum resonances can be calculated using dissipation-less ideal magnetohydrodynamics provided that the poles due to these resonances are properly treated. We describe a singular finite element technique for calculating the continuum damping of Alfvén waves. A Frobenius expansion is used to determine appropriate finite element basis functions on an inner region surrounding a pole due to the continuum resonance. The location of the pole due to the continuum resonance and mode frequency is calculated iteratively using a Galerkin method. This method is used to find the complex frequency and mode structure of a toroidicity-induced Alfvén eigenmode in a large aspect ratio circular tokamak and is shown to agree closely with a complex contour technique.

  13. Electrostatics

    SciTech Connect

    Wallace, John P.; Wallace, Michael J.

    2015-12-04

    Quantum mechanics should be able to generate the basic properties of a particle. One of the most basic properties are charge and the associated electrostatic electric field. Electrostatic force is a fundamental characteristics of a charged fermion and should have its nature described by the fermion’s structure. To produce the particle properties require two spaces that define both their dynamics and their base structure. Relativity and the conservation of energy dictate how these two separate spaces are connected and the differential equations that describe behavior within these two spaces. The main static characteristic of an elementary fermion are mass and charge. Mass represents a scale measure of the fermion and it appears that charge results from the detailed structure of the fermion, which must merge into the electric field description of Maxwell. Coulomb’s law is a good approximation for large distances, but it is a poor approximation at dimension on the order of a particle’s Compton wavelength. The relativistic description of the fermion in its own frame of reference contains the information required for producing the electrostatic field over all space without a singularity as a source. With this description it is possible to understand the first order correction to the ionization energy of hydrogen. The role of nuclear effects on ionization energies can now be better defined for nuclei heavier than hydrogen.

  14. Edge energies : atomistic calculations of a continuum quantity.

    SciTech Connect

    Hamilton, John C.

    2005-06-01

    Controlling the properties of self-assembled nanostructures requires controlling their shape. Size-dependent shape transitions, frequently observed at nanolength scales, are commonly attributed to edge energy effects. To rigorously test such theories against experiment, quantitative atomistic calculations of edge energies are essential, yet none exist. I describe a fundamental ambiguity in the atomistic definition of edge energies, propose a definition based on equimolar dividing surfaces, and present an atomistic calculation of edge energies for Pd clusters.

  15. Fast electrostatic force calculation on parallel computer clusters

    SciTech Connect

    Kia, Amirali Kim, Daejoong Darve, Eric

    2008-10-01

    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.

  16. Continuum calculations of continental deformation in transcurrent environments

    NASA Technical Reports Server (NTRS)

    Sonder, L. J.; England, P. C.; Houseman, G. A.

    1986-01-01

    A thin viscous sheet approximation is used to investigate continental deformation near a strike-slip boundary. The vertically averaged velocity field is calculated for a medium characterized by a power law rheology with stress exponent n. Driving stresses include those applied along boundaries of the sheet and those arising from buoyancy forces related to lateral differences in crustal thickness. Exact and approximate analytic solutions for a region with a sinusoidal strike-slip boundary condition are compared with solutions for more geologically relevant boundary conditions obtained using a finite element technique. The across-strike length scale of the deformation is approximately 1/4pi x sq rt n times the dominant wavelength of the imposed strike-slip boundary condition for both the analytic and the numerical solutions; this result is consistent with length scales observed in continental regions of large-scale transcurrent faulting. An approximate, linear relationship between displacement and rotation is found that depends only on the deformation length scale and the rheology. Calculated displacements, finite rotations, and distribution of crustal thicknesses are consistent with those observed in the region of the Pacific-North America plate boundary in California.

  17. Calculation of continuum damping of Alfvén eigenmodes in tokamak and stellarator equilibria

    SciTech Connect

    Bowden, G. W.; Hole, M. J.; Könies, A.

    2015-09-15

    In an ideal magnetohydrodynamic (MHD) plasma, shear Alfvén eigenmodes may experience dissipationless damping due to resonant interaction with the shear Alfvén continuum. This continuum damping can make a significant contribution to the overall growth/decay rate of shear Alfvén eigenmodes, with consequent implications for fast ion transport. One method for calculating continuum damping is to solve the MHD eigenvalue problem over a suitable contour in the complex plane, thereby satisfying the causality condition. Such an approach can be implemented in three-dimensional ideal MHD codes which use the Galerkin method. Analytic functions can be fitted to numerical data for equilibrium quantities in order to determine the value of these quantities along the complex contour. This approach requires less resolution than the established technique of calculating damping as resistivity vanishes and is thus more computationally efficient. The complex contour method has been applied to the three-dimensional finite element ideal MHD Code for Kinetic Alfvén waves. In this paper, we discuss the application of the complex contour technique to calculate the continuum damping of global modes in tokamak as well as torsatron, W7-X and H-1NF stellarator cases. To the authors' knowledge, these stellarator calculations represent the first calculation of continuum damping for eigenmodes in fully three-dimensional equilibria. The continuum damping of global modes in W7-X and H-1NF stellarator configurations investigated is found to depend sensitively on coupling to numerous poloidal and toroidal harmonics.

  18. On the proper calculation of electrostatic interactions in solid-supported bilayer systems

    NASA Astrophysics Data System (ADS)

    Yeh, In-Chul; Wallqvist, Anders

    2011-02-01

    Modeling systems that are not inherently isotropic, e.g., extended bilayers, using molecular simulation techniques poses a potential problem. Since these methods rely on a finite number of atoms and molecules to describe the system, periodic boundary conditions are implemented to avoid edge effects and capture long-range electrostatic interactions. Systems consisting of a solvated bilayer adsorbed on a solid surface and exposed to an air/vacuum interface occur in many experimental settings and present some unique challenges in this respect. Here, we investigated the effects of implementing different electrostatic boundary conditions on the structural and electrostatic properties of a quartz/water/vacuum interface and a similar quartz-supported hydrated lipid bilayer exposed to vacuum. Since these interfacial systems have a net polarization, implementing the standard Ewald summation with the conducting boundary condition for the electrostatic long-range interactions introduced an artificial periodicity in the out-of-plane dimension. In particular, abnormal orientational polarizations of water were observed with the conducting boundary condition. Implementing the Ewald summation technique with the planar vacuum boundary condition and calculating electrostatic properties compatible with the implemented electrostatic boundary condition removed these inconsistencies. This formulation is generally applicable to similar interfacial systems in bulk solution.

  19. Analytical transformed harmonic oscillator basis for continuum discretized coupled channels calculations

    SciTech Connect

    Moro, A. M.; Arias, J. M.; Gomez-Camacho, J.; Perez-Bernal, F.

    2009-11-15

    A new method for continuum discretization in continuum-discretized coupled-channels calculations is proposed. The method is based on an analytic local-scale transformation of the harmonic-oscillator wave functions proposed for other purposes in a recent work [Karatagladis et al., Phys. Rev. C 71, 064601 (2005)]. The new approach is compared with the standard method of continuum discretization in terms of energy bins for the reactions d+{sup 58}Ni at 80 MeV, {sup 6}Li+{sup 40}Ca at 156 MeV, and {sup 6}He+{sup 208}Pb at 22 MeV and 240 MeV/nucleon. In all cases very good agreement between both approaches is found.

  20. Numerical calculations of the intrinsic electrostatic resonances of artificial dielectric heterostructures

    NASA Astrophysics Data System (ADS)

    Mejdoubi, Abdelilah; Brosseau, Christian

    2007-04-01

    In order to study the intrinsic electrostatic resonances (ERs) of artificial dielectric heterostructures, we develop an efficient effective-medium-based method for modeling the effective permittivity, with careful attention paid to several key factors controlling ERs. Our method relies on finite element modeling and is applicable to inclusions with complex boundaries, e.g., fractal inclusion. A series of isolated and square arrays of several types of negative-permittivity media is considered. The inclusion shapes investigated can be considered as cross sections of infinite three-dimensional objects, where the properties and characteristics are invariant along the perpendicular cross-sectional plane. The continuum model used in this work is accurate only if the homogeneous representation of the composite structure makes sense, i.e., quasistatic approximation. It is found, among the conclusions of the article, that the effective permittivity of the composite (lossless) structures versus surface fraction curves presents a sharp peak, which occurs precisely at ER. For lossy inclusions, the primary signature of the ER is seen in the peak in the imaginary part of the complex permittivity or as an inflexion in the curve of the real part of the complex permittivity. The focus in this effort is on the analysis of intrinsic ER as a function of the shape and permittivity of the inclusion. The variations in the effective permittivity related to the iteration number show the following hierarchy for Sierpinski's square and triangle: the higher the iteration number of the inclusion the smaller value of ϕ2 corresponding to the ER. In the vicinity of the ER peak, field enhancement is observed, which consists of enormous changes in the local electric field. Differences between the ER characteristics for aperiodic and periodic orders through the introduction of localized voids in the structure are also noteworthy. In addition, our approach performs well for fractal-shaped inclusions

  1. Effects of Long-Range Electrostatics on Time-Dependent Stokes Shift Calculations.

    PubMed

    Furse, Kristina E; Corcelli, Steven A

    2009-08-11

    Molecular dynamics simulations are essential to the correct interpretation of the response measured in time-dependent Stokes shift (TDSS) experiments of fluorescent probe molecules in biological environments. Within linear response theory, the TDSS response is the time correlation function of the fluctuations of ΔE(t), the difference between the solute environment interaction energy with the probe, modeled in both its electronically excited and ground states. ΔE(t) is dominated by electrostatic interactions between the environment and the ground- and excited-state charge distributions of the probe. The treatment of the long-ranged electrostatics in the calculation of the TDSS response in MD simulations is systematically investigated for three probes in aqueous solution: a model diatomic, coumarin 102, and Hoechst 33258. Nine different protocols for the treatment of the electrostatics were compared to particle mesh Ewald (PME), which was utilized as a reference standard. A computationally efficient pairwise alternative to PME, the damped shifted force method, was shown to reproduce the TDSS response calculated with PME for all three systems. In contrast, neglecting the role of the long-ranged electrostatics in the calculation of the TDSS response results in artifacts.

  2. Quantitative assessment of electrostatic embedding in Density Functional Theory calculations of biomolecular systems

    SciTech Connect

    Fattebert, J; Law, R J; Bennion, B; Lau, E Y; Schwegler, E; Lightstone, F C

    2009-04-24

    We evaluate the accuracy of density functional theory quantum calculations of biomolecular subsystems using a simple electrostatic embedding scheme. Our scheme is based on dividing the system of interest into a primary and secondary subsystem. A finite difference discretization of the Kohn-Sham equations is used for the primary subsystem, while its electrostatic environment is modeled with a simple one-electron potential. Force-field atomic partial charges are used to generate smeared Gaussian charge densities and to model the secondary subsystem. We illustrate the utility of this approach with calculations of truncated dipeptide chains. We analyze quantitatively the accuracy of this approach by calculating atomic forces and comparing results with fullQMcalculations. The impact of the choice made in terminating dangling bonds at the frontier of the QM region is also investigated.

  3. Extension and evaluation of the multilevel summation method for fast long-range electrostatics calculations.

    PubMed

    Moore, Stan G; Crozier, Paul S

    2014-06-21

    Several extensions and improvements have been made to the multilevel summation method (MSM) of computing long-range electrostatic interactions. These include pressure calculation, an improved error estimator, faster direct part calculation, extension to non-orthogonal (triclinic) systems, and parallelization using the domain decomposition method. MSM also allows fully non-periodic long-range electrostatics calculations which are not possible using traditional Ewald-based methods. In spite of these significant improvements to the MSM algorithm, the particle-particle particle-mesh (PPPM) method was still found to be faster for the periodic systems we tested on a single processor. However, the fast Fourier transforms (FFTs) that PPPM relies on represent a major scaling bottleneck for the method when running on many cores (because the many-to-many communication pattern of the FFT becomes expensive) and MSM scales better than PPPM when using a large core count for two test problems on Sandia's Redsky machine. This FFT bottleneck can be reduced by running PPPM on only a subset of the total processors. MSM is most competitive for relatively low accuracy calculations. On Sandia's Chama machine, however, PPPM is found to scale better than MSM for all core counts that we tested. These results suggest that PPPM is usually more efficient than MSM for typical problems running on current high performance computers. However, further improvements to MSM algorithm could increase its competitiveness for calculation of long-range electrostatic interactions.

  4. DFT-based simulations of amide I' IR spectra of a small protein in solution using empirical electrostatic map with a continuum solvent model.

    PubMed

    Welch, William R W; Kubelka, Jan

    2012-09-06

    A continuum solvent model was tested for simulations of amide I' IR spectra for a 40-residue subdomain of P22 viral coat protein in aqueous solution. Spectra obtained using DFT (BPW91/6-31G**) parameters for a reduced all-Ala representation of the protein were corrected by an electrostatic potential map obtained from the solvent cavity surface and AMBER99 side-chain atom partial charges. Various cavity sizes derived from van der Waals atomic radii with an added effective solvent radius up to 2.0 Å were tested. The interplay of the side-chain and solvent electrostatic effects was investigated by considering the side chains and solvent separately as well as together. The sensitivity to side-chain conformational fluctuations and to the parametrization of C(β) group partial charges was also tested. Simulation results were compared to the experimental amide I' spectra of P22 subdomain, including two (13)C isotopically edited variants, as well as to the previous simulations based on the molecular dynamics trajectory in explicit solvent. For small cavity sizes, between van der Waals and that with added solvent radius of 0.5 Å, better qualitative agreement with experiment was obtained than with the explicit solvent representation, in particular for the (13)C-labeled spectra. Larger protein cavities led to progressively worse predictions due to increasingly stronger electrostatic effects of side chains, which could no longer be well compensated for by the solvent potential. Balance between side-chain and solvent electrostatic effects is important in determining the width and shape of the simulated amide I', which is also virtually unaffected by side-chain-geometry fluctuations. The continuum solvent model combined with the electrostatic map is a computationally efficient and potentially robust approach for the simulations of IR spectra of proteins in solution.

  5. Charge Compensation and Electrostatic Transferability in Three Entropy Stabilized Oxides: Results from Density Functional Theory Calculations

    DTIC Science & Technology

    2016-09-06

    Charge compensation and electrostatic transferability in three entropy-stabilized oxides: Results from density functional theory calculations Zs. Rak...North Carolina State University, Raleigh, North Carolina 27695-7907, USA 2Department of Mechanical Engineering and Materials Science and Center for...random structures. For J14, Bader charges are transferable between the binary, ternary, and random structures. For J14þSc and J14þLi, average Bader

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

    SciTech Connect

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

    2011-04-02

    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/.

  7. DelPhi webserver: Comprehensive suite for electrostatic calculations of biological macromolecules and their complexes

    NASA Astrophysics Data System (ADS)

    Witham, Shawn; Boylen, Brett; Owesen, Barr; Rocchia, Walter; Alexov, Emil

    2011-03-01

    Electrostatic forces and energies are two of the major components that contribute to the stability, function and interaction of biological macromolecules. The calculations of the electrostatic potential distribution in such systems, which are comprised of irregularly shaped objects immersed in a water phase, is not a trivial task. In addition, an accurate model requires any missing hydrogen atoms of the corresponding structural files (Protein Data Bank, or, PDB files) to be generated in silico and, if necessary, missing atoms or residues to be predicted as well. Here we report a comprehensive suite, an academic DelPhi webserver, which allows the users to upload their structural file, calculate the components of the electrostatic energy, generate the corresponding potential (and/or concentration/dielectric constant) distribution map, and choose the appropriate force field. The webserver utilizes modern technology to take user input and construct an algorithm that suits the users specific needs. The webserver uses Clemson University's Palmetto Supercomputer Cluster to handle the DelPhi calculations, which can range anywhere from small and short computation times, to extensive and computationally demanding runtimes. The work was supported by a grant from NIGMS, NIH, grant number 1R01GM093937-01.

  8. ICSM: An order N method for calculating electrostatic interactions added to TINKER

    NASA Astrophysics Data System (ADS)

    Baker, Katherine; Baumketner, Andrij; Lin, Yuchun; Deng, Shaozhong; Jacobs, Donald; Cai, Wei

    2013-01-01

    We present an order N method for calculating electrostatic interactions that has been integrated into the molecular dynamics portion of the TINKER Molecular Modeling package. This method, introduced in a previous paper [Y. Lin, A. Baumketner, S. Deng, Z. Xu, D. Jacobs, W. Cai, An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions, J. Chem. Phys. 131 (2009) 154103] and termed the Image-Charge Solvation Model (ICSM), is a hybrid electrostatic approach that combines the strengths of both explicit and implicit representations of the solvent. A multiple-image method is used to calculate reaction fields due to the implicit part while the Fast Multipole Method (FMM) is used to calculate the Coulomb interactions for all charges, including the explicit part. The integrated package is validated through test simulations of liquid water. The results are compared with those obtained by the Particle Mesh Ewald (PME) method that is built in the TINKER package. Timing performance of TINKER with the integrated ICSM is benchmarked on bulk water as a function of the size of the system. In particular, timing analysis results show that the ICSM outperforms the PME for sufficiently large systems with the break-even point at around 30,000 particles in the simulated system.

  9. Four-body continuum-discretized coupled-channels calculations using a transformed harmonic oscillator basis

    SciTech Connect

    Rodriguez-Gallardo, M.; Arias, J. M.; Gomez-Camacho, J.; Moro, A. M.; Johnson, R. C.; Tostevin, J. A.; Thompson, I. J.

    2008-06-15

    The scattering of a weakly bound three-body system by a target is discussed. A transformed harmonic oscillator basis is used to provide an appropriate discrete and finite basis for treating the continuum part of the spectrum of the projectile. The continuum-discretized coupled-channels framework is used for the scattering calculations. The formalism is applied to different reactions, {sup 6}He+{sup 12}C at 229.8 MeV, {sup 6}He+{sup 64}Zn at 10 and 13.6 MeV, and {sup 6}He+{sup 208}Pb at 22 MeV, induced by the Borromean nucleus {sup 6}He. Both the Coulomb and nuclear interactions with a target are taken into account.

  10. A new smoothing function to introduce long-range electrostatic effects in QM/MM calculations

    SciTech Connect

    Fang, Dong; Duke, Robert E.; Andrés Cisneros, G.

    2015-07-28

    A new method to account for long range electrostatic contributions is proposed and implemented for quantum mechanics/molecular mechanics long range electrostatic correction (QM/MM-LREC) calculations. This method involves the use of the minimum image convention under periodic boundary conditions and a new smoothing function for energies and forces at the cutoff boundary for the Coulomb interactions. Compared to conventional QM/MM calculations without long-range electrostatic corrections, the new method effectively includes effects on the MM environment in the primary image from its replicas in the neighborhood. QM/MM-LREC offers three useful features including the avoidance of calculations in reciprocal space (k-space), with the concomitant avoidance of having to reproduce (analytically or approximately) the QM charge density in k-space, and the straightforward availability of analytical Hessians. The new method is tested and compared with results from smooth particle mesh Ewald (PME) for three systems including a box of neat water, a double proton transfer reaction, and the geometry optimization of the critical point structures for the rate limiting step of the DNA dealkylase AlkB. As with other smoothing or shifting functions, relatively large cutoffs are necessary to achieve comparable accuracy with PME. For the double-proton transfer reaction, the use of a 22 Å cutoff shows a close reaction energy profile and geometries of stationary structures with QM/MM-LREC compared to conventional QM/MM with no truncation. Geometry optimization of stationary structures for the hydrogen abstraction step by AlkB shows some differences between QM/MM-LREC and the conventional QM/MM. These differences underscore the necessity of the inclusion of the long-range electrostatic contribution.

  11. A new smoothing function to introduce long-range electrostatic effects in QM/MM calculations.

    PubMed

    Fang, Dong; Duke, Robert E; Cisneros, G Andrés

    2015-07-28

    A new method to account for long range electrostatic contributions is proposed and implemented for quantum mechanics/molecular mechanics long range electrostatic correction (QM/MM-LREC) calculations. This method involves the use of the minimum image convention under periodic boundary conditions and a new smoothing function for energies and forces at the cutoff boundary for the Coulomb interactions. Compared to conventional QM/MM calculations without long-range electrostatic corrections, the new method effectively includes effects on the MM environment in the primary image from its replicas in the neighborhood. QM/MM-LREC offers three useful features including the avoidance of calculations in reciprocal space (k-space), with the concomitant avoidance of having to reproduce (analytically or approximately) the QM charge density in k-space, and the straightforward availability of analytical Hessians. The new method is tested and compared with results from smooth particle mesh Ewald (PME) for three systems including a box of neat water, a double proton transfer reaction, and the geometry optimization of the critical point structures for the rate limiting step of the DNA dealkylase AlkB. As with other smoothing or shifting functions, relatively large cutoffs are necessary to achieve comparable accuracy with PME. For the double-proton transfer reaction, the use of a 22 Å cutoff shows a close reaction energy profile and geometries of stationary structures with QM/MM-LREC compared to conventional QM/MM with no truncation. Geometry optimization of stationary structures for the hydrogen abstraction step by AlkB shows some differences between QM/MM-LREC and the conventional QM/MM. These differences underscore the necessity of the inclusion of the long-range electrostatic contribution.

  12. A new smoothing function to introduce long-range electrostatic effects in QM/MM calculations

    NASA Astrophysics Data System (ADS)

    Fang, Dong; Duke, Robert E.; Cisneros, G. Andrés

    2015-07-01

    A new method to account for long range electrostatic contributions is proposed and implemented for quantum mechanics/molecular mechanics long range electrostatic correction (QM/MM-LREC) calculations. This method involves the use of the minimum image convention under periodic boundary conditions and a new smoothing function for energies and forces at the cutoff boundary for the Coulomb interactions. Compared to conventional QM/MM calculations without long-range electrostatic corrections, the new method effectively includes effects on the MM environment in the primary image from its replicas in the neighborhood. QM/MM-LREC offers three useful features including the avoidance of calculations in reciprocal space (k-space), with the concomitant avoidance of having to reproduce (analytically or approximately) the QM charge density in k-space, and the straightforward availability of analytical Hessians. The new method is tested and compared with results from smooth particle mesh Ewald (PME) for three systems including a box of neat water, a double proton transfer reaction, and the geometry optimization of the critical point structures for the rate limiting step of the DNA dealkylase AlkB. As with other smoothing or shifting functions, relatively large cutoffs are necessary to achieve comparable accuracy with PME. For the double-proton transfer reaction, the use of a 22 Å cutoff shows a close reaction energy profile and geometries of stationary structures with QM/MM-LREC compared to conventional QM/MM with no truncation. Geometry optimization of stationary structures for the hydrogen abstraction step by AlkB shows some differences between QM/MM-LREC and the conventional QM/MM. These differences underscore the necessity of the inclusion of the long-range electrostatic contribution.

  13. Optimizing electrostatic field calculations with the adaptive Poisson-Boltzmann Solver to predict electric fields at protein-protein interfaces. I. Sampling and focusing.

    PubMed

    Ritchie, Andrew W; Webb, Lauren J

    2013-10-03

    Continuum electrostatics methods are commonly used to calculate electrostatic potentials in proteins and at protein-protein interfaces to aid many types of biophysical studies. Despite their ubiquity throughout the biophysical literature, these calculations are difficult to test against experimental data to determine their accuracy and validity. To address this, we have calculated the Boltzmann-weighted electrostatic field at the midpoint of a nitrile bond placed at a variety of locations on the surface of the protein RalGDS, both in its monomeric form as well as when docked to four different constructs of the protein Rap, and compared the computation results to vibrational absorption energy measurements of the nitrile oscillator. This was done by generating a statistical ensemble of protein structures using enhanced molecular dynamics sampling with the Amber03 force field, followed by solving the linear Poisson-Boltzmann equation for each structure using the Applied Poisson-Boltzmann Solver (APBS) software package. Using a two-stage focusing strategy, we examined numerous second stage box dimensions, grid point densities, box locations, and compared the numerical result to the result obtained from the sum of the numeric reaction field and the analytic Coulomb field. It was found that the reaction field method yielded higher correlation with experiment for the absolute calculation of fields, while the numeric solutions yielded higher correlation with experiment for the relative field calculations. Finer grid spacing typically improved the calculation, although this effect was less pronounced in the reaction field method. These sorts of calculations were also very sensitive to the box location, particularly for the numeric calculations of absolute fields using a 10(3) Å(3) box.

  14. The calculation of electrostatic interactions and their role in determining the energies and geometries of explosive molecular crystals

    SciTech Connect

    Ritchie, J.P.; Kober, E.M.; Copenhaver, A.S.

    1993-01-01

    Three different procedures were used to calculate electrostatic interactions in explosive molecular crystals. The use of Potential Derived Charges (PDC's) and atom-centered multipole expansions (ACME's) provides reasonable fits of the molecular electrostatic potential. The ability of these approaches to reproduce observed crystal structures was also evaluated.

  15. Resolution of a Challenge for Solvation Modeling: Calculation of Dicarboxylic Acid Dissociation Constants Using Mixed Discrete-Continuum Solvation Models

    SciTech Connect

    Marenich, Aleksandr; Ding, Wendu; Cramer, Christopher J.; Truhlar, Donald G.

    2012-06-07

    First and second dissociation constants (pKa values) of oxalic acid, malonic acid, and adipic acid were computed by using a number of theoretical protocols based on density functional theory and using both continuum solvation models and mixed discrete-continuum solvation models. We show that fully implicit solvation models (in which the entire solvent is represented by a dielectric continuum) fail badly for dicarboxylic acids with mean unsigned errors averaged over six pKa values) of 2.4-9.0 log units, depending on the particular implicit model used. The use of water-solute clusters and accounting for multiple conformations in solution significantly improve the performance of both generalized Born solvation models and models that solve the nonhomogeneous dielectric Poisson equation for bulk electrostatics. The four most successful models have mean unsigned errors of only 0.6-0.8 log units.

  16. Transfer to the continuum calculations of quasifree (p,pn) and (p,2p) reactions

    NASA Astrophysics Data System (ADS)

    Gomez-Ramos, M.; Moro, A. M.

    2016-05-01

    Nucleon removal (p, pn) and (p, 2p) reactions at intermediate energies have gained renewed attention in recent years as a tool to extract information from exotic nuclei. The information obtained from these experiments is expected to be sensitive to deeper portions of the wave function of the removed nucleon than knockout reactions with heavier targets. In this contribution, we present calculations for (p, 2p) and (p, pn) reactions performed within the so-called transfer to the continuum method (TR*). Results for stable and unstable nuclei are presented, and compared with experimental data, when available.

  17. Electrostatic embedding in large-scale first principles quantum mechanical calculations on biomolecules.

    PubMed

    Fox, Stephen J; Pittock, Chris; Fox, Thomas; Tautermann, Christofer S; Malcolm, Noj; Skylaris, Chris-Kriton

    2011-12-14

    Biomolecular simulations with atomistic detail are often required to describe interactions with chemical accuracy for applications such as the calculation of free energies of binding or chemical reactions in enzymes. Force fields are typically used for this task but these rely on extensive parameterisation which in cases can lead to limited accuracy and transferability, for example for ligands with unusual functional groups. These limitations can be overcome with first principles calculations with methods such as density functional theory (DFT) but at a much higher computational cost. The use of electrostatic embedding can significantly reduce this cost by representing a portion of the simulated system in terms of highly localised charge distributions. These classical charge distributions are electrostatically coupled with the quantum system and represent the effect of the environment in which the quantum system is embedded. In this paper we describe and evaluate such an embedding scheme in which the polarisation of the electronic density by the embedding charges occurs self-consistently during the calculation of the density. We have implemented this scheme in a linear-scaling DFT program as our aim is to treat with DFT entire biomolecules (such as proteins) and large portions of the solvent. We test this approach in the calculation of interaction energies of ligands with biomolecules and solvent and investigate under what conditions these can be obtained with the same level of accuracy as when the entire system is described by DFT, for a variety of neutral and charged species.

  18. Point charge representation of multicenter multipole moments in calculation of electrostatic properties

    NASA Technical Reports Server (NTRS)

    Sokalski, W. A.; Shibata, M.; Ornstein, R. L.; Rein, R.

    1993-01-01

    Distributed Point Charge Models (PCM) for CO, (H2O)2, and HS-SH molecules have been computed from analytical expressions using multi-center multipole moments. The point charges (set of charges including both atomic and non-atomic positions) exactly reproduce both molecular and segmental multipole moments, thus constituting an accurate representation of the local anisotropy of electrostatic properties. In contrast to other known point charge models, PCM can be used to calculate not only intermolecular, but also intramolecular interactions. Comparison of these results with more accurate calculations demonstrated that PCM can correctly represent both weak and strong (intramolecular) interactions, thus indicating the merit of extending PCM to obtain improved potentials for molecular mechanics and molecular dynamics computational methods.

  19. Full QM Calculation of RNA Energy Using Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps Method.

    PubMed

    Jin, Xinsheng; Zhang, John Z H; He, Xiao

    2017-03-30

    In this study, the electrostatically embedded generalized molecular fractionation with conjugate caps (concaps) method (EE-GMFCC) was employed for efficient linear-scaling quantum mechanical (QM) calculation of total energies of RNAs. In the EE-GMFCC approach, the total energy of RNA is calculated by taking a proper combination of the QM energy of each nucleotide-centric fragment with large caps or small caps (termed EE-GMFCC-LC and EE-GMFCC-SC, respectively) deducted by the energies of concaps. The two-body QM interaction energy between non-neighboring ribonucleotides which are spatially in close contact are also taken into account for the energy calculation. Numerical studies were carried out to calculate the total energies of a number of RNAs using the EE-GMFCC-LC and EE-GMFCC-SC methods at levels of the Hartree-Fock (HF) method, density functional theory (DFT), and second-order many-body perturbation theory (MP2), respectively. The results show that the efficiency of the EE-GMFCC-SC method is about 3 times faster than the EE-GMFCC-LC method with minimal accuracy sacrifice. The EE-GMFCC-SC method is also applied for relative energy calculations of 20 different conformers of two RNA systems using HF and DFT, respectively. Both single-point and relative energy calculations demonstrate that the EE-GMFCC method has deviations from the full system results of only a few kcal/mol.

  20. A marching method for calculating line and continuum radiation in high energy flow fields

    NASA Technical Reports Server (NTRS)

    Bolz, C. W., Jr.

    1979-01-01

    A method is presented for calculating nongrey radiative fluxes and intensities in a highly ionized, low temperature plasma with extreme line broadening. The method was developed to study radiative heating phenomena in the mass-injected hypersonic shock-layer environments characteristic of outer planet atmospheric entry, although it is not limited to such studies. The radiative properties model assumed local thermodynamic equilibrium and used standard continuum and molecular band models. The atomic line model, however, used a frequency-marching method for the frequency integration, which not only accounted completely for line overlapping (reabsorption) effects, but compared favorably in economy with the best equivalent-width methods. An assessment of hydrogen line-far-wing treatments, with recommendations for engineering models, is also presented.

  1. Lattice QCD calculation of the proton decay matrix element in the continuum limit

    SciTech Connect

    Tsutsui, N.; Hashimoto, S.; Kaneko, T.; Kuramashi, Y.; Aoki, S.; Kanaya, K.; Taniguchi, Y.; Fukugita, M.; Ishikawa, K-I.; Okawa, M.; Ishizuka, N.; Iwasaki, Y.; Ukawa, A.; Yoshie, T.; Onogi, T.

    2004-12-01

    We present a quenched lattice QCD calculation of the {alpha} and {beta} parameters of the proton decay matrix element. The simulation is carried out using the Wilson quark action at three values of the lattice spacing in the range a{approx_equal}0.1-0.064 fm to study the scaling violation effect. We find only mild scaling violation when the lattice scale is determined by the nucleon mass. We obtain in the continuum limit, vertical bar {alpha}(NDR,2 GeV) vertical bar=0.0090(09)(+5-19) GeV{sup 3} and vertical bar{beta}(NDR,2 GeV)vertical bar=0.0096(09)(+6-20) GeV{sup 3} with {alpha} and {beta} in a relatively opposite sign, where the first error is statistical and the second is due to the uncertainty in the determination of the physical scale.

  2. Electronic coupling calculations with transition charges, dipoles, and quadrupoles derived from electrostatic potential fitting

    SciTech Connect

    Fujimoto, Kazuhiro J.

    2014-12-07

    A transition charge, dipole, and quadrupole from electrostatic potential (TrESP-CDQ) method for electronic coupling calculations is proposed. The TrESP method is based on the classical description of electronic Coulomb interaction between transition densities for individual molecules. In the original TrESP method, only the transition charge interactions were considered as the electronic coupling. In the present study, the TrESP method is extended to include the contributions from the transition dipoles and quadrupoles as well as the transition charges. Hence, the self-consistent transition density is employed in the ESP fitting procedure. To check the accuracy of the present approach, several test calculations are performed to a helium dimer, a methane dimer, and an ethylene dimer. As a result, the TrESP-CDQ method gives a much improved description of the electronic coupling, compared with the original TrESP method. The calculated results also show that the self-consistent treatment to the transition densities contributes significantly to the accuracy of the electronic coupling calculations. Based on the successful description of the electronic coupling, the contributions to the electronic coupling are also analyzed. This analysis clearly shows a negligible contribution of the transition charge interaction to the electronic coupling. Hence, the distribution of the transition density is found to strongly influence the magnitudes of the transition charges, dipoles, and quadrupoles. The present approach is useful for analyzing and understanding the mechanism of excitation-energy transfer.

  3. Pyridine adsorbed on H-Faujasite zeolite: Electrostatic effect of the infinite crystal lattice calculated from a point charge representation

    NASA Astrophysics Data System (ADS)

    Injan, Natcha; Pannorad, Narong; Probst, Michael; Limtrakul, Jumras

    Calculations on cluster models of infinite systems require less computational effort and are technically simpler than periodic calculations, but they neglect, among other contributions, the effect of long-range electrostatic interaction from the infinite crystal lattice. In the case of zeolites, such contributions can be important for adsorption processes and surface reactions. We test a simple method for including this effect into the calculation by generating a finite number of point charges placed on the lattice sites. These point charges reproduce the infinite electrostatic potential at the chemically important region of the zeolite. We apply this method to the adsorption of pyridine on H-Faujasite zeolite. The embedding method gives an adsorption energy of -42.8 kcal/mol, which agrees well with the experimental value of -43.1 ± 1 kcal/mol. Without the electrostatic effect of the crystal field, the value is ˜9 kcal/mol higher.

  4. Electrostatic forces in two lysozymes: calculations and measurements of histidine pKa values.

    PubMed

    Takahashi, T; Nakamura, H; Wada, A

    1992-08-01

    In order to examine the electrostatic forces in globular proteins, pKa values and their ionic strength dependence of His residues of hen egg white lysozyme (HEWL) and human lysozyme (HUML) were measured, and they were compared with those calculated numerically. pKa values of His residues in HEWL, HUML, and short oligopeptides were determined from chemical shift changes of His side chains by 1H-nmr measurements. The associated changes in pKa values in HEWL and HUML were calculated by solving the Poisson-Boltzmann equations numerically for macroscopic dielectric models. The calculated pKa changes and their ionic strength dependence agreed fairly well with the observed ones. The contribution from each residue of each alpha-helix dipole to the pKa values and their ionic strength dependence was analyzed using Green's reciprocity theorem. The results indicate that (1) the pKa of His residues are largely affected by surrounding ionized and polar groups; (2) the ionic strength dependence of the pKa values is determined by the overall charge distributions and their accessibilities to solvent; and (3) alpha-helix dipoles make a significant contribution to the pKa, when the His residue is close to the helix terminus and not fully exposed to the solvent.

  5. On the calculations of interaction energies and induced electric properties within the polarizable continuum model.

    PubMed

    Zawada, Agnieszka; Góra, Robert W; Mikołajczyk, Mikołaj M; Bartkowiak, Wojciech

    2012-05-03

    In this work we investigate the influence of a polarizable environment on the interaction energies and the interaction-induced (excess) static electric dipole properties for the selected model hydrogen-bonded complexes. The excess properties were estimated for water and hydrogen fluoride dimers using the supermolecular approach and assuming the polarizable continuum model (PCM) as a representation of the polarizable environment. We analyze in this context the performance of the counterpoise correction and the consequences of various possible monomer cavity choices. The polarizable environment reduces the absolute magnitudes of interaction energies and interaction-induced dipole moments, whereas an increase is observed for the absolute magnitudes of induced polarizabilities and first hyperpolarizabilities. Our results indicate that the use of either monomeric (MC) or dimeric (DC) cavities in calculations of monomer properties does not change qualitatively the resultant excess properties. We conclude that the DC scheme is more consistent with the definition of the interaction energy and consequently also the interaction-induced property, whereas the MC scheme corresponds to the definition of stabilization energy. Our results indicate also a good performance of the counterpoise correction scheme for the self-consistent methods in the case of all studied properties.

  6. Electrostatic interaction in atomic force microscopy

    PubMed Central

    Butt, Hans-Jüurgen

    1991-01-01

    In atomic force microscopy, the stylus experiences an electrostatic force when imaging in aqueous medium above a charged surface. This force has been calculated numerically with continuum theory for a silicon nitrite or silicon oxide stylus. For comparison, the Van der Waals force was also calculated. In contrast to the Van der Waals attraction, the electrostatic force is repulsive. At a distance of 0.5 nm the electrostatic force is typically 10-12-10-10 N and thus comparable in strength to the Van der Waals force. The electrostatic force increases with increasing surface charge density and decreases roughly exponentially with distance. It can be reduced by imaging in high salt concentrations. Below surface potentials of ≈50 mV, a simple analytical approximation of the electrostatic force is described. PMID:19431803

  7. General methodology to optimize damping functions to account for charge penetration effects in electrostatic calculations using multicentered multipolar expansions.

    PubMed

    Werneck, Araken S; Filho, Tarcísio M Rocha; Dardenne, Laurent E

    2008-01-17

    We developed a methodology to optimize exponential damping functions to account for charge penetration effects when computing molecular electrostatic properties using the multicentered multipolar expansion method (MME). This methodology is based in the optimization of a damping parameter set using a two-step fast local fitting procedure and the ab initio (Hartree-Fock/6-31G** and 6-31G**+) electrostatic potential calculated in a set of concentric grid of points as reference. The principal aspect of the methodology is a first local fitting step which generates a focused initial guess to improve the performance of a simplex method avoiding the use of multiple runs and the choice of initial guesses. Three different strategies for the determination of optimized damping parameters were tested in the following studies: (1) investigation of the error in the calculation of the electrostatic interaction energy for five hydrogen-bonded dimers at standard and nonstandard hydrogen-bonded geometries and at nonequilibrium geometries; (2) calculation of the electrostatic molecular properties (potential and electric field) for eight small molecular systems (methanol, ammonia, water, formamide, dichloromethane, acetone, dimethyl sulfoxide, and acetonitrile) and for the 20 amino acids. Our results show that the methodology performs well not only for small molecules but also for relatively larger molecular systems. The analysis of the distinct parameter sets associated with different optimization strategies show that (i) a specific parameter set is more suitable and more general for electrostatic interaction energy calculations, with an average absolute error of 0.46 kcal/mol at hydrogen-bond geometries; (ii) a second parameter set is more suitable for electrostatic potential and electric field calculations at and outside the van der Waals (vdW) envelope, with an average error decrease >72% at the vdW surface. A more general amino acid damping parameter set was constructed from the

  8. Alternative basis functions for L sup 2 calculations on the molecular continuum. I. The basic prototype integrals

    SciTech Connect

    Fortunelli, A.; Carravetta, V. )

    1992-04-01

    Alternative square-integrable ({ital L}{sup 2}) basis functions, the oscillating Hermite Gaussian functions (OHGF's), are proposed for describing the continuum orbitals in {ital L}{sup 2} calculations on molecules. Each function is the product of a Hermite Gaussian function (HGF), which gives the proper dumping and angular factor, and a radial trigonometric function, cos({ital kr}), which describes the oscillating asymptotic behavior of a continuum orbital. Analytic expressions for the one- and two-electron integrals involving {ital s}-type OHGF's and many-center {ital s}-type HGF's are derived and their numerical implementation is discussed in detail. The present proposal of adopting a mixed basis set of OHGF's and many-center HGF's for the {ital L}{sup 2} description of bound and continuum molecular states is compared with the other types of basis functions currently employed. With respect to these, it requires a greater computational effort in the integral evaluation, but it also allows an accurate description of the electronic continuum in general polyatomic systems.

  9. Confusing Aspects in the Calculation of the Electrostatic Potential of an Infinite Line of Charge

    ERIC Educational Resources Information Center

    Jimenez, J. L.; Campos, I.; Roa-Neri, J. A. E.

    2012-01-01

    In this work we discuss the trick of eliminating infinite potential of reference arguing that it corresponds to a constant of integration, in the problem of determining the electrostatic potential of an infinite line of charge with uniform density, and show how the problem must be tackled properly. The usual procedure is confusing for most…

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

    PubMed

    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.

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

    PubMed Central

    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

  12. Prediction of the most favorable configuration in the ACBP-membrane interaction based on electrostatic calculations.

    PubMed

    Vallejo, Diego F; Zamarreño, Fernando; Guérin, Diego M A; Grigera, J Raul; Costabel, Marcelo D

    2009-03-01

    Acyl-CoA binding proteins (ACBPs) are highly conserved 10 kDa cytosolic proteins that bind medium- and long-chain acyl-CoA esters. They act as intracellular carriers of acyl-CoA and play a role in acyl-CoA metabolism, gene regulation, acyl-CoA-mediated cell signaling, transport-mediated lipid synthesis, membrane trafficking and also, ACBPs were indicated as a possible inhibitor of diazepam binding to the GABA-A receptor. To estimate the importance of the non-specific electrostatic energy in the ACBP-membrane interaction, we computationally modeled the interaction of HgACBP with both anionic and neutral membranes. To compute the Free Electrostatic Energy of Binding (dE), we used the Finite Difference Poisson Boltzmann Equation (FDPB) method as implemented in APBS. In the most energetically favorable orientation, ACBP brings charged residues Lys18 and Lys50 and hydrophobic residues Met46 and Leu47 into membrane surface proximity. This conformation suggests that these four ACBP amino acids are most likely to play a leading role in the ACBP-membrane interaction and ligand intake. Thus, we propose that long range electrostatic forces are the first step in the interaction mechanism between ACBP and membranes.

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

    PubMed

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

    2013-01-01

    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.

  14. Alternative basis functions for L sup 2 calculations on the molecular continuum. II. Integrals with higher-order functions

    SciTech Connect

    Fortunelli, A.; Carravetta, V. )

    1992-04-01

    By differentiation of the expressions for the basic {ital s}-type integrals previously presented, analytic expressions are here derived for integrals, relevant for quantum-chemistry calculations, involving oscillating Hermite Gaussian functions (OHGF's) and many-center Hermite Gaussian functions (HGF's) of any order. The OHGF is the product of a HGF and a radial trigonometric factor cos({ital kr}), and has been proposed for describing the continuum orbitals in {ital L}{sup 2} calculations on molecules. The resulting expressions are compact and particularly suitable for numerical implementation on a computer, while the increase in the computational effort of the integral evaluation with respect to the {ital s}-type functions is estimated to be of the same order as that found in the standard case of simple Gaussian functions. Applications of the OHGF basis to the calculation of continuum states are presented and compared to the exact results for test cases: the hydrogen atom and the H{sub 2}{sup +} molecule, in order to discuss advantages and limitations of the proposed approach.

  15. AFMPB: An Adaptive Fast Multipole Poisson-Boltzmann Solver for Calculating Electrostatics in Biomolecular Systems

    PubMed Central

    Lu, Benzhuo; Cheng, Xiaolin; Huang, Jingfang; McCammon, J. Andrew

    2010-01-01

    A Fortran program package is introduced for rapid evaluation of the electrostatic potentials and forces in biomolecular systems modeled by the linearized Poisson-Boltzmann equation. The numerical solver utilizes a well-conditioned boundary integral equation (BIE) formulation, a node-patch discretization scheme, a Krylov subspace iterative solver package with reverse communication protocols, and an adaptive new version of fast multipole method in which the exponential expansions are used to diagonalize the multipole to local translations. The program and its full description, as well as several closely related libraries and utility tools are available at http://lsec.cc.ac.cn/lubz/afmpb.html and a mirror site at http://mccammon.ucsd.edu/. This paper is a brief summary of the program: the algorithms, the implementation and the usage. PMID:20532187

  16. Experimental Measurements and Density Functional Theory Calculations of Continuum Lowering in Strongly Coupled Plasmas

    NASA Astrophysics Data System (ADS)

    Vinko, Sam

    2014-10-01

    An accurate description of the ionization potential depression (IPD) of ions in plasmas due to their interaction with the environment is a fundamental problem in plasma physics, playing a key role in determining the ionization balance, charge state distribution, opacity and plasma equation of state. Here I present the first experimental investigation of the IPD as a function of ionic charge state in a range of dense Mg, Al and Si plasmas, using the Linac Coherent Light Source X-ray free-electron laser. The measurements show significantly larger IPDs than are predicted by the most commonly used models, such as that of Stewart-Pyatt, or the ion-sphere model of Zimmerman-More. Instead, plasma simulations using finite-temperature density functional theory with excited-state projector augmented-wave potentials show excellent agreement with the experimental results and explain the stronger-than-expected continuum lowering through the electronic structure of the valence states in these strong-coupling conditions, which retain much of their atomic characteristics close to the ion core regions. These results have a profound impact on the understanding and modelling of plasmas over a wide range of warm- and hot-dense matter conditions.

  17. Protonation state and free energy calculation of HIV-1 protease-inhibitor complex based on electrostatic polarisation effect

    NASA Astrophysics Data System (ADS)

    Yang, Maoyou; Jiang, Xiaonan; Jiang, Ning

    2014-06-01

    The protonation states of catalytic Asp25/25‧ residues remarkably affect the binding mechanism of the HIV-1 protease-inhibitor complex. Here we report a molecular dynamics simulation study, which includes electrostatic polarisation effect, to investigate the influence of Asp25/25‧ protonation states upon the binding free energy of the HIV-1 protease and a C2-symmetric inhibitor. Good agreements are obtained on inhibitor structure, hydrogen bond network, and binding free energy between our theoretical calculations and the experimental data. The calculations show that the Asp25 residue is deprotonated, and the Asp25‧ residue is protonated. Our results reveal that the Asp25/25‧ residues can have different protonation states when binding to different inhibitors although the protease and the inhibitors have the same symmetry. This study offers some insights into understanding the protonation state of HIV-1 protease-inhibitor complex, which could be helpful in designing new inhibitor molecules.

  18. ElectroShape: fast molecular similarity calculations incorporating shape, chirality and electrostatics

    NASA Astrophysics Data System (ADS)

    Armstrong, M. Stuart; Morris, Garrett M.; Finn, Paul W.; Sharma, Raman; Moretti, Loris; Cooper, Richard I.; Richards, W. Graham

    2010-09-01

    We present ElectroShape, a novel ligand-based virtual screening method, that combines shape and electrostatic information into a single, unified framework. Building on the ultra-fast shape recognition (USR) approach for fast non-superpositional shape-based virtual screening, it extends the method by representing partial charge information as a fourth dimension. It also incorporates the chiral shape recognition (CSR) method, which distinguishes enantiomers. It has been validated using release 2 of the Directory of useful decoys (DUD), and shows a near doubling in enrichment ratio at 1% over USR and CSR, and improvements as measured by Receiver Operating Characteristic curves. These improvements persisted even after taking into account the chemotype redundancy in the sets of active ligands in DUD. During the course of its development, ElectroShape revealed a difference in the charge allocation of the DUD ligand and decoy sets, leading to several new versions of DUD being generated as a result. ElectroShape provides a significant addition to the family of ultra-fast ligand-based virtual screening methods, and its higher-dimensional shape recognition approach has great potential for extension and generalisation.

  19. AFMPB: An adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems

    NASA Astrophysics Data System (ADS)

    Lu, Benzhuo; Cheng, Xiaolin; Huang, Jingfang; McCammon, J. Andrew

    2013-11-01

    A Fortran program package is introduced for rapid evaluation of the electrostatic potentials and forces in biomolecular systems modeled by the linearized Poisson-Boltzmann equation. The numerical solver utilizes a well-conditioned boundary integral equation (BIE) formulation, a node-patch discretization scheme, a Krylov subspace iterative solver package with reverse communication protocols, and an adaptive new version of the fast multipole method in which the exponential expansions are used to diagonalize the multipole-to-local translations. The program and its full description, as well as several closely related libraries and utility tools are available at http://lsec.cc.ac.cn/~lubz/afmpb.html and a mirror site at http://mccammon.ucsd.edu/. This paper is a brief summary of the program: the algorithms, the implementation and the usage. Restrictions: Only three or six significant digits options are provided in this version. Unusual features: Most of the codes are in Fortran77 style. Memory allocation functions from Fortran90 and above are used in a few subroutines. Additional comments: The current version of the codes is designed and written for single core/processor desktop machines. Check http://lsec.cc.ac.cn/lubz/afmpb.html for updates and changes. Running time: The running time varies with the number of discretized elements (N) in the system and their distributions. In most cases, it scales linearly as a function of N.

  20. Rydberg and continuum states of the HeH+ molecular ion: Variational R -matrix and multichannel quantum defect theory calculations

    NASA Astrophysics Data System (ADS)

    Bouhali, I.; Bezzaouia, S.; Telmini, M.; Jungen, Ch.

    2016-08-01

    Variational ab initio R -matrix theory combined with generalized multichannel quantum defect theory is used to calculate singly excited Rydberg states of the hydrohelium molecular ion, HeH+, for Σ,3+1,Π,31,Δ,31,Φ,31, and Γ,31 symmetry. Bound levels are calculated for n values up to n ≈10 , and continuum states up to ≈3 eV above the HeH2 + threshold. The calculations span the range of internuclear distances R from 1 to 5 bohrs. The present work follows a preliminary study on the Δ,31 states of HeH+ [Bouhali, Bezzaouia, Telmini, and Jungen, EPJ Web Conf. 84, 04004 (2015), 10.1051/epjconf/20158404004] which was also based on R -matrix theory. Further—although limited to rather small R values—the present work extends the recent ab initio computations of Jungen and Jungen [Mol. Phys. 113, 2333 (2015), 10.1080/00268976.2015.1040094] to higher excitation energies which are not accessible to standard quantum-chemical methods. Where a comparison with the calculations of Jungen and Jungen and other older results can be made, namely for n ≤5 , very good agreement with previous ab initio results is obtained.

  1. Robust computational method for fast calculations of multicharged ions lineshapes affected by a low-frequency electrostatic plasma turbulence

    NASA Astrophysics Data System (ADS)

    Dalimier, E.; Oks, E.

    2017-01-01

    Transport phenomena in plasmas, such as, e.g., resistivity, can be affected by electrostatic turbulence that frequently occurs in various kinds of laboratory and astrophysical plasmas. Transport phenomena are affected most significantly by a low-frequency electrostatic turbulence—such as, e.g., ion acoustic waves, also known as ionic sound—causing anomalous resistivity. In this case, for computing profiles of spectral lines, emitted by plasma ions, by any appropriate code for diagnostic purposes, it is necessary to calculate the distribution of the total quasistatic field. For a practically important situation, where the average turbulent field is much greater than the characteristic ion microfield, we develop a robust computational method valid for any appropriate distribution of the ion microfield at a charged point. We show that the correction to the Rayleigh distribution of the turbulent field is controlled by the behavior of the ion microfield distribution at large fields—in distinction to the opposite (and therefore, erroneous) result in the literature. We also obtain a universal analytical expression for the correction to the Rayleigh distribution based on the asymptotic of the ion microfield distribution at large fields at a charged point. By comparison with various known distributions of the ion microfield, we show that our asymptotic formula has a sufficiently high accuracy. Also exact computations are used to verify the high accuracy of the method. This robust approximate, but accurate method yields faster computational results than the exact calculations and therefore should be important for practical situations requiring simultaneous computations of a large number of spectral lineshapes (e.g., for calculating opacities)—especially for laser-produced plasmas.

  2. AFMPB: An adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems

    NASA Astrophysics Data System (ADS)

    Lu, Benzhuo; Cheng, Xiaolin; Huang, Jingfang; McCammon, J. Andrew

    2010-06-01

    A Fortran program package is introduced for rapid evaluation of the electrostatic potentials and forces in biomolecular systems modeled by the linearized Poisson-Boltzmann equation. The numerical solver utilizes a well-conditioned boundary integral equation (BIE) formulation, a node-patch discretization scheme, a Krylov subspace iterative solver package with reverse communication protocols, and an adaptive new version of fast multipole method in which the exponential expansions are used to diagonalize the multipole-to-local translations. The program and its full description, as well as several closely related libraries and utility tools are available at http://lsec.cc.ac.cn/~lubz/afmpb.html and a mirror site at http://mccammon.ucsd.edu/. This paper is a brief summary of the program: the algorithms, the implementation and the usage. Program summaryProgram title: AFMPB: Adaptive fast multipole Poisson-Boltzmann solver Catalogue identifier: AEGB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGB_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL 2.0 No. of lines in distributed program, including test data, etc.: 453 649 No. of bytes in distributed program, including test data, etc.: 8 764 754 Distribution format: tar.gz Programming language: Fortran Computer: Any Operating system: Any RAM: Depends on the size of the discretized biomolecular system Classification: 3 External routines: Pre- and post-processing tools are required for generating the boundary elements and for visualization. Users can use MSMS ( http://www.scripps.edu/~sanner/html/msms_home.html) for pre-processing, and VMD ( http://www.ks.uiuc.edu/Research/vmd/) for visualization. Sub-programs included: An iterative Krylov subspace solvers package from SPARSKIT by Yousef Saad ( http://www-users.cs.umn.edu/~saad/software/SPARSKIT/sparskit.html), and the fast multipole methods subroutines from FMMSuite ( http

  3. Optimizing electrostatic field calculations with the Adaptive Poisson-Boltzmann Solver to predict electric fields at protein-protein interfaces II: explicit near-probe and hydrogen-bonding water molecules.

    PubMed

    Ritchie, Andrew W; Webb, Lauren J

    2014-07-17

    We have examined the effects of including explicit, near-probe solvent molecules in a continuum electrostatics strategy using the linear Poisson-Boltzmann equation with the Adaptive Poisson-Boltzmann Solver (APBS) to calculate electric fields at the midpoint of a nitrile bond both at the surface of a monomeric protein and when docked at a protein-protein interface. Results were compared to experimental vibrational absorption energy measurements of the nitrile oscillator. We examined three methods for selecting explicit water molecules: (1) all water molecules within 5 Å of the nitrile nitrogen; (2) the water molecule closest to the nitrile nitrogen; and (3) any single water molecule hydrogen-bonding to the nitrile. The correlation between absolute field strengths with experimental absorption energies were calculated and it was observed that method 1 was only an improvement for the monomer calculations, while methods 2 and 3 were not significantly different from the purely implicit solvent calculations for all protein systems examined. Upon taking the difference in calculated electrostatic fields and comparing to the difference in absorption frequencies, we typically observed an increase in experimental correlation for all methods, with method 1 showing the largest gain, likely due to the improved absolute monomer correlations using that method. These results suggest that, unlike with quantum mechanical methods, when calculating absolute fields using entirely classical models, implicit solvent is typically sufficient and additional work to identify hydrogen-bonding or nearest waters does not significantly impact the results. Although we observed that a sphere of solvent near the field of interest improved results for relative field calculations, it should not be consider a panacea for all situations.

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

    SciTech Connect

    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.

  5. Uncertainties in Properties Calculated from Fitted Potential Functions and Determining Potential Functions from FITS to Bound to Continuum Intensity Data

    NASA Astrophysics Data System (ADS)

    Le Roy, Robert J.

    2013-06-01

    In recent years it has become increasingly common to analyse spectroscopic data by using ``direct potential fits" of simulated data generated from analytic potential energy functions to experiment to optimize the parameters defining that potential energy function. This has the advantages of circumventing use of the semiclassical approximations associated with traditional methodologies, and of directly yielding a closed-form expression that is the most compact and comprehensive way to summarize what we know about a molecule. A question which then arises is: What are the uncertainties in properties computed using this potential? It turns out that this question is very closely related to the question of how to apply this simulation/fitting method efficiently to the analysis of bound to continuum intensity data. Both depend upon being able to answer the question: What are the partial derivatives of a wavefunction with respect to the parameters defining the potential energy function from which it is generated? It will be shown that such partial derivatives may be obtained readily as the `particular' solutions of linear inhomogeneous differential equations of a type that is routinely solved in another context for calculating the centrifugal distortion constants of diatomic molecules. Applications of this technique have been incorporated into the publicly available bound-state data analysis and simulation program DPotFit and the distributed bound to continuum simulation/fitting program BCONT. J.M. Hutson, J. Phys. B (At. Mol. Phys) {14}, 851 (1981). J. Tellinghuisen, J. Mol. Spectrosc. {122}, 455 (1987). See http://leroy.uwaterloo.ca/programs/

  6. Interplay among electrostatic, dispersion and steric interactions: Spectroscopy and quantum chemical calculations of π-hydrogen bonded complexes.

    PubMed

    Kumar, Sumit; Singh, Santosh Kumar; Vaishnav, Jamuna Kanaram; Hill, J Grant; Das, Aloke

    2017-01-26

    π-hydrogen bonding interactions are ubiquitous in both materials and biology. Despite their relatively weak nature great progress has been made in their investigation by experimental and theoretical methods, but this becomes significantly more complicated when secondary intermolecular interactions are present. In this study the effect of successive methyl substitution on the supramolecular structure and interaction energy of indole⋯methylated benzene (ind⋯n-mb, n = 1-6) complexes is probed through a combination of supersonic jet experiment and benchmark quality quantum chemical calculations. It is demonstrated that additional secondary interactions introduce a subtle interplay among electrostatic and dispersion forces, as well as steric repulsion, which fine-tunes the overall structural motif. Resonant Two-Photon Ionization (R2PI) and IR-UV double resonance spectroscopy techniques were used to probe jet-cooled ind⋯n-mb (n = 2, 3, 6) complexes, with red-shifting of the N-H IR stretching frequency showing that increasing the degree of methyl substitution increases the strength of the primary N-H⋯π interaction. Ab initio harmonic frequency and binding energy calculations confirm this trend for all six complexes. Electronic spectra of the three dimers are broad and structureless, with quantum chemical calculations revealing that this is likely due to multiple tilted conformations of each dimer possessing similar stabilization energies.

  7. A self-consistent, microenvironment modulated screened coulomb potential approximation to calculate pH-dependent electrostatic effects in proteins.

    PubMed Central

    Mehler, E L; Guarnieri, F

    1999-01-01

    An improved approach is presented for calculating pH-dependent electrostatic effects in proteins using sigmoidally screened Coulomb potentials (SCP). It is hypothesized that a key determinant of seemingly aberrant behavior in pKa shifts is due to the properties of the unique microenvironment around each residue. To help demonstrate this proposal, an approach is developed to characterize the microenvironments using the local hydrophobicity/hydrophilicity around each residue of the protein. The quantitative characterization of the microenvironments shows that the protein is a complex mosaic of differing dielectric regions that provides a physical basis for modifying the dielectric screening functions: in more hydrophobic microenvironments the screening decreases whereas the converse applies to more hydrophilic regions. The approach was applied to seven proteins providing more than 100 measured pKa values and yielded a root mean square deviation of 0.5 between calculated and experimental values. The incorporation of the local hydrophobicity characteristics into the algorithm allowed the resolution of some of the more intractable problems in the calculation of pKa. Thus, the divergent shifts of the pKa of Glu-35 and Asp-66 in hen egg white lysozyme, which are both about 90% buried, was correctly predicted. Mechanistically, the divergence occurs because Glu-35 is in a hydrophobic microenvironment, while Asp-66 is in a hydrophilic microenvironment. Furthermore, because the calculation of the microenvironmental effects takes very little CPU time, the computational speed of the SCP formulation is conserved. Finally, results from different crystal structures of a given protein were compared, and it is shown that the reliability of the calculated pKa values is sufficient to allow identification of conformations that may be more relevant for the solution structure. PMID:10388736

  8. Efficient calculation of many-body induced electrostatics in molecular systems.

    PubMed

    McLaughlin, Keith; Cioce, Christian R; Pham, Tony; Belof, Jonathan L; Space, Brian

    2013-11-14

    Potential energy functions including many-body polarization are in widespread use in simulations of aqueous and biological systems, metal-organics, molecular clusters, and other systems where electronically induced redistribution of charge among local atomic sites is of importance. The polarization interactions, treated here via the methods of Thole and Applequist, while long-ranged, can be computed for moderate-sized periodic systems with extremely high accuracy by extending Ewald summation to the induced fields as demonstrated by Nymand, Sala, and others. These full Ewald polarization calculations, however, are expensive and often limited to very small systems, particularly in Monte Carlo simulations, which may require energy evaluation over several hundred-thousand configurations. For such situations, it shall be shown that sufficiently accurate computation of the polarization energy can be produced in a fraction of the central processing unit (CPU) time by neglecting the long-range extension to the induced fields while applying the long-range treatments of Ewald or Wolf to the static fields; these methods, denoted Ewald E-Static and Wolf E-Static (WES), respectively, provide an effective means to obtain polarization energies for intermediate and large systems including those with several thousand polarizable sites in a fraction of the CPU time. Furthermore, we shall demonstrate a means to optimize the damping for WES calculations via extrapolation from smaller trial systems.

  9. Electrostatic effects in macromolecules: fundamental concepts and practical modeling.

    PubMed

    Warshel, A; Papazyan, A

    1998-04-01

    The past few years have seen an exponential growth in the calculations of electrostatic energies of macromolecules and an increased recognition of the crucial role of electrostatic effects. This review considers the current state of the field. Focus is placed on calculations of pKas, redox potentials and binding energies in macromolecules and clarification of the fact that the value of the dielectric 'constant' of a protein depends on its definition and that small dielectric constants should not be used in describing charge-charge interactions by current continuum models.

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

    PubMed

    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.

  11. Calculating pKa values for substituted phenols and hydration energies for other compounds with the first-order Fuzzy-Border continuum solvation model.

    PubMed

    Sharma, Ity; Kaminski, George A

    2012-11-15

    We have computed pK(a) values for 11 substituted phenol compounds using the continuum Fuzzy-Border (FB) solvation model. Hydration energies for 40 other compounds, including alkanes, alkenes, alkynes, ketones, amines, alcohols, ethers, aromatics, amides, heterocycles, thiols, sulfides, and acids have been calculated. The overall average unsigned error in the calculated acidity constant values was equal to 0.41 pH units and the average error in the solvation energies was 0.076 kcal/mol. We have also reproduced pK(a) values of propanoic and butanoic acids within about 0.1 pH units from the experimental values by fitting the solvation parameters for carboxylate ion carbon and oxygen atoms. The FB model combines two distinguishing features. First, it limits the amount of noise which is common in numerical treatment of continuum solvation models by using fixed-position grid points. Second, it uses either second- or first-order approximation for the solvent polarization, depending on a particular implementation. These approximations are similar to those used for solute and explicit solvent fast polarization treatment which we developed previously. This article describes results of using the first-order technique. This approximation places the presented methodology between the Generalized Born and Poisson-Boltzmann continuum solvation models with respect to their accuracy of reproducing the many-body effects in modeling a continuum solvent.

  12. Hybrid Gaussian-discrete-variable representation for one- and two-active-electron continuum calculations in molecules

    NASA Astrophysics Data System (ADS)

    Yip, F. L.; McCurdy, C. W.; Rescigno, T. N.

    2014-12-01

    A combined basis of analytic Gaussian functions and grid-based finite element-discrete variable representation spherical harmonic expansion is specialized for the description of continuum electron dynamics in the presence of electrons held fixed in core molecular orbitals. The applicability of this hybrid representation designed for general problems involving accurate determination of molecular continua wave functions is illustrated for photoionization of second-row diatomic molecules. Accurate descriptions of such electron continuum dynamics are a necessary step towards analyzing correlated double continua photoejections. Examination of this hybrid method in comparison to a more computationally expensive pure grid-based single-center expansion reveals several key advantages that by design make it attractive for describing processes involving one or more electrons moved to the continuum.

  13. Continuum and atomistic modeling of ion partitioning into a peptide nanotube.

    PubMed Central

    Asthagiri, D; Bashford, D

    2002-01-01

    Continuum and atomistic descriptions of the partitioning of ions into a self-assembled (D,L)-octapeptide nanotube, cyclo[-(L-Ala-D-Ala)(4)-], are presented. Perturbation free energy calculations, including Ewald electrostatics, are used to estimate the electrostatic component of the excess free energy of charging Li(+), Na(+), Rb(+), and Cl(minus sign) ions inside the nanotube. The radial density and orientational distribution of water around the ion is calculated for the ion at two different positions inside the tube; it is seen that the calculated distributions are sensitive to the location of the ions. Two different continuum electrostatic models are formulated to describe the ion solvation inside the nanotube. When enhanced orientational structuring of water dipoles is evidenced, explicitly including the first solvation shell as part of the low dielectric nanotube environment provides good agreement with molecular dynamics simulations. When water orientational structuring is as in the reference bulk solvent, we find that treating the first shell water explicitly or as a high dielectric continuum leads to similar results. These results are discussed, and their importance for continuum electrostatic modeling of ion channels are highlighted. PMID:11867436

  14. 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

    SciTech Connect

    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{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

  15. 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

    PubMed Central

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

    2013-01-01

    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

  16. Polarizable Atomic Multipole Solutes in a Generalized Kirkwood Continuum.

    PubMed

    Schnieders, Michael J; Ponder, Jay W

    2007-11-01

    The generalized Born (GB) model of continuum electrostatics is an analytic approximation to the Poisson equation useful for predicting the electrostatic component of the solvation free energy for solutes ranging in size from small organic molecules to large macromolecular complexes. This work presents a new continuum electrostatics model based on Kirkwood's analytic result for the electrostatic component of the solvation free energy for a solute with arbitrary charge distribution. Unlike GB, which is limited to monopoles, our generalized Kirkwood (GK) model can treat solute electrostatics represented by any combination of permanent and induced atomic multipole moments of arbitrary degree. Here we apply the GK model to the newly developed Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field, which includes permanent atomic multipoles through the quadrupole and treats polarization via induced dipoles. A derivation of the GK gradient is presented, which enables energy minimization or molecular dynamics of an AMOEBA solute within a GK continuum. For a series of 55 proteins, GK electrostatic solvation free energies are compared to the Polarizable Multipole Poisson-Boltzmann (PMPB) model and yield a mean unsigned relative difference of 0.9%. Additionally, the reaction field of GK compares well to that of the PMPB model, as shown by a mean unsigned relative difference of 2.7% in predicting the total solvated dipole moment for each protein in this test set. The CPU time needed for GK relative to vacuum AMOEBA calculations is approximately a factor of 3, making it suitable for applications that require significant sampling of configuration space.

  17. A semi-analytical calculation of the electrostatic pair interaction between nonuniformly charged colloidal spheres at an air-water interface.

    PubMed

    Lian, Zengju

    2016-07-07

    We study the electrostatic pair interaction between two nonuniformly like-charged colloidal spheres trapped in an air-water interface. Under the linear Poisson-Boltzmann approximation, a general form of the electrostatic potential for the system is shown in terms of multipole expansions. After combining the translation-rotation transform of the coordinates with the numerical multipoint collection, we give a semi-analytical result of the electrostatic pair interaction between the colloids. The pair interaction changes quantitatively or even qualitatively with different distributions of the surface charges on the particles. Because of the anisotropic distribution of the surface charge and the asymmetric dielectric medium, the dipole moment of the ion cloud associating with the particle orients diagonally to the air-water interface with an angle α. When the angle is large, the colloids interact repulsively, while they attract each other when the angle is small. The attractive colloids may be "Janus-like" charged and be arranged with some specific configurations. Whatever the repulsions or the attractions, they all decay asymptotically ∝1/d(3) (d is the center-center distance of the particles) which is consistent with our general acknowledge. The calculation results also provide an insight of the effect of the ion concentration, particle size, and the total charge of the particle on the pair interaction between the particles.

  18. Combined atomistic-continuum model for simulation of laser interaction with metals: application in the calculation of melting thresholds in Ni targets of varying thickness

    NASA Astrophysics Data System (ADS)

    Ivanov, D. S.; Zhigilei, L. V.

    The threshold laser fluence for the onset of surface melting is calculated for Ni films of different thicknesses and for a bulk Ni target using a combined atomistic-continuum computational model. The model combines the classical molecular dynamics (MD) method for simulation of non-equilibrium processes of lattice superheating and fast phase transformations with a continuum description of the laser excitation and subsequent relaxation of the conduction band electrons based on the two-temperature model (TTM). In the hybrid TTM-MD method, MD substitutes the TTM equation for the lattice temperature, and the diffusion equation for the electron temperature is solved simultaneously with MD integration of the equations of motion of atoms. The dependence of the threshold fluence on the film thickness predicted in TTM-MD simulations qualitatively agrees with TTM calculations, while the values of the thresholds for thick films and bulk targets are 10% higher in TTM-MD. The quantitative differences between the predictions of TTM and TTM-MD demonstrate that the kinetics of laser melting as well as the energy partitioning between the thermal energy of atomic vibrations and energy of the collective atomic motion driven by the relaxation of the laser-induced pressure should be taken into account in interpretation of experimental results on surface melting.

  19. TI-59 programmable calculator programs for in-stack opacity, venturi scrubbers, and electrostatic precipitators. User manual Jul 78-Jul 79

    SciTech Connect

    Cowen, S.J.; Ensor, D.S.; Sparks, L.E.

    1980-05-01

    The report explains the basic concepts of in-stack opacity as measured by in-stack opacity monitors. Also included are calculator programs that model the performance of venturi scrubbers and electrostatic precipitators. The effect of particulate control devices on in-stack opacity can be predicted by using these programs. The size distribution data input can be either in lognormal or histogram format. The opacity is calculated using Deirmendjian's approximation to Mie series to obtain extinction efficiencies. An alternative opacity program employing the exact Mie series solution is also described. The running time for this program is about 8 hours; that for the approximation program is 30 minutes. The accuracy of these programs is as good as the measured data input.

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

    SciTech Connect

    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.

  1. Thermodynamic properties and solidification kinetics of intermetallic Ni7Zr2 alloy investigated by electrostatic levitation technique and theoretical calculations

    NASA Astrophysics Data System (ADS)

    Li, L. H.; Hu, L.; Yang, S. J.; Wang, W. L.; Wei, B.

    2016-01-01

    The thermodynamic properties, including the density, volume expansion coefficient, ratio of specific heat to emissivity of intermetallic Ni7Zr2 alloy, have been measured using the non-contact electrostatic levitation technique. These properties vary linearly with temperature at solid and liquid states, even down to the obtained maximum undercooling of 317 K. The enthalpy, glass transition, diffusion coefficient, shear viscosity, and surface tension were obtained by using molecular dynamics simulations. Ni7Zr2 has a relatively poor glass forming ability, and the glass transition temperature is determined as 1026 K. The inter-diffusivity of Ni7Zr2 alloy fitted by Vogel-Fulcher-Tammann law yields a fragility parameter of 8.49, which indicates the fragile nature of this alloy. Due to the competition of increased thermodynamic driving force and decreased atomic diffusion, the dendrite growth velocity of Ni7Zr2 compound exhibits double-exponential relationship to the undercooling. The maximum growth velocity is predicted to be 0.45 m s-1 at the undercooling of 335 K. Theoretical analysis reveals that the dendrite growth is a diffusion-controlled process and the atomic diffusion speed is only 2.0 m s-1.

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

    SciTech Connect

    Fukuda, Ryoichi Ehara, Masahiro

    2015-12-31

    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.

  3. Spectroscopy (FT-IR, FT-Raman), hydrogen bonding, electrostatic potential and HOMO-LUMO analysis of tioxolone based on DFT calculations

    NASA Astrophysics Data System (ADS)

    Tao, Yaping; Li, Xiaofeng; Han, Ligang; Zhang, Weiying; Liu, Zhaojun

    2016-10-01

    Tioxolone possess antipsoriatic and antibacterial properties. Therefore, it has been used in treating various skin and scalp disorders for many years. Spectroscopic analysis of tioxolone was presented by using density functional theory (DFT) calculations and experiments (FT-IR, FT-Raman and UV-Vis). Molecular geometry and vibrational wavenumbers of tioxolone were investigated by using B3LYP method with aug-cc-pVTZ basis set. A complete vibrational spectra was made to analyze the potential energy distributions (PED). In addition, analysis of frontier molecular orbitals, electrostatic potential (ESP) and thermodynamic properties (heat capacity, entropy, enthalpy and Gibbs free energy) was presented with the same basis-set. Furthermore, the nature of molecular association through hydrogen bonding were discussed using atoms in molecules (AIM) and reduced density gradient (RDG) methods.

  4. Continuum-atomistic simulation of picosecond laser heating of copper with electron heat capacity from ab initio calculation

    NASA Astrophysics Data System (ADS)

    Ji, Pengfei; Zhang, Yuwen

    2016-03-01

    On the basis of ab initio quantum mechanics (QM) calculation, the obtained electron heat capacity is implemented into energy equation of electron subsystem in two temperature model (TTM). Upon laser irradiation on the copper film, energy transfer from the electron subsystem to the lattice subsystem is modeled by including the electron-phonon coupling factor in molecular dynamics (MD) and TTM coupled simulation. The results show temperature and thermal melting difference between the QM-MD-TTM integrated simulation and pure MD-TTM coupled simulation. The successful construction of the QM-MD-TTM integrated simulation provides a general way that is accessible to other metals in laser heating.

  5. Electronic excitation spectra of molecules in solution calculated using the symmetry-adapted cluster-configuration interaction method in the polarizable continuum model with perturbative approach

    SciTech Connect

    Fukuda, Ryoichi Ehara, Masahiro; Cammi, Roberto

    2014-02-14

    A perturbative approximation of the state specific polarizable continuum model (PCM) symmetry-adapted cluster-configuration interaction (SAC-CI) method is proposed for efficient calculations of the electronic excitations and absorption spectra of molecules in solutions. This first-order PCM SAC-CI method considers the solvent effects on the energies of excited states up to the first-order with using the zeroth-order wavefunctions. This method can avoid the costly iterative procedure of the self-consistent reaction field calculations. The first-order PCM SAC-CI calculations well reproduce the results obtained by the iterative method for various types of excitations of molecules in polar and nonpolar solvents. The first-order contribution is significant for the excitation energies. The results obtained by the zeroth-order PCM SAC-CI, which considers the fixed ground-state reaction field for the excited-state calculations, are deviated from the results by the iterative method about 0.1 eV, and the zeroth-order PCM SAC-CI cannot predict even the direction of solvent shifts in n-hexane for many cases. The first-order PCM SAC-CI is applied to studying the solvatochromisms of (2,2{sup ′}-bipyridine)tetracarbonyltungsten [W(CO){sub 4}(bpy), bpy = 2,2{sup ′}-bipyridine] and bis(pentacarbonyltungsten)pyrazine [(OC){sub 5}W(pyz)W(CO){sub 5}, pyz = pyrazine]. The SAC-CI calculations reveal the detailed character of the excited states and the mechanisms of solvent shifts. The energies of metal to ligand charge transfer states are significantly sensitive to solvents. The first-order PCM SAC-CI well reproduces the observed absorption spectra of the tungsten carbonyl complexes in several solvents.

  6. Cluster-continuum quasichemical theory calculation of the lithium ion solvation in water, acetonitrile and dimethyl sulfoxide: an absolute single-ion solvation free energy scale.

    PubMed

    Carvalho, Nathalia F; Pliego, Josefredo R

    2015-10-28

    Absolute single-ion solvation free energy is a very useful property for understanding solution phase chemistry. The real solvation free energy of an ion depends on its interaction with the solvent molecules and on the net potential inside the solute cavity. The tetraphenyl arsonium-tetraphenyl borate (TATB) assumption as well as the cluster-continuum quasichemical theory (CC-QCT) approach for Li(+) solvation allows access to a solvation scale excluding the net potential. We have determined this free energy scale investigating the solvation of the lithium ion in water (H2O), acetonitrile (CH3CN) and dimethyl sulfoxide (DMSO) solvents via the CC-QCT approach. Our calculations at the MP2 and MP4 levels with basis sets up to the QZVPP+diff quality, and including solvation of the clusters and solvent molecules by the dielectric continuum SMD method, predict the solvation free energy of Li(+) as -116.1, -120.6 and -123.6 kcal mol(-1) in H2O, CH3CN and DMSO solvents, respectively (1 mol L(-1) standard state). These values are compatible with the solvation free energy of the proton of -253.4, -253.2 and -261.1 kcal mol(-1) in H2O, CH3CN and DMSO solvents, respectively. Deviations from the experimental TATB scale are only 1.3 kcal mol(-1) in H2O and 1.8 kcal mol(-1) in DMSO solvents. However, in the case of CH3CN, the deviation reaches a value of 9.2 kcal mol(-1). The present study suggests that the experimental TATB scale is inconsistent for CH3CN. A total of 125 values of the solvation free energy of ions in these three solvents were obtained. These new data should be useful for the development of theoretical solvation models.

  7. Calculation of the Gibbs Free Energy of Solvation and Dissociation of HCl in Water via Monte Carlo Simulations and Continuum Solvation Models

    SciTech Connect

    McGrath, Matthew; Kuo, I-F W.; Ngouana, Brice F.; Ghogomu, Julius N.; Mundy, Christopher J.; Marenich, Aleksandr; Cramer, Christopher J.; Truhlar, Donald G.; Siepmann, Joern I.

    2013-08-28

    The free energy of solvation and dissociation of hydrogen chloride in water is calculated through a combined molecular simulation quantum chemical approach at four temperatures between T = 300 and 450 K. The free energy is first decomposed into the sum of two components: the Gibbs free energy of transfer of molecular HCl from the vapor to the aqueous liquid phase and the standard-state free energy of acid dissociation of HCl in aqueous solution. The former quantity is calculated using Gibbs ensemble Monte Carlo simulations using either Kohn-Sham density functional theory or a molecular mechanics force field to determine the system’s potential energy. The latter free energy contribution is computed using a continuum solvation model utilizing either experimental reference data or micro-solvated clusters. The predicted combined solvation and dissociation free energies agree very well with available experimental data. CJM was supported by the US Department of Energy,Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.

  8. Continuum kinetic modeling of the tokamak plasma edge

    SciTech Connect

    Dorf, M. A.; Dorr, M.; Rognlien, T.; Hittinger, J.; Cohen, R.

    2016-03-10

    In this study, the first 4D (axisymmetric) high-order continuum gyrokinetic transport simulations that span the magnetic separatrix of a tokamak are presented. The modeling is performed with the COGENT code, which is distinguished by fourth-order finite-volume discretization combined with mapped multiblock grid technology to handle the strong anisotropy of plasmatransport and the complex X-point divertor geometry with high accuracy. The calculations take into account the effects of fully nonlinear Fokker-Plank collisions, electrostatic potential variations, and anomalous radial transport. Topics discussed include: (a) ion orbit loss and the associated toroidal rotation and (b) edge plasma relaxation in the presence of anomalous radial transport.

  9. Continuum kinetic modeling of the tokamak plasma edge

    NASA Astrophysics Data System (ADS)

    Dorf, M. A.; Dorr, M. R.; Hittinger, J. A.; Cohen, R. H.; Rognlien, T. D.

    2016-05-01

    The first 4D (axisymmetric) high-order continuum gyrokinetic transport simulations that span the magnetic separatrix of a tokamak are presented. The modeling is performed with the COGENT code, which is distinguished by fourth-order finite-volume discretization combined with mapped multiblock grid technology to handle the strong anisotropy of plasma transport and the complex X-point divertor geometry with high accuracy. The calculations take into account the effects of fully nonlinear Fokker-Plank collisions, electrostatic potential variations, and anomalous radial transport. Topics discussed include: (a) ion orbit loss and the associated toroidal rotation and (b) edge plasma relaxation in the presence of anomalous radial transport.

  10. DAPI binding to the DNA minor groove: a continuum solvent analysis.

    PubMed

    De Castro, L F Pineda; Zacharias, M

    2002-01-01

    A continuum solvent model based on the generalized Born (GB) or finite-difference Poisson-Boltzmann (FDPB) approaches has been employed to compare the binding of 4'-6-diamidine-2-phenyl indole (DAPI) to the minor groove of various DNA sequences. Qualitative agreement between the results of GB and FDPB approaches as well as between calculated and experimentally observed trends regarding the sequence specificity of DAPI binding to B-DNA was obtained. Calculated binding energies were decomposed into various contributions to solvation and DNA-ligand interaction. DNA conformational adaptation was found to make a favorable contribution to the calculated total interaction energy but did not change the DAPI binding affinity ranking of different DNA sequences. The calculations indicate that closed complex formation is mainly driven by nonpolar contributions and was found to be disfavored electrostatically due to a desolvation penalty that outbalances the attractive Coulomb interaction. The calculated penalty was larger for DAPI binding to GC-rich sequences compared with AT-rich target sequences and generally larger for the FDPB vs the GB continuum model. A radial interaction profile for DAPI at different distances from the DNA minor groove revealed an electrostatic energy minimum a few Angstroms farther away from the closed binding geometry. The calculated electrostatic interaction up to this distance is attractive and it may stabilize a nonspecific binding arrangement.

  11. Electrostatic Toys.

    ERIC Educational Resources Information Center

    Greenslade, Thomas B., Jr.

    1982-01-01

    Describes typical electrostatic toys which may be used to show students phenomena associated with sparks, sudden drops in potential, induction, and forces between bodies of like and opposite charges. Many of these demonstrations are suitable for student projects. (Author/JN)

  12. Continuum effects in nuclear transfer reactions

    SciTech Connect

    Marta, H. D.; Donangelo, R.; Fernandez Niello, J. O.; Pacheco, A. J.

    2007-02-12

    We develop a semiclassical calculation for nuclear transfer reactions where the continuum is treated in an exact way, and compare the results with those of a treatment in which the continuum is neglected. We conclude that the influence of the continuum is very important for weakly bound reactants.

  13. Four-body continuum-discretized coupled-channels calculations: Application to {sup 6}He+{sup 64}Zn at 13.6 MeV

    SciTech Connect

    Rodriguez-Gallardo, M.; Arias, J. M.; Moro, A. M.; Gomez-Camacho, J.; Thompson, I. J.; Tostevin, J. A.

    2010-04-26

    The recently developed four-body continuum-discretized coupled-channels (CDCC) method, making use of the binning procedure, is applied to the reaction {sup 6}He+{sup 64}Zn at 13.6 MeV (around the Coulomb barrier). Excellent agreement with available elastic data is found.

  14. Continuum radiation in planetary magnetospheres

    NASA Technical Reports Server (NTRS)

    Kurth, W. S.

    1991-01-01

    With the completion of the Voyager tour of the outer planets, radio and plasma wave instruments have executed the first survey of the wave spectra of Earth, Jupiter, Saturn, Uranus, and Neptune. One of the most notable conclusions of this survey is that there is a great deal of qualitative similarity in both the plasma wave and radio wave spectra from one magnetosphere to the next. In particular, in spite of detailed differences, most of the radio emissions at each of the planets have been tentatively classified into two primary categories. First, the most intense emissions are generally associated with the cyclotron maser instability. Second, a class of weaker emissions can be found at each of the magnetospheres which appears to be the result of conversion from intense electrostatic emissions at the upper hybrid resonance frequency into (primarily) ordinary mode radio emission. It is this second category, often referred to as nonthermal continuum radiation, which we will discuss in this review. We review the characteristics of the continuum spectrum at each of the planets, discuss the source region and direct observations of the generation of the emissions where available, and briefly describe the theories for the generation of the emissions. Over the past few years evidence has increased that the linear mode conversion of electrostatic waves into the ordinary mode can account for at least some of the continuum radiation observed. There is no definitive evidence which precludes the possibility that a nonlinear mechanism may also be important.

  15. Electrostatic monitoring

    DOEpatents

    Orr, Christopher Henry; Luff, Craig Janson; Dockray, Thomas; Macarthur, Duncan Whittemore

    2001-01-01

    The apparatus and method provide a technique for more simply measuring alpha and/or beta emissions arising from items or locations. The technique uses indirect monitoring of the emissions by detecting ions generated by the emissions, the ions being attracted electrostatically to electrodes for discharge of collection. The apparatus and method employ a chamber which is sealed around the item or location during monitoring with no air being drawn into or expelled from the chamber during the monitoring process. A simplified structure and operations arises as a result, but without impairing the efficiency and accuracy of the detection technique.

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

    PubMed Central

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

    2013-01-01

    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 (J Comput Chem. 2012 Sep 15; 33(24):1960–6.) 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, multi-threading, 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. PMID:23733490

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

    PubMed

    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.

  18. Continuum effects in transfer reactions induced by heavy ions

    SciTech Connect

    Marta, H.D.; Donangelo, R.; Fernandez Niello, J.O.; Pacheco, A.J.

    2006-02-15

    In the usual treatment of transfer nuclear reactions, the continuum states of the transferred particle are neglected. Here we perform a semiclassical calculation that treats the continuum in an exact way. For comparison purposes, we perform a second calculation in which the continuum is completely disregarded. The results of these two calculations indicates that the influence of the continuum states may be very important in systems with weakly bound reactants.

  19. Electrostatic Return of Contaminants

    NASA Technical Reports Server (NTRS)

    Rantanen, R.; Gordon, T.

    2003-01-01

    A Model has been developed capable of calculating the electrostatic return of spacecraft-emitted molecules that are ionized and attracted back to the spacecraft by the spacecraft electric potential on its surfaces. The return of ionized contaminant molecules to charged spacecraft surfaces is very important to all altitudes. It is especially important at geosynchronous and interplanetary environments, since it may be the only mechanism by which contaminants can degrade a surface. This model is applicable to all altitudes and spacecraft geometries. In addition to results of the model will be completed to cover a wide range of potential space systems.

  20. Continuum kinetic modeling of the tokamak plasma edge

    DOE PAGES

    Dorf, M. A.; Dorr, M.; Rognlien, T.; ...

    2016-03-10

    In this study, the first 4D (axisymmetric) high-order continuum gyrokinetic transport simulations that span the magnetic separatrix of a tokamak are presented. The modeling is performed with the COGENT code, which is distinguished by fourth-order finite-volume discretization combined with mapped multiblock grid technology to handle the strong anisotropy of plasmatransport and the complex X-point divertor geometry with high accuracy. The calculations take into account the effects of fully nonlinear Fokker-Plank collisions, electrostatic potential variations, and anomalous radial transport. Topics discussed include: (a) ion orbit loss and the associated toroidal rotation and (b) edge plasma relaxation in the presence of anomalousmore » radial transport.« less

  1. Explicit solvent models in protein pKa calculations.

    PubMed

    Gibas, C J; Subramaniam, S

    1996-07-01

    Continuum methods for calculation of protein electrostatics treat buried and ordered water molecules by one of two approximations; either the dielectric constant of regions containing ordered water molecules is equal to the bulk solvent dielectric constant, or it is equal to the protein dielectric constant though no fixed atoms are used to represent water molecules. A method for calculating the titration behavior of individual residues in proteins has been tested on models of hen egg white lysozyme containing various numbers of explicit water molecules. Water molecules were included based on hydrogen bonding, solvent accessibility, and/or proximity to titrating groups in the protein. Inclusion of water molecules significantly alters the calculated titration behavior of individual titrating sites, shifting calculated pKa values by up to 0.5 pH unit. Our results suggest that approximately one water molecule within hydrogen-bonding distance of each charged group should be included in protein electrostatics calculations.

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

    NASA Technical Reports Server (NTRS)

    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.

  3. A unified electrostatic and cavitation model for first-principles molecular dynamics in solution

    SciTech Connect

    Scherlis, D A; Fattebert, J; Gygi, F; Cococcioni, M; Marzari, N

    2005-11-14

    The electrostatic continuum solvent model developed by Fattebert and Gygi is combined with a first-principles formulation of the cavitation energy based on a natural quantum-mechanical definition for the surface of a solute. Despite its simplicity, the cavitation contribution calculated by this approach is found to be in remarkable agreement with that obtained by more complex algorithms relying on a large set of parameters. The model allows for very efficient Car-Parrinello simulations of finite or extended systems in solution, and demonstrates a level of accuracy as good as that of established quantum-chemistry continuum solvent methods. They apply this approach to the study of tetracyanoethylene dimers in dichloromethane, providing valuable structural and dynamical insights on the dimerization phenomenon.

  4. Thermodynamic properties and solidification kinetics of intermetallic Ni{sub 7}Zr{sub 2} alloy investigated by electrostatic levitation technique and theoretical calculations

    SciTech Connect

    Li, L. H.; Hu, L.; Yang, S. J.; Wang, W. L.; Wei, B.

    2016-01-21

    The thermodynamic properties, including the density, volume expansion coefficient, ratio of specific heat to emissivity of intermetallic Ni{sub 7}Zr{sub 2} alloy, have been measured using the non-contact electrostatic levitation technique. These properties vary linearly with temperature at solid and liquid states, even down to the obtained maximum undercooling of 317 K. The enthalpy, glass transition, diffusion coefficient, shear viscosity, and surface tension were obtained by using molecular dynamics simulations. Ni{sub 7}Zr{sub 2} has a relatively poor glass forming ability, and the glass transition temperature is determined as 1026 K. The inter-diffusivity of Ni{sub 7}Zr{sub 2} alloy fitted by Vogel–Fulcher–Tammann law yields a fragility parameter of 8.49, which indicates the fragile nature of this alloy. Due to the competition of increased thermodynamic driving force and decreased atomic diffusion, the dendrite growth velocity of Ni{sub 7}Zr{sub 2} compound exhibits double-exponential relationship to the undercooling. The maximum growth velocity is predicted to be 0.45 m s{sup −1} at the undercooling of 335 K. Theoretical analysis reveals that the dendrite growth is a diffusion-controlled process and the atomic diffusion speed is only 2.0 m s{sup −1}.

  5. Electrostatic potential map modelling with COSY Infinity

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

    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.

  6. Continuum electromechanical modeling of protein-membrane interactions.

    PubMed

    Zhou, Y C; Lu, Benzhuo; Gorfe, Alemayehu A

    2010-10-01

    A continuum electromechanical model is proposed to describe the membrane curvature induced by electrostatic interactions in a solvated protein-membrane system. The model couples the macroscopic strain energy of membrane and the electrostatic solvation energy of the system, and equilibrium membrane deformation is obtained by minimizing the electroelastic energy functional with respect to the dielectric interface. The model is illustrated with the systems with increasing geometry complexity and captures the sensitivity of membrane curvature to the permanent and mobile charge distributions.

  7. Four-component relativistic calculations in solution with the polarizable continuum model of solvation: theory, implementation, and application to the group 16 dihydrides H2X (X = O, S, Se, Te, Po).

    PubMed

    Remigio, Roberto Di; Bast, Radovan; Frediani, Luca; Saue, Trond

    2015-05-28

    We present a formulation of four-component relativistic self-consistent field (SCF) theory for a molecular solute described within the framework of the polarizable continuum model (PCM) for solvation. The linear response function for a four-component PCM-SCF state is also derived, as well as the explicit form of the additional contributions to the first-order response equations. The implementation of such a four-component PCM-SCF model, as carried out in a development version of the DIRAC program package, is documented. In particular, we present the newly developed application programming interface PCMSolver used in the actual implementation with DIRAC. To demonstrate the applicability of the approach, we present and analyze calculations of solvation effects on the geometries, electric dipole moments, and static electric dipole polarizabilities for the group 16 dihydrides H2X (X = O, S, Se, Te, Po).

  8. Electrostatically screened, voltage-controlled electrostatic chuck

    DOEpatents

    Klebanoff, Leonard Elliott

    2001-01-01

    Employing an electrostatically screened, voltage-controlled electrostatic chuck particularly suited for holding wafers and masks in sub-atmospheric operations will significantly reduce the likelihood of contaminant deposition on the substrates. The electrostatic chuck includes (1) an insulator block having a outer perimeter and a planar surface adapted to support the substrate and comprising at least one electrode (typically a pair of electrodes that are embedded in the insulator block), (2) a source of voltage that is connected to the at least one electrode, (3) a support base to which the insulator block is attached, and (4) a primary electrostatic shield ring member that is positioned around the outer perimeter of the insulator block. The electrostatic chuck permits control of the voltage of the lithographic substrate; in addition, it provides electrostatic shielding of the stray electric fields issuing from the sides of the electrostatic chuck. The shielding effectively prevents electric fields from wrapping around to the upper or front surface of the substrate, thereby eliminating electrostatic particle deposition.

  9. Electrostatic properties of fullerenes under an external electric field: First-principles calculations of energetics for all IPR isomers from C60 to C78

    NASA Astrophysics Data System (ADS)

    Sorimachi, Jun-ya; Okada, Susumu

    2016-08-01

    Based on first-principles total energy calculations, we analyze the energetics of the fullerene isomers from C60 to C78, all of which satisfy the isolated pentagon rule, under a parallel electric field. Our calculations show that the total energy of the fullerene is proportional to the square of the external electric field. On the other hand, the coefficient of the quadratic energy profile is sensitive to the fullerene species and their orientation. Furthermore, fullerenes possessing lower symmetry exhibit asymmetric quadratic energy profiles with respect to the field, indicating that they possess intrinsic polarization along particular molecular orientations.

  10. Continuum Kinetic Modeling of the Tokamak Plasma Edge

    NASA Astrophysics Data System (ADS)

    Dorf, Mikhail

    2015-11-01

    The problem of edge plasma transport provides substantial challenges for analytical or numerical analysis due to (a) complex magnetic geometry including both open and closed magnetic field lines B, (b) steep radial gradients comparable to ion drift-orbit excursions, and (c) a variation in the collision mean-free path along B from long to short compared to the magnetic connection length. Here, the first 4D continuum drift-kinetic transport simulations that span the magnetic separatrix of a tokamak are presented, motivated in part by the success of continuum kinetic codes for core physics and in part by the potential for high accuracy. The calculations include fully-nonlinear Fokker-Plank collisions and electrostatic potential variations. The problem of intrinsic toroidal rotation driven by ion orbit loss is addressed in detail. The code, COGENT, developed by the Edge Simulation Laboratory collaboration, is distinguished by a fourth-order finite-volume discretization combined with mapped multiblock grid technology to handle the strong anisotropy of plasma transport and the complex magnetic X-point divertor geometry with high accuracy. Previously, successful performance of high-order algorithms has been demonstrated in a simpler closed magnetic-flux-surface geometry for the problems of neoclassical transport and collisionless relaxation of geodesic acoustic modes in a tokamak pedestal, including the effects of a strong radial electric field under H-mode conditions. Work performed for USDOE, at LLNL under contract DE-AC52-07NA27344.

  11. NNWSI unit evaluation at Yucca Mountain, Nevada Test Site: Near field mechanical calculations using a continuum jointed rock moel in the JAC code

    SciTech Connect

    Thomas, R.K.

    1987-05-01

    The Nevada Nuclear Waste Storage Investigations (NNWSI) Project, managed by the Nevada Operations Office of the US Department of Energy, is examining the feasibility of siting a repository for high level nuclear wastes at Yucca Mountain on and adjacent to the Nevada Test Site (NTS). The work reported herein was done to support the selection, on a technical basis, of a single target repository horizon upon which to concentrate future activities. Presented in this report are the results of a comparative study between two candidate horizons: the devitrified Topopah Spring member of the Paintbrush Tuff and the nonwelded, zeolitized Tuffaceous Beds of Calico Hills. Performance of a repository sited in each candidate horizon was assessed by conducting structural calculations using a two-dimensional room-and-pillar geometry and average and limit material properties. The computer code JAC, with a constitutive model for jointed rock masses, was used to make the calculations. Based on analyses of the confining pressures in the pillar and the joint movement near the room, it is concluded that the Topopah Spring unit is more suitable than the Calico Hills unit for the placement of a nuclear waste repository. Finally, a comparison is made with a similar mine geometry sited in the Grouse Canyon Tuff, a horizon of known performance characteristics, using properties from G-Tunnel at NTS.

  12. Compact electrostatic comb actuator

    DOEpatents

    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).

  13. A robust, coupled approach for atomistic-continuum simulation.

    SciTech Connect

    Aubry, Sylvie; Webb, Edmund Blackburn, III; Wagner, Gregory John; Klein, Patrick A.; Jones, Reese E.; Zimmerman, Jonathan A.; Bammann, Douglas J.; Hoyt, Jeffrey John; Kimmer, Christopher J.

    2004-09-01

    This report is a collection of documents written by the group members of the Engineering Sciences Research Foundation (ESRF), Laboratory Directed Research and Development (LDRD) project titled 'A Robust, Coupled Approach to Atomistic-Continuum Simulation'. Presented in this document is the development of a formulation for performing quasistatic, coupled, atomistic-continuum simulation that includes cross terms in the equilibrium equations that arise due to kinematic coupling and corrections used for the calculation of system potential energy to account for continuum elements that overlap regions containing atomic bonds, evaluations of thermo-mechanical continuum quantities calculated within atomistic simulations including measures of stress, temperature and heat flux, calculation used to determine the appropriate spatial and time averaging necessary to enable these atomistically-defined expressions to have the same physical meaning as their continuum counterparts, and a formulation to quantify a continuum 'temperature field', the first step towards constructing a coupled atomistic-continuum approach capable of finite temperature and dynamic analyses.

  14. Continuum description for jointed media

    SciTech Connect

    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.

  15. The Suicide Prevention Continuum

    PubMed Central

    Caldwell, Dawn

    2010-01-01

    The suicide prevention continuum illustrates a practical approach to the complex issue of suicide prevention. The continuum evolved from discussions with two Aboriginal communities in Atlantic Canada about suicide and the different types of interventions available. The continuum offers a framework and reference tool to differentiate between the different stages of suicide risk. It illustrates where the Aboriginal Community Youth Resilience Network (ACYRN) fits into suicide prevention and how it contributes to prevention knowledge, capacity building, and policy development. PMID:20835376

  16. Quantum mechanical/molecular mechanical/continuum style solvation model: Linear response theory, variational treatment, and nuclear gradients

    NASA Astrophysics Data System (ADS)

    Li, Hui

    2009-11-01

    Linear response and variational treatment are formulated for Hartree-Fock (HF) and Kohn-Sham density functional theory (DFT) methods and combined discrete-continuum solvation models that incorporate self-consistently induced dipoles and charges. Due to the variational treatment, analytic nuclear gradients can be evaluated efficiently for these discrete and continuum solvation models. The forces and torques on the induced point dipoles and point charges can be evaluated using simple electrostatic formulas as for permanent point dipoles and point charges, in accordance with the electrostatic nature of these methods. Implementation and tests using the effective fragment potential (EFP, a polarizable force field) method and the conductorlike polarizable continuum model (CPCM) show that the nuclear gradients are as accurate as those in the gas phase HF and DFT methods. Using B3LYP/EFP/CPCM and time-dependent-B3LYP/EFP/CPCM methods, acetone S0→S1 excitation in aqueous solution is studied. The results are close to those from full B3LYP/CPCM calculations.

  17. Elucidating the Conformational Dependence of Calculated pKa Values.

    PubMed

    Livesay, Dennis R; Jacobs, Donald J; Kanjanapangka, Julie; Chea, Eric; Cortez, Hector; Garcia, Jorge; Kidd, Patrick; Marquez, Mario Pulido; Pande, Swati; Yang, David

    2006-07-01

    The variability within calculated protein residue pKa values calculated using Poisson-Boltzmann continuum theory with respect to small conformational fluctuations is investigated. As a general rule, sites buried in the protein core have the largest pKa fluctuations but the least amount of conformational variability; conversely, sites on the protein surface generally have large conformational fluctuations but very small pKa fluctuations. These results occur because of the heterogeneous or uniform nature of the electrostatic microenvironments at the protein core or surface, respectively. Atypical surface sites with large pKa fluctuations occur at the interfaces between significant anionic and cationic potentials.

  18. Continuum methods in lattice perturbation theory

    SciTech Connect

    Becher, Thomas G

    2002-11-15

    We show how methods of continuum perturbation theory can be used to simplify perturbative lattice calculations. We use the technique of asymptotic expansions to expand lattice loop integrals around the continuum limit. After the expansion, all nontrivial dependence on momenta and masses is encoded in continuum loop integrals and the only genuine lattice integrals left are tadpole integrals. Using integration-by-parts relations all of these can be expressed in terms of a small number of master integrals. Four master integrals are needed for bosonic one loop integrals, sixteen in QCD with Wilson or staggered fermions.

  19. Electrostatic Levitator Electrodes

    NASA Technical Reports Server (NTRS)

    1998-01-01

    Electrostatic levitation system inside Electrostatic Levitator (ESL) vacuum chamber. 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.

  20. Oral Language Continuum.

    ERIC Educational Resources Information Center

    Fresno County Dept. of Education, Fresno, CA.

    An oral language continuum designed to help elementary students develop techniques for a variety of speech situations, learn to listen, and learn to be aware of the responsibility of the speaker is presented. The continuum is divided into four sections. Student needs, implications for teaching, and suggested activities are arranged sequentially.…

  1. ELECTROSTATIC POWER GENERATOR.

    DTIC Science & Technology

    ELECTROSTATIC GENERATORS , POWER EQUIPMENT, ELECTRIC GOVERNORS, CIRCUITS, VACUUM SEALS, ELECTRICAL INSULATION, VACUUM, ELECTRODES, FINISHES, SURFACE...FINISHING, SURFACE PROPERTIES, HARDNESS, PULSE GENERATORS , TRANSFORMERS, FIELD EMISSION.

  2. ELECTROSTATIC POWER GENERATOR.

    DTIC Science & Technology

    ELECTROSTATIC GENERATORS , POWER EQUIPMENT, ELECTRICAL INSULATION, FIELD EMISSION, ELECTRODES, VACUUM, SURFACE PROPERTIES, ANODES, CATHODES, POLISHES...DIELECTRICS, COATINGS, PRESSURE, HARDNESS, PULSE GENERATORS , TRANSFORMERS, VACUUM SEALS, EQUATIONS.

  3. Electrostatic Environment of Hemes in Proteins: pKas of Hydroxyl Ligands†

    PubMed Central

    Song, Yifan; Mao, Junjun; Gunner, M. R.

    2009-01-01

    The pKas of ferric aquo–heme and aquo–heme electrochemical midpoints (Ems) at pH 7 in sperm whale myoglobin, Aplysia myoblogin, hemoglobin I, heme oxygenase 1, horseradish peroxidase and cytochrome c oxidase were calculated with Multi-Conformation Continuum Electrostatics (MCCE). The pKas span 3.3 pH units from 7.6 in heme oxygenase 1 to 10.9 in peroxidase, and the Ems range from −250 mv in peroxidase to 125 mV in Aplysia myoglobin. Proteins with higher in situ ferric aquo–heme pKas tend to have lower Ems. Both changes arise from the protein stabilizing a positively charged heme. However, compared with values in solution, the protein shifts the aquo–heme Ems more than the pKas. Thus, the protein has a larger effective dielectric constant for the protonation reaction, showing that electron and proton transfers are coupled to different conformational changes that are captured in the MCCE analysis. The calculations reveal a breakdown in the classical continuum electrostatic analysis of pairwise interactions. Comparisons with DFT calculations show that Coulomb’s law overestimates the large unfavorable interactions between the ferric water–heme and positively charged groups facing the heme plane by as much as 60%. If interactions with CuB in cytochrome c oxidase and Arg 38 in horseradish peroxidase are not corrected, the pKa calculations are in error by as much as 6 pH units. With DFT corrected interactions calculated pKas and Ems differ from measured values by less than 1 pH unit or 35 mV, respectively. The in situ aquo–heme pKa is important for the function of cytochrome c oxidase since it helps to control the stoichiometry of proton uptake coupled to electron transfer PMID:16800621

  4. Continuum radiation at Uranus

    SciTech Connect

    Kurth, W.S.; Gurnett, D.A. ); Desch, M.D. )

    1990-02-01

    Uranus has proven to be a radio source of remarkable complexity with as many as six distinctly different types of emission. One Uranian radio emission which has thus far escaped attention is an analog of continuum radiation at Earth, Jupiter, and Saturn. The emission is found to be propagating in the ordinary mode in the range of one to a few kHz on the inbound leg of the Voyager 2 encounter, shortly after the magnetopause crossing. The continuum radiation spectrum at Uranus also includes bands with frequencies as high as 12 kHz or greater on both the inbound and outbound legs. The Uranian continuum radiation is notably weak, making it more like that detected at Saturn than the extremely intense Jovian continuum radiation. The Uranian emission shows some evidence for narrow-band components lying in the same frequency regime as the continuum, completing the analogy with the other planets, which also show narrow-band components superimposed on the continuum spectrum. The authors argue that the low intensity of the Uranian continuum is most likely related to the lack of a density cavity within the Uranian magnetosphere that is deep relative to the solar wind plasma density.

  5. Electrostatic Levitator (ESL)

    NASA Technical Reports Server (NTRS)

    1998-01-01

    Dr. Rulison of Space System LORAl working with the Electrostatic Levitation (ESL) prior to the donation. Space System/LORAL donated the electrostatic containerless processing system to NASA's Marshall Space Flight Center (MSFC). The official hand over took place in July 1998.

  6. Edutainment Science: Electrostatics

    ERIC Educational Resources Information Center

    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…

  7. Continuum description of ionic and dielectric shielding for molecular-dynamics simulations of proteins in solution.

    PubMed

    Egwolf, Bernhard; Tavan, Paul

    2004-01-22

    We extend our continuum description of solvent dielectrics in molecular-dynamics (MD) simulations, which has provided an efficient and accurate solution of the Poisson equation, to ionic solvents as described by the linearized Poisson-Boltzmann (LPB) equation. We start with the formulation of a general theory for the electrostatics of an arbitrarily shaped molecular system, which consists of partially charged atoms and is embedded in a LPB continuum. This theory represents the reaction field induced by the continuum in terms of charge and dipole densities localized within the molecular system. Because these densities cannot be calculated analytically for systems of arbitrary shape, we introduce an atom-based discretization and a set of carefully designed approximations. This allows us to represent the densities by charges and dipoles located at the atoms. Coupled systems of linear equations determine these multipoles and can be rapidly solved by iteration during a MD simulation. The multipoles yield the reaction field forces and energies. Finally, we scrutinize the quality of our approach by comparisons with an analytical solution restricted to perfectly spherical systems and with results of a finite difference method.

  8. A Geometric and Electrostatic Study of the [4Fe-4S] Cluster of Adenosine-5´-Phosphosulfate Reductase from Broken Symmetry Density Functional Calculations and Extended X-ray Absorption Fine Structure Spectroscopy

    PubMed Central

    Bhave, Devayani P.; Han, Wen-Ge; Pazicni, Samuel; Penner-Hahn, James E.; Carroll, Kate S.; Noodleman, Louis

    2011-01-01

    Adenosine-5’-phosphosulfate reductase (APSR) is an iron-sulfur protein that catalyses the reduction of adenosine-5’-phosphosulfate (APS) to sulfite. APSR coordinates to a [4Fe-4S] cluster via a conserved CC-X~80-CXXC motif and the cluster is essential for catalysis. Despite extensive functional, structural and spectroscopic studies, the exact role of the iron-sulfur cluster in APS reduction remains unknown. To gain an understanding into the role of the cluster, density functional theory (DFT) analysis and extended X-ray fine structure spectroscopy (EXAFS) have been performed to reveal insights into the coordination, geometry and electrostatics of the [4Fe-4S] cluster. XANES data confirms that the cluster is in the [4Fe-4S]2+ state in both native and substrate-bound APSR while EXAFS data recorded at ~0.1 Å resolution indicates that there is no significant change in the structure of the [4Fe-4S] cluster between the native and substrate-bound forms of the protein. On the other hand, DFT calculations provide an insight into the subtle differences between the geometry of the cluster in the native and APS-bound forms of APSR. A comparison between models with and without the tandem cysteine pair coordination of the cluster suggests a role for the unique coordination in facilitating a compact geometric structure and ‘fine-tuning’ the electronic structure to prevent reduction of the cluster. Further, calculations using models in which residue Lys144 is mutated to Ala confirm the finding that Lys144 serves as a crucial link in the interactions involving the [4Fe-4S] cluster and APS. PMID:21678934

  9. Continuum Absorption Coefficient of Atoms and Ions

    NASA Technical Reports Server (NTRS)

    Armaly, B. F.

    1979-01-01

    The rate of heat transfer to the heat shield of a Jupiter probe has been estimated to be one order of magnitude higher than any previously experienced in an outer space exploration program. More than one-third of this heat load is due to an emission of continuum radiation from atoms and ions. The existing computer code for calculating the continuum contribution to the total load utilizes a modified version of Biberman's approximate method. The continuum radiation absorption cross sections of a C - H - O - N ablation system were examined in detail. The present computer code was evaluated and updated by being compared with available exact and approximate calculations and correlations of experimental data. A detailed calculation procedure, which can be applied to other atomic species, is presented. The approximate correlations can be made to agree with the available exact and experimental data.

  10. Efficient optimization of electrostatic interactions between biomolecules.

    SciTech Connect

    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.

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

    PubMed Central

    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

  12. An improved proximity force approximation for electrostatics

    SciTech Connect

    Fosco, Cesar D.; Lombardo, Fernando C.; Mazzitelli, Francisco D.

    2012-08-15

    A quite straightforward approximation for the electrostatic interaction between two perfectly conducting surfaces suggests itself when the distance between them is much smaller than the characteristic lengths associated with their shapes. Indeed, in the so called 'proximity force approximation' the electrostatic force is evaluated by first dividing each surface into a set of small flat patches, and then adding up the forces due two opposite pairs, the contributions of which are approximated as due to pairs of parallel planes. This approximation has been widely and successfully applied in different contexts, ranging from nuclear physics to Casimir effect calculations. We present here an improvement on this approximation, based on a derivative expansion for the electrostatic energy contained between the surfaces. The results obtained could be useful for discussing the geometric dependence of the electrostatic force, and also as a convenient benchmark for numerical analyses of the tip-sample electrostatic interaction in atomic force microscopes. - Highlights: Black-Right-Pointing-Pointer The proximity force approximation (PFA) has been widely used in different areas. Black-Right-Pointing-Pointer The PFA can be improved using a derivative expansion in the shape of the surfaces. Black-Right-Pointing-Pointer We use the improved PFA to compute electrostatic forces between conductors. Black-Right-Pointing-Pointer The results can be used as an analytic benchmark for numerical calculations in AFM. Black-Right-Pointing-Pointer Insight is provided for people who use the PFA to compute nuclear and Casimir forces.

  13. Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum

    NASA Astrophysics Data System (ADS)

    Schnieders, Michael J.; Baker, Nathan A.; Ren, Pengyu; Ponder, Jay W.

    2007-03-01

    Modeling the change in the electrostatics of organic molecules upon moving from vacuum into solvent, due to polarization, has long been an interesting problem. In vacuum, experimental values for the dipole moments and polarizabilities of small, rigid molecules are known to high accuracy; however, it has generally been difficult to determine these quantities for a polar molecule in water. A theoretical approach introduced by Onsager [J. Am. Chem. Soc. 58, 1486 (1936)] used vacuum properties of small molecules, including polarizability, dipole moment, and size, to predict experimentally known permittivities of neat liquids via the Poisson equation. Since this important advance in understanding the condensed phase, a large number of computational methods have been developed to study solutes embedded in a continuum via numerical solutions to the Poisson-Boltzmann equation. Only recently have the classical force fields used for studying biomolecules begun to include explicit polarization in their functional forms. Here the authors describe the theory underlying a newly developed polarizable multipole Poisson-Boltzmann (PMPB) continuum electrostatics model, which builds on the atomic multipole optimized energetics for biomolecular applications (AMOEBA) force field. As an application of the PMPB methodology, results are presented for several small folded proteins studied by molecular dynamics in explicit water as well as embedded in the PMPB continuum. The dipole moment of each protein increased on average by a factor of 1.27 in explicit AMOEBA water and 1.26 in continuum solvent. The essentially identical electrostatic response in both models suggests that PMPB electrostatics offers an efficient alternative to sampling explicit solvent molecules for a variety of interesting applications, including binding energies, conformational analysis, and pKa prediction. Introduction of 150mM salt lowered the electrostatic solvation energy between 2 and 13kcal /mole, depending on

  14. Electrostatic Field Invisibility Cloak

    PubMed Central

    Lan, Chuwen; Yang, Yuping; Geng, Zhaoxin; Li, Bo; Zhou, Ji

    2015-01-01

    The invisibility cloak has been drawing much attention due to its new concept for manipulating many physical fields, from oscillating wave fields (electromagnetic, acoustic and elastic) to static magnetic fields, dc electric fields, and diffusive fields. Here, an electrostatic field invisibility cloak has been theoretically investigated and experimentally demonstrated to perfectly hide two dimensional objects without disturbing their external electrostatic fields. The desired cloaking effect has been achieved via both cancelling technology and transformation optics (TO). This study demonstrates a novel way for manipulating electrostatic fields, which shows promise for a wide range of potential applications. PMID:26552343

  15. The electrostatic storage tube

    NASA Technical Reports Server (NTRS)

    Rutherford, R. E., Jr.

    1973-01-01

    An electrostatic camera system is discussed which is based on the electrostatic storage tube. The development of the system was begun following a series of experiments which indicated that the device offers signficantly improved performance over currently available devices. The approach used in developing the high performance camera involves: converting the input image to an electron image at low loss, applying a low noise gain process, and storing the resulting charge pattern in a low-loss target. The basic processes and elements of the electrostatic storage tube are illustrated and discussed. Graphs that depict the camera performance characteristics are included.

  16. Continuum-continuum transitions between resonant states using the RABITT technique

    NASA Astrophysics Data System (ADS)

    Jiménez, A.; Argenti, L.; Martín, F.

    2014-04-01

    We present a study of radiative continuum-continuum transitions in helium in the presence of doubly-excited states by using the attosecond RABITT technique beyond the Single Active Electron approximation. On the one hand, transition amplitudes between correlated continuum states are calculated both by direct numerical solution of the time-dependent Schrodinger equation as well as with a two-photon perturbative model. The effect of autoionizing states on the sideband phaseshift is thus analyzed. On the other hand, we apply the soft-photon approximation to quantify the effects the IR probe intensity on the sideband non-resonant overtone components.

  17. Micromachined electrostatic vertical actuator

    DOEpatents

    Lee, Abraham P.; Sommargren, Gary E.; McConaghy, Charles F.; Krulevitch, Peter A.

    1999-10-19

    A micromachined vertical actuator utilizing a levitational force, such as in electrostatic comb drives, provides vertical actuation that is relatively linear in actuation for control, and can be readily combined with parallel plate capacitive position sensing for position control. The micromachined electrostatic vertical actuator provides accurate movement in the sub-micron to micron ranges which is desirable in the phase modulation instrument, such as optical phase shifting. For example, compact, inexpensive, and position controllable micromirrors utilizing an electrostatic vertical actuator can replace the large, expensive, and difficult-to-maintain piezoelectric actuators. A thirty pound piezoelectric actuator with corner cube reflectors, as utilized in a phase shifting diffraction interferometer can be replaced with a micromirror and a lens. For any very precise and small amplitudes of motion` micromachined electrostatic actuation may be used because it is the most compact in size, with low power consumption and has more straightforward sensing and control options.

  18. More Electrostatic Explorations.

    ERIC Educational Resources Information Center

    Stewart, Gay; Gallai, Ditta

    1998-01-01

    Presents worksheet activities that enable students to explore the concept of electrostatic induction and learn the meaning of grounding. Students build two classic devices, the electrophorus and the leaf electroscope. (DDR)

  19. Graphene Electrostatic Microphone

    NASA Astrophysics Data System (ADS)

    Zhou, Qin; Onishi, Seita; Zettl, A.

    2015-03-01

    We demonstrate a wideband electrostatic graphene microphone displaying flat frequency response over the entire human audible region as well as into the ultrasonic regime. Using the microphone, low-level ultrasonic bat calls are successfully recorded. The microphone can be paired with a similarly constructed electrostatic graphene loudspeaker to create a wideband ultrasonic radio. Materials Sciences Division, Lawrence Berkeley National Laboratory Kavli Energy NanoSciences Institute at the University of California - Berkeley.

  20. Electrostatic discharge test apparatus

    NASA Technical Reports Server (NTRS)

    Smith, William Conrad (Inventor)

    1988-01-01

    Electrostatic discharge properties of materials are quantitatively measured and ranked. Samples are rotated on a turntable beneath selectable, co-available electrostatic chargers, one being a corona charging element and the other a sample-engaging triboelectric charging element. Samples then pass under a voltage meter to measure the amount of residual charge on the samples. After charging is discontinued, measurements are continued to record the charge decay history over time.

  1. Electrostatic Levitator in Use

    NASA Technical Reports Server (NTRS)

    1998-01-01

    Metal droplet levitated inside the Electrostatic Levitator (ESL). 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.

  2. Electrostatic Levitator Electrode Layout

    NASA Technical Reports Server (NTRS)

    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.

  3. Electrostatic Levitator Layout

    NASA Technical Reports Server (NTRS)

    1998-01-01

    General oayout of Electrostatic Levitator (ESL). 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.

  4. Examining the Psychosis Continuum

    PubMed Central

    DeRosse, Pamela; Karlsgodt, Katherine H.

    2015-01-01

    The notion that psychosis may exist on a continuum with normal experience has been proposed in multiple forms throughout the history of psychiatry. However, in recent years there has been an exponential increase in efforts aimed at elucidating what has been termed the ‘psychosis continuum’. The present review seeks to summarize some of the more basic characteristics of this continuum and to present some of the recent findings that provide support for its validity. While there is still considerable work to be done, the emerging data holds considerable promise for advancing our understanding of both risk and resilience to psychiatric disorders characterized by psychosis. PMID:26052479

  5. Electrostatics at the nanoscale.

    PubMed

    Walker, David A; Kowalczyk, Bartlomiej; de la Cruz, Monica Olvera; Grzybowski, Bartosz A

    2011-04-01

    Electrostatic forces are amongst the most versatile interactions to mediate the assembly of nanostructured materials. Depending on experimental conditions, these forces can be long- or short-ranged, can be either attractive or repulsive, and their directionality can be controlled by the shapes of the charged nano-objects. This Review is intended to serve as a primer for experimentalists curious about the fundamentals of nanoscale electrostatics and for theorists wishing to learn about recent experimental advances in the field. Accordingly, the first portion introduces the theoretical models of electrostatic double layers and derives electrostatic interaction potentials applicable to particles of different sizes and/or shapes and under different experimental conditions. This discussion is followed by the review of the key experimental systems in which electrostatic interactions are operative. Examples include electroactive and "switchable" nanoparticles, mixtures of charged nanoparticles, nanoparticle chains, sheets, coatings, crystals, and crystals-within-crystals. Applications of these and other structures in chemical sensing and amplification are also illustrated.

  6. Large electrostatic accelerators

    SciTech Connect

    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.

  7. The Continuum of Listening

    ERIC Educational Resources Information Center

    Rud, A. G.; Garrison, Jim

    2007-01-01

    The distinction between "apophatic" and "cataphatic" listening is defined and analyzed. "Apophatic" listening is more or less devoid of cognitivist claims, whereas "cataphatic" listening involves cognition and questioning. Many of the papers in this volume are discussed along the continuum determined by these two types of listening.…

  8. The Creativity Continuum

    ERIC Educational Resources Information Center

    Walling, Donovan R.

    2009-01-01

    Children are innately creative, and the youngest often are the most original because they have yet to be influenced by the creativity of others. One way to think of creative expression is as a continuum. At one end is originality, or the creation of something wholly new, "original." At the other end is replication, or the re-creation of something…

  9. DEPPDB - DNA electrostatic potential properties database. Electrostatic properties of genome DNA elements.

    PubMed

    Osypov, Alexander A; Krutinin, Gleb G; Krutinina, Eugenia A; Kamzolova, Svetlana G

    2012-04-01

    Electrostatic properties of genome DNA are important to its interactions with different proteins, in particular, related to transcription. DEPPDB - DNA Electrostatic Potential (and other Physical) Properties Database - provides information on the electrostatic and other physical properties of genome DNA combined with its sequence and annotation of biological and structural properties of genomes and their elements. Genomes are organized on taxonomical basis, supporting comparative and evolutionary studies. Currently, DEPPDB contains all completely sequenced bacterial, viral, mitochondrial, and plastids genomes according to the NCBI RefSeq, and some model eukaryotic genomes. Data for promoters, regulation sites, binding proteins, etc., are incorporated from established DBs and literature. The database is complemented by analytical tools. User sequences calculations are available. Case studies discovered electrostatics complementing DNA bending in E.coli plasmid BNT2 promoter functioning, possibly affecting host-environment metabolic switch. Transcription factors binding sites gravitate to high potential regions, confirming the electrostatics universal importance in protein-DNA interactions beyond the classical promoter-RNA polymerase recognition and regulation. Other genome elements, such as terminators, also show electrostatic peculiarities. Most intriguing are gene starts, exhibiting taxonomic correlations. The necessity of the genome electrostatic properties studies is discussed.

  10. First-principles electrostatic potentials for reliable alignment at interfaces and defects.

    PubMed

    Sundararaman, Ravishankar; Ping, Yuan

    2017-03-14

    The alignment of electrostatic potential between different atomic configurations is necessary for first-principles calculations of band offsets across interfaces and formation energies of charged defects. However, strong oscillations of this potential at the atomic scale make alignment challenging, especially when atomic geometries change considerably from bulk to the vicinity of defects and interfaces. We introduce a method to suppress these strong oscillations by eliminating the deep wells in the potential at each atom. We demonstrate that this method considerably improves the system-size convergence of a wide range of first-principles predictions that depend on the alignment of electrostatic potentials, including band offsets at solid-liquid interfaces, and formation energies of charged vacancies in solids and at solid surfaces in vacuum. Finally, we use this method in conjunction with continuum solvation theories to investigate energetics of charged vacancies at solid-liquid interfaces. We find that for the example of an NaCl (001) surface in water, solvation reduces the formation energy of charged vacancies by 0.5 eV: calculation of this important effect was previously impractical due to the computational cost in molecular-dynamics methods.

  11. Electrostatic solvation energy for two oppositely charged ions in a solvated protein system: salt bridges can stabilize proteins.

    PubMed

    Gong, Haipeng; Freed, Karl F

    2010-02-03

    Born-type electrostatic continuum methods have been an indispensable ingredient in a variety of implicit-solvent methods that reduce computational effort by orders of magnitude compared to explicit-solvent MD simulations and thus enable treatment using larger systems and/or longer times. An analysis of the limitations and failures of the Born approaches serves as a guide for fundamental improvements without diminishing the importance of prior works. One of the major limitations of the Born theory is the lack of a liquidlike description of the response of solvent dipoles to the electrostatic field of the solute and the changes therein, a feature contained in the continuum Langevin-Debye (LD) model applied here to investigate how Coulombic interactions depend on the location of charges relative to the protein/water boundary. This physically more realistic LD model is applied to study the stability of salt bridges. When compared head to head using the same (independently measurable) physical parameters (radii, dielectric constants, etc.), the LD model is in good agreement with observations, whereas the Born model is grossly in error. Our calculations also suggest that a salt bridge on the protein's surface can be stabilizing when the charge separation is < or =4 A.

  12. Electrostatic graphene loudspeaker

    NASA Astrophysics Data System (ADS)

    Zhou, Qin; Zettl, A.

    2013-06-01

    Graphene has extremely low mass density and high mechanical strength, and key qualities for efficient wide-frequency-response electrostatic audio speaker design. Low mass ensures good high frequency response, while high strength allows for relatively large free-standing diaphragms necessary for effective low frequency response. Here, we report on construction and testing of a miniaturized graphene-based electrostatic audio transducer. The speaker/earphone is straightforward in design and operation and has excellent frequency response across the entire audio frequency range (20 Hz-20 kHz), with performance matching or surpassing commercially available audio earphones.

  13. Electrostatic Levitator Vacuum Chamber

    NASA Technical Reports Server (NTRS)

    1998-01-01

    Optical ports ring the Electrostatic Levitator (ESL) vacuum chamber to admit light from the heating laser (beam passes through the window at left), positioning lasers (one port is at center), and lamps to allow diagnostic instruments to view the sample. 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.

  14. Electrostatic Levitator Inspected

    NASA Technical Reports Server (NTRS)

    1998-01-01

    Larry Savage, Dr. Jan Rogers, Dr. Michael Robinson (All NASA) and Doug Huie (Mevatec) inspect the Electrostatic Levitator (ESL) at NASA's Marshall Space Flight Center (MSFC). 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.

  15. Electrostatic Levitator (ESL) Undercooling

    NASA Technical Reports Server (NTRS)

    1998-01-01

    Graph depicting Electrostatic Levitator (ESL) heating and cooling cycle to achieve undercooling of liquid metals. The ESL uses static electricity to suspend an object (about 3-4 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 contracting the container or any instruments, conditions that would alter the readings. The electrostatic Levitator is one of several tools used in NASA's microgravity matierials sciences program.

  16. Electrostatic Levitator at Work

    NASA Technical Reports Server (NTRS)

    2000-01-01

    A 3 mm drop of nickel-zirconium, heated to incandescence, hovers between electrically charged plates inside the Electrostatic Levitator (ESL). 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.

  17. Electrostatic contribution to the thermodynamic and kinetic stability of the homotrimeric coiled coil Lpp-56: A computational study.

    PubMed

    Bjelić, Sasa; Wieninger, Silke; Jelesarov, Ilian; Karshikoff, Andrey

    2008-02-15

    The protein moiety of the Braun's E. coli outer membrane lipoprotein (Lpp-56) is an attractive object of biophysical investigation in several aspects. It is a homotrimeric, parallel coiled coil, a class of coiled coils whose stability and folding have been studied only occasionally. Lpp-56 possesses unique structural properties and exhibits extremely low rates of folding and unfolding. It is natural to ask how the specificity of the structure determines the extraordinary physical chemical properties of this protein. Recently, a seemingly controversial data on the stability and unfolding rate of Lpp-56 have been published (Dragan et al., Biochemistry 2004;43: 14891-14900; Bjelic et al., Biochemistry 2006;45:8931-8939). The unfolding rate constant measured using GdmCl as the denaturing agent, though extremely low, was substantially higher than that obtained on the basis of thermal unfolding. If this large difference arises from the effect of screening of electrostatic interactions induced by GdmCl, electrostatic interactions would appear to be an important factor determining the unusual properties of Lpp-56. We present here a computational analysis of the electrostatic properties of Lpp-56 combining molecular dynamics simulations and continuum pK calculations. The pH-dependence of the unfolding free energy is predicted in good agreement with the experimental data: the change in DeltaG between pH 3 and pH 7 is approximately 60 kJ mol(-1). The results suggest that the difference in the stability of the protein observed using different experimental methods is mainly because of the effect of the reduction of electrostatic interactions when the salt (GdmCl) concentration increases. We also find that the occupancy of the interhelical salt bridges is unusually high. We hypothesize that electrostatic interactions, and the interhelical salt bridges in particular, are an important factor determining the low unfolding rate of Lpp-56.

  18. Continuum modeling of charging process and piezoelectricity of ferroelectrets

    NASA Astrophysics Data System (ADS)

    Xu, Bai-Xiang; von Seggern, Heinz; Zhukov, Sergey; Gross, Dietmar

    2013-09-01

    Ferroelectrets in the form of electrically charged micro-porous foams exhibit a very large longitudinal piezoelectric coefficient d33. The structure has hence received wide application interests as sensors particularly in acoustic devices. During charging process, electrical breakdown (Paschen breakdown) takes place in the air pores of the foam and introduces free charge pairs. These charges are separated by electrostatic forces and relocated at the interfaces between the polymer and the electrically broken-down medium, where they are trapped quasistatically. The development of this trapped charge density along the interfaces is key for enabling the piezoelectricity of ferroelectrets. In this article, an internal variable based continuum model is proposed to calculate the charge density development at the interfaces, whereas a Maxwell stress based electromechanical model is used for the bulk behavior, i.e., of the polymer and of the medium where the Paschen breakdown takes place. In the modeling, the electrostatic forces between the separated charge pairs are included, as well as the influence of deformation of the solid layers. The material models are implemented in a nonlinear finite element scheme, which allows a detailed analysis of different geometries. A ferroelectret unit with porous expanded polytetrafluoroethylene (ePTFE) surrounded by fluorinated ethylene propylene is studied first. The simulated hysteresis curves of charge density at the surfaces and the calculated longitudinal piezoelectric constant are in good agreement with experimental results. Simulations show a strong dependency of the interface charge development and thus the remnant charges on the thicknesses of the layers and the permittivity of the materials. According to the calculated relation between d33 and the Young's modulus of ePTFE, the value of the Young's modulus of ePTFE is identified to be around 0.75 MPa, which lies well in the predicted range of 0.45 to 0.80 MPa, determined from

  19. Self-consistent treatment of the local dielectric permittivity and electrostatic potential in solution for polarizable macromolecular force fields

    PubMed Central

    Hassan, Sergio A.

    2012-01-01

    A self-consistent method is presented for the calculation of the local dielectric permittivity and electrostatic potential generated by a solute of arbitrary shape and charge distribution in a polar and polarizable liquid. The structure and dynamics behavior of the liquid at the solute/liquid interface determine the spatial variations of the density and the dielectric response. Emphasis here is on the treatment of the interface. The method is an extension of conventional methods used in continuum protein electrostatics, and can be used to estimate changes in the static dielectric response of the liquid as it adapts to charge redistribution within the solute. This is most relevant in the context of polarizable force fields, during electron structure optimization in quantum chemical calculations, or upon charge transfer. The method is computationally efficient and well suited for code parallelization, and can be used for on-the-fly calculations of the local permittivity in dynamics simulations of systems with large and heterogeneous charge distributions, such as proteins, nucleic acids, and polyelectrolytes. Numerical calculation of the system free energy is discussed for the general case of a liquid with field-dependent dielectric response. PMID:22920098

  20. Nanoscale Electrostatics in Mitosis

    NASA Astrophysics Data System (ADS)

    Gagliardi, L. John; West, Patrick Michael

    2001-04-01

    Primitive biological cells had to divide with very little biology. This work simulates a physicochemical mechanism, based upon nanoscale electrostatics, which explains the anaphase A poleward motion of chromosomes. In the cytoplasmic medium that exists in biological cells, electrostatic fields are subject to strong attenuation by Debye screening, and therefore decrease rapidly over a distance equal to several Debye lengths. However, the existence of microtubules within cells changes the situation completely. Microtubule dimer subunits are electric dipolar structures, and can act as intermediaries that extend the reach of the electrostatic interaction over cellular distances. Experimental studies have shown that intracellular pH rises to a peak at mitosis, and decreases through cytokinesis. This result, in conjunction with the electric dipole nature of microtubule subunits and the Debye screened electrostatic force is sufficient to explain and unify the basic events during mitosis and cytokinesis: (1) assembly of asters, (2) motion of the asters to poles, (3) poleward motion of chromosomes (anaphase A), (4) cell elongation, and (5) cytokinesis. This paper will focus on a simulation of the dynamics if anaphase A motion based on this comprehensive model. The physicochemical mechanisms utilized by primitive cells could provide important clues regarding our understanding of cell division in modern eukaryotic cells.

  1. Magnetosheath electrostatic turbulence

    NASA Technical Reports Server (NTRS)

    Rodriquez, P.

    1977-01-01

    The spectrum of electrostatic plasma waves in the terrestrial magnetosheath was studied using the plasma wave experiment on the IMP-6 satellite. Electrostatic plasma wave turbulence is almost continuously present throughout the magnetosheath with broadband (20 Hz- 70 kHz) r.m.s. field intensities typically 0.01 - 1.0 millivolts/m. Peak intensities of about 1.0 millivolts/m near the electron plasma frequency (30 - 60 kHz) were detected occasionally. The components usually identified in the spectrum of magnetosheath electrostatic turbulence include a high frequency ( or = 30 kHz) component peaking at the electron plasma frequency f sub pe, a low frequency component with a broad intensity maximum below the nominal ion plasma frequency f sub pi (approximately f sub pe/43), and a less well defined intermediate component in the range f sub pi f f sub pe. 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.

  2. Electrostatics of Rigid Polyelectrolytes

    SciTech Connect

    Wong, G.C.L.

    2009-06-04

    The organization of rigid biological polyelectrolytes by multivalent ions and macroions are important for many fundamental problems in biology and biomedicine, such as cytoskeletal regulation and antimicrobial sequestration in cystic fibrosis. These polyelectrolytes have been used as model systems for understanding electrostatics in complex fluids. Here, we review some recent results in theory, simulations, and experiments.

  3. Using electrostatic modelling to study cone discharges

    NASA Astrophysics Data System (ADS)

    Azizi, W.

    2015-10-01

    Cone discharges, also known as bulking brush discharges, can arise when charged insulating powder accumulates in a heap in silos. They can be an effective ignition source to relatively ignition sensitive powders and therefore represent a possible electrostatic hazard. The current international guidance on control of electrostatic hazards (IEC/TS 60079-32-1 [1]), endorses the usage of electrostatic modelling to estimate the electric field above the powder heap. “Such model calculations should be based on the charge to mass ratio, bulk density and filling rate of the powder, the relative permittivity and resistivity of the bulked powder as well as the silo geometry.” This study shows a practical demonstration of this modelling technique. It also examines whether the shape of the heap affects the strength of the electric field above the powder heap, and thus the likelihood of cone discharges from occurring.

  4. Isostaticity in Cosserat Continuum

    DTIC Science & Technology

    2012-01-01

    Research Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 15. SUBJECT TERMS Isostaticity, Cosserat, Granular, Force chains Antoinette ...TELEPHONE NUMBER Antoinette Tordesillas 038-344-9685 3. DATES COVERED (From - To) Standard Form 298 (Rev 8/98) Prescribed by ANSI Std. Z39.18...Cosserat continuum Antoinette Tordesillas · Jingyu Shi · John F. Peters Received: 29 August 2011 / Published online: 16 March 2012 © Springer-Verlag 2012

  5. Optimizing electrostatic affinity in ligand-receptor binding: Theory, computation, and ligand properties

    NASA Astrophysics Data System (ADS)

    Kangas, Erik; Tidor, Bruce

    1998-11-01

    The design of a tight-binding molecular ligand involves a tradeoff between an unfavorable electrostatic desolvation penalty incurred when the ligand binds a receptor in aqueous solution and the generally favorable intermolecular interactions made in the bound state. Using continuum electrostatic models we have developed a theoretical framework for analyzing this problem and have shown that the ligand-charge distribution can be optimized to produce the most favorable balance of these opposing free energy contributions [L.-P. Lee and B. Tidor, J. Chem. Phys. 106, 8681 (1997)]. Herein the theoretical framework is extended and calculations are performed for a wide range of model receptors. We examine methods for computing optimal ligands (including cases where there is conformational change) and the resulting properties of optimized ligands. In particular, indicators are developed to aid in the determination of the deficiencies in a specific ligand or basis. A connection is established between the optimization problem here and a generalized image problem, from which an inverse-image basis set can be defined; this basis is shown to perform very well in optimization calculations. Furthermore, the optimized ligands are shown to have favorable electrostatic binding free energies (in contrast to many natural ligands), there is a strong correlation between the receptor desolvation penalty and the optimized binding free energy for fixed geometry, and the ligand and receptor cannot generally be mutually optimal. Additionally, we introduce the display of complementary desolvation and interaction potentials and the deviation of their relationship from ideal as a useful tool for judging effective complementarity. Scripts for computing and displaying these potentials with GRASP are available at http://mit.edu/tidor.

  6. Electrostatic properties of graphitic nanostructures

    NASA Astrophysics Data System (ADS)

    Erbahar, Dogan

    2014-03-01

    Carbon nanostructures are considered to be one of the most important candidates of circuit elements for future nanoelectronics. However, being one of the main issues of conventional circuitry used today, charge accumulation on circuit elements can also be expected to have important effects on the performance of the nanoscale devices. In this work we investigated charge accumulation on various graphitic systems by simulated charge doping. We report ab initio density functional theory (DFT) calculations of electrostatically charged multilayered carbon nano structures. We investigate the effect of total and background charge on charge distribution profiles on the systems under consideration varying from multilayered graphene to multiwalled carbon nanotubes. We show that the charge distribution profile on the inner layers are mainly induced from the background charge which is imposed by the code on periodic systems. Our population anaylsis indicates that the outermost two layers effectively shields the inner layers electrostatically. Illuminating the typical skin depth of those systems our results could give important insights for designing the nanocircuit elements.

  7. Electron-ion continuum-continuum mixing in dissociative recombination

    NASA Technical Reports Server (NTRS)

    Guberman, Steven L.

    1993-01-01

    In recent calculations on the dissociative recombination (DR) of the v=1 vibrational level of the ground state of N2(+), N2(+)(v=1) + e(-) yields N + N, we have observed an important continuun-continuum mixing process involving the open channels on both sides of N2(+)(v=1) + e(-) yields N2(+)(v=0) + e(-). In vibrational relaxation by electron impact (immediately above) the magnitude of the cross section depends upon the strength of the interaction between these continua. In DR of the v=1 ion level, these continua can also interact in the entrance channel, and the mixing can have a profound effect upon the DR cross section from v=1, as we illustrate in this paper. In our theoretical calculations of N2(+) DR using multichannel quantum defect theory (MQDT), the reactants and products in the two above equations are described simultaneously. This allows us to calculate vibrational relaxation and excitation cross sections as well as DR cross sections. In order to understand the mixing described above, we first present a brief review of the prior results for DR of the v=0 level of N2(+).

  8. Continuum Nuclear Structure via

    NASA Astrophysics Data System (ADS)

    Templon, Jeffrey A.

    1993-01-01

    Nuclear spectra are generally well-understood for excitation energies below the particle-emission threshold. Above this threshold, excited states decay preferentially by emission of nucleons or nucleon clusters. These resonant excitations are short-lived, producing continuum spectra of overlapping states accompanied by non-resonant, probe -dependent background processes. The resonant excitations' properties are difficult to deduce from these spectra. Many important advances in nuclear physics require understanding of such excitations. (e,e^' X) coincidence experiments have established the utility of angular correlation measurements of particle (X) emitted by decaying resonances for continuum studies. However, electron-induced reactions excite only a subset of the total nuclear response. Hadronic probes are necessary for a complete study. This dissertation describes a (p,p^' X) coincidence experiment, the first at intermediate energies where microscopic theories apply. The reaction's utility was investigated and applied to ^{12 }C. The experiment was performed using a 156 MeV polarized proton beam. A magnetic spectrometer was used to detect scattered protons. An array of eight silicon-detector telescopes was constructed and used to measure the angular correlation of charged particles (X). Inclusive (p,p ^') and exclusive (p,p ^' X) data were acquired simultaneously. The momentum transfer range (0.6<= q<= 1.2 fm^{-1}) was covered in three spectrometer angle settings. The excitation energy range spanned the region from sharp states to quasifree processes. Analyzing powers and cross sections were measured for both inclusive and exclusive data. A simple reaction model was developed which suggested a Legendre-polynomial series should describe the sigma(theta_{X}) data. The model relates the polynomial coefficients to nuclear structure information. A result of this work is that this series was found to satisfactorily describe the data and provided new information about

  9. Biobriefcase electrostatic aerosol collector

    DOEpatents

    Bell, Perry M.; Christian, Allen T.; Bailey, Christopher G.; Willis, Ladona; Masquelier, Donald A.; Nasarabadi, Shanavaz L.

    2009-03-17

    A system for sampling air and collecting particles entrained in the air comprising a receiving surface, a liquid input that directs liquid to the receiving surface and produces a liquid surface, an air input that directs the air so that the air with particles entrained in the air impact the liquid surface, and an electrostatic contact connected to the liquid that imparts an electric charge to the liquid. The particles potentially including bioagents become captured in the liquid by the air with particles entrained in the air impacting the liquid surface. Collection efficiency is improved by the electrostatic contact electrically charging the liquid. The effects of impaction and adhesion due to electrically charging the liquid allows a unique combination in a particle capture medium that has a low fluid consumption rate while maintaining high efficiency.

  10. Automated Electrostatics Environmental Chamber

    NASA Technical Reports Server (NTRS)

    Calle, Carlos; Lewis, Dean C.; Buchanan, Randy K.; Buchanan, Aubri

    2005-01-01

    The Mars Electrostatics Chamber (MEC) is an environmental chamber designed primarily to create atmospheric conditions like those at the surface of Mars to support experiments on electrostatic effects in the Martian environment. The chamber is equipped with a vacuum system, a cryogenic cooling system, an atmospheric-gas replenishing and analysis system, and a computerized control system that can be programmed by the user and that provides both automation and options for manual control. The control system can be set to maintain steady Mars-like conditions or to impose temperature and pressure variations of a Mars diurnal cycle at any given season and latitude. In addition, the MEC can be used in other areas of research because it can create steady or varying atmospheric conditions anywhere within the wide temperature, pressure, and composition ranges between the extremes of Mars-like and Earth-like conditions.

  11. Electrostatically clean solar array

    NASA Technical Reports Server (NTRS)

    Stern, Theodore Garry (Inventor); Krumweide, Duane Eric (Inventor)

    2004-01-01

    Provided are methods of manufacturing an electrostatically clean solar array panel and the products resulting from the practice of these methods. The preferred method uses an array of solar cells, each with a coverglass where the method includes machining apertures into a flat, electrically conductive sheet so that each aperture is aligned with and undersized with respect to its matched coverglass sheet and thereby fashion a front side shield with apertures (FSA). The undersized portion about each aperture of the bottom side of the FSA shield is bonded to the topside portions nearest the edges of each aperture's matched coverglass. Edge clips are attached to the front side aperture shield edges with the edge clips electrically and mechanically connecting the tops of the coverglasses to the solar panel substrate. The FSA shield, edge clips and substrate edges are bonded so as to produce a conductively grounded electrostatically clean solar array panel.

  12. Electrostatic analysis of nanoelectromechanical systems

    NASA Astrophysics Data System (ADS)

    Xu, Yang

    We present a multiscale method, seamlessly combining semiclassical, effective-mass Schrodinger (EMS), and tight-binding (TB) theories proposed for electrostatic analysis of silicon nanoelectromechanical systems (NEMS). By using appropriate criteria, we identify the physical models that are accurate in each local region. If the local physical model is semiclassical, the charge density is directly computed by the semiclassical theory. If the local physical model is quantum-mechanical (EMS or TB model), the charge density is calculated by using the theory of local density of states (LDOS). The LDOS is efficiently calculated from Green's function by using Haydock's recursion method where the Green's function is expressed as a continued fraction based on the local Hamiltonian. Once the charge density is determined, a Poisson equation is solved self-consistently to determine the electronic properties. The accuracy and efficiency of the multiscale method are demonstrated by considering several NEMS examples. The multiscale method can be used to compute the effect of surface and interior defects such as vacancies and broken bonds on the performance of microelectromechanical systems (MEMS). By combining multiscale electrostatic analysis with mechanical analysis, we compute the capacitance-voltage and pull-in/pull-out voltages of MEMS switches in the presence of defects in the dielectric oxide layer. Our results indicate that both surface and interior defects can change the pull-in/pull-out voltages significantly. These voltage offsets can lead to an eventual failure of the MEMS switches. The self-consistent TB method is used to investigate carbon nanotube (CNT)-based sensors. We compute the screening effects of semiconducting and metallic single-wall carbon nanotubes (SWNTs) when water molecules and various ions pass through the nanotubes. The trajectories of ions and water molecules are obtained from molecular dynamics (MD) simulations. It is shown that metallic SWNTs have

  13. Electrostatic Levitator Operations

    NASA Technical Reports Server (NTRS)

    1998-01-01

    Dr. Jan Rogers (left) and Larry Savage (foreground) of the Science Directorate at NASA's Marshall Space Flight Center are joined by Dr. Richard Weber (Center) and April Hixon of Containerless Research Inc. of Evanston, Ill., in conducting an experiment run of the Electrostatic Levitator (ESL) using insulating materials. Materials researchers use unique capability of the facility to levitate and study the properties of various materials important in manufacturing processes.

  14. Micromachined silicon electrostatic chuck

    SciTech Connect

    Anderson, R.A.; Seager, C.H.

    1994-12-31

    In the field of microelectronics, and in particular the fabrication of microelectronics during plasma etching processes, electrostatic chucks have been used to hold silicon wafers during the plasma etching process. Current electrostatic chucks that operate by the {open_quotes}Johnson-Rahbek Effect{close_quotes} consist of a metallic base plate that is typically coated with a thick layer of slightly conductive dielectric material. A silicon wafer of approximately the same size as the chuck is placed on top of the chuck and a potential difference of several hundred volts is applied between the silicon and the base plate of the electrostatic chuck. This causes an electrostatic attraction proportional to the square of the electric field in the gap between the silicon wafer and the chuck face. When the chuck is used in a plasma filled chamber the electric potential of the wafer tends to be fixed by the effective potential of the plasma. The purpose of the dielectric layer on the chuck is to prevent the silicon wafer from coming into direct electrical contact with the metallic part of the chuck and shorting out the potential difference. On the other hand, a small amount of conductivity appears to be desirable in the dielectric coating so that much of its free surface between points of contact with the silicon wafer is maintained near the potential of the metallic base plate; otherwise, a much larger potential difference would be needed to produce a sufficiently large electric field in the vacuum gap between the wafer and chuck. Typically, the face of the chuck has a pattern of grooves in which about 10 torr pressure of helium gas is maintained. This gas provides cooling (thermal contact) between the wafer and the chuck. A pressure of 10 torr is equivalent to about 0.2 psi.

  15. Continuum Edge Gyrokinetic Theory and Simulations

    SciTech Connect

    Xu, X Q; Xiong, Z; Dorr, M R; Hittinger, J A; Bodi, K; Candy, J; Cohen, B I; Cohen, R H; Colella, P; Kerbel, G D; Krasheninnikov, S; Nevins, W M; Qin, H; Rognlien, T D; Snyder, P B; Umansky, M V

    2007-01-09

    The following results are presented from the development and application of TEMPEST, a fully nonlinear (full-f) five dimensional (3d2v) gyrokinetic continuum edge-plasma code. (1) As a test of the interaction of collisions and parallel streaming, TEMPEST is compared with published analytic and numerical results for endloss of particles confined by combined electrostatic and magnetic wells. Good agreement is found over a wide range of collisionality, confining potential, and mirror ratio; and the required velocity space resolution is modest. (2) In a large-aspect-ratio circular geometry, excellent agreement is found for a neoclassical equilibrium with parallel ion flow in the banana regime with zero temperature gradient and radial electric field. (3) The four-dimensional (2d2v) version of the code produces the first self-consistent simulation results of collisionless damping of geodesic acoustic modes and zonal flow (Rosenbluth-Hinton residual) with Boltzmann electrons using a full-f code. The electric field is also found to agree with the standard neoclassical expression for steep density and ion temperature gradients in the banana regime. In divertor geometry, it is found that the endloss of particles and energy induces parallel flow stronger than the core neoclassical predictions in the SOL. (5) Our 5D gyrokinetic formulation yields a set of nonlinear electrostatic gyrokinetic equations that are for both neoclassical and turbulence simulations.

  16. Electrostatics of Granular Materials

    NASA Technical Reports Server (NTRS)

    Marshall, John

    2004-01-01

    The purpose of the research was to continue developing an understanding of electrostatic phenomena in preparation for any future flight opportunities of the EGM experiment, originally slated for a 2004 Space Station deployment. Work would be based on theoretical assessments, ground-based lab experiments, and reduced-gravity experiments. The ability to examine dipoles in the lab proved to be elusive, and thus, effort was concentrated on monopoles -how materials become charged, the fate of the charge, the role of material type, and so forth. Several significant milestones were achieved in this regard. In regard of the dipoles, experiments were designed in collaboration with the University of Chicago school district who had access to reduced gravity on the KC-135 aircraft. Two experiments were slated to fly last year but were cancelled after the Columbia accident. One of the experiments has been given a second life and will fly sometime in 2005 if the Shuttle flights resume. There remains active interest in the question of electrostatic dipoles within the educational community, and experiments using magnetic dipoles as a substitute are to be examined. The KC-135 experiments will also examine dispersion methods for particles as a verification of possible future techniques in microgravity. Both laboratory and theoretical work established a number of breakthroughs in our understanding of electrostatic phenomena. These breakthroughs are listed in this paper.

  17. Electrostatic Plasma Accelerator (EPA)

    NASA Technical Reports Server (NTRS)

    Brophy, John R.; Aston, Graeme

    1989-01-01

    The Electrostatic Plasma Accelerator (EPA) is a thruster concept which promises specific impulse levels between low power arcjets and those of the ion engine while retaining the relative simplicity of the arcjet. The EPA thruster produces thrust through the electrostatic acceleration of a moderately dense plasma. No accelerating electrodes are used and the specific impulse is a direct function of the applied discharge voltage and the propellant atomic mass. The goal of the present program is to demonstrate feasibility of the EPA thruster concept through experimental and theoretical investigations of the EPA acceleration mechanism and discharge chamber performance. Experimental investigations will include operating the test bed ion (TBI) engine as an EPA thruster and parametrically varying the thruster geometry and operating conditions to quantify the electrostatic plasma acceleration effect. The theoretical investigations will include the development of a discharge chamber model which describes the relationships between the engine size, plasma properties, and overall performance. For the EPA thruster to be a viable propulsion concept, overall thruster efficiencies approaching 30% with specific impulses approaching 1000 s must be achieved.

  18. Electrostatic space radiation shielding

    NASA Astrophysics Data System (ADS)

    Tripathi, Ram K.; Wilson, John W.; Youngquist, Robert C.

    2008-09-01

    For the success of NASA’s new vision for space exploration to Moon, Mars and beyond, exposures from the hazards of severe space radiation in deep space long duration missions is ‘a must solve’ problem. The payload penalty demands a very stringent requirement on the design of the spacecrafts for human deep space missions. The exploration beyond low Earth orbit (LEO) to enable routine access of space will require protection from the hazards of the accumulated exposures of space radiation, Galactic Cosmic Rays (GCR) and Solar Particle Events (SPE), and minimizing the production of secondary radiation is a great advantage. There is a need to look to new horizons for newer technologies. The present investigation revisits electrostatic active radiation shielding and explores the feasibility of using the electrostatic shielding in concert with the state-of-the-art materials shielding and protection technologies. The full space radiation environment has been used, for the first time, to explore the feasibility of electrostatic shielding. The goal is to repel enough positive charge ions so that they miss the spacecraft without attracting thermal electrons. Conclusions are drawn for the future directions of space radiation protection.

  19. The Response Continuum

    SciTech Connect

    Caltagirone, Sergio; Frincke, Deborah A.

    2005-06-17

    Active response is a sequence of actions per- formed speci¯cally to mitigate a detected threat. Response decisions always follow detection: a decision to take `no ac- tion' remains a response decision. However, active response is a complex subject that has received insu±cient formal attention. To facilitate discussion, this paper provides a framework that proposes a common de¯nition, describes the role of response and the major issues surrounding response choices, and ¯nally, provides a model for the process of re- sponse. This provides a common starting point for discus- sion of the full response continuum as an integral part of contemporary computer security.

  20. Innovative Electrostatic Adhesion Technologies

    NASA Technical Reports Server (NTRS)

    Bryan, Tom; Macleod, Todd; Gagliano, Larry; Williams, Scott; McCoy, Brian

    2015-01-01

    Developing specialized Electro-Static grippers (commercially used in Semiconductor Manufacturing and in package handling) will allow gentle and secure Capture, Soft Docking, and Handling of a wide variety of materials and shapes (such as upper-stages, satellites, arrays, and possibly asteroids) without requiring physical features or cavities for a pincher or probe or using harpoons or nets. Combined with new rigid boom mechanisms or small agile chaser vehicles, flexible, high speed Electro-Static Grippers can enable compliant capture of spinning objects starting from a safe stand-off distance. Electroadhesion (EA) can enable lightweight, ultra-low-power, compliant attachment in space by using an electrostatic force to adhere similar and dissimilar surfaces. A typical EA enabled device is composed of compliant space-rated materials, such as copper-clad polyimide encapsulated by polymers. Attachment is induced by strong electrostatic forces between any substrate material, such as an exterior satellite panel and a compliant EA gripper pad surface. When alternate positive and negative charges are induced in adjacent planar electrodes in an EA surface, the electric fields set up opposite charges on the substrate and cause an electrostatic adhesion between the electrodes and the induced charges on the substrate. Since the electrodes and the polymer are compliant and can conform to uneven or rough surfaces, the electrodes can remain intimately close to the entire surface, enabling high clamping pressures. Clamping pressures of more than 3 N/cm2 in shear can be achieved on a variety of substrates with ultra-low holding power consumption (measured values are less than 20 microW/Newton weight held). A single EA surface geometry can be used to clamp both dielectric and conductive substrates, with slightly different physical mechanisms. Furthermore EA clamping requires no normal force be placed on the substrate, as conventional docking requires. Internally funded research and

  1. Innovative Electrostatic Adhesion Technologies

    NASA Astrophysics Data System (ADS)

    Gagliano, L.; Bryan, T.; Williams, S.; McCoy, B.; MacLeod, T.

    Developing specialized Electro-Static grippers (commercially used in Semiconductor Manufacturing and in package handling) will allow gentle and secure Capture, Soft Docking, and Handling of a wide variety of materials and shapes (such as upper-stages, satellites, arrays, and possibly asteroids) without requiring physical features or cavities for a pincher or probe or using harpoons or nets. Combined with new rigid boom mechanisms or small agile chaser vehicles, flexible, high speed Electro-Static Grippers can enable compliant capture of spinning objects starting from a safe stand-off distance. Electroadhesion (EA) can enable lightweight, ultra-low-power, compliant attachment in space by using an electrostatic force to adhere similar and dissimilar surfaces. A typical EA enabled device is composed of compliant space-rated materials, such as copper-clad polyimide encapsulated by polymers. Attachment is induced by strong electrostatic forces between any substrate material, such as an exterior satellite panel and a compliant EA surface. When alternate positive and negative charges are induced in adjacent planar electrodes in an EA surface, the electric fields set up opposite charges on the substrate and cause an electrostatic adhesion between the electrodes and the induced charges on the substrate. Since the electrodes and the polymer are compliant and can conform to uneven or rough surfaces, the electrodes can remain intimately close to the entire surface, enabling high clamping pressures. Clamping pressures of more than 3 N/cm2 in shear can be achieved on a variety of substrates with ultra-low holding power consumption (measured values are less than 20 microW/Newton weight held). A single EA surface geometry can be used to clamp both dielectric and conductive substrates, with slightly different physical mechanisms. Furthermore EA clamping requires no normal force be placed on the substrate, as conventional docking requires. Internally funded research and development

  2. Kilometric Continuum Radiation

    NASA Technical Reports Server (NTRS)

    Green, James L.; Boardsen, Scott

    2006-01-01

    Kilometric continuum (KC) is the high frequency component (approximately 100 kHz to approximately 800 kHz) of nonthermal continuum (NTC). Unlike the lower frequency portion of NTC (approximately 5 kHz to approximately 100 kHz) whose source is around the dawn sector, the source of KC occurs at all magnetic local times. The latitudinal beaming of KC as observed by GEOTAIL is, for most events, restricted to plus or minus 15 degrees magnetic latitude. KC has been observed during periods of both low and strong geomagnetic activity, with no significant correlation of wave intensity with K(sub p), index. However statistically the maximum observed frequency of KC emission tends to increase with K(sub p) index, the effect is more pronounced around solar maximum, but is also detected near solar minimum. There is strong evidence that the source region of KC is from the equatorial plasmapause during periods when a portion of the plasmapause moves significantly inwards from its nominal position. Case studies have shown that KC emissions are nearly always associated with plasmaspheric notches, shoulders, and tails. There is a recent focus on trying to understand the banded frequency structure of this emission and its relationship to plasmaspheric density ducts and irregularities in the source region.

  3. Electrostatic evaluation of isosteric analogues

    NASA Astrophysics Data System (ADS)

    Sayle, Roger; Nicholls, Anthony

    2006-04-01

    A method is presented for enumerating a large number of isosteric analogues of a ligand from a known protein-ligand complex structure and then rapidly calculating an estimate of their binding energies. This approach takes full advantage of the observed crystal structure, by reusing the atomic co-ordinates determined experimentally for one ligand, to approximate those of similar compounds that have approximately the same shape. By assuming that compounds with similar shapes adopt similar binding poses, and that entropic and protein flexibility effects are approximately constant across such an isosteric series ("the frozen ligand approximation"), it is possible to order their binding affinities relatively accurately. Additionally, the constraint that the atomic coordinates are invariant allows for a dramatic simplification in the Poisson-Boltzmann method used to calculation the electrostatic component of the binding energy. This algorithmic improvement allows for the calculation of tens of thousands of binding energies per second for drug-like molecules, enabling this technique to be used in screening large virtual libraries of isosteric analogues. Most significantly, this procedure is shown to be able to reproduce SAR effects of subtle medicinal chemistry substitutions. Finally, this paper reports the results of the proposed methodology on␣seven model systems; dihydrofolate reductase, Lck␣kinase, ribosome inactivating protein, l-arabinose binding protein, neuraminidase, HIV-1 reverse transcriptase and COX-2.

  4. Elasticity and Electrostatics of Plectonemic DNA

    PubMed Central

    Clauvelin, N.; Audoly, B.; Neukirch, S.

    2009-01-01

    We present a self-contained theory for the mechanical response of DNA in single molecule experiments. Our model is based on a one-dimensional continuum description of the DNA molecule and accounts both for its elasticity and for DNA-DNA electrostatic interactions. We consider the classical loading geometry used in experiments where one end of the molecule is attached to a substrate and the other one is pulled by a tensile force and twisted by a given number of turns. We focus on configurations relevant to the limit of a large number of turns, which are made up of two phases, one with linear DNA and the other one with superhelical DNA. The model takes into account thermal fluctuations in the linear phase and electrostatic interactions in the superhelical phase. The values of the torsional stress, of the supercoiling radius and angle, and key features of the experimental extension-rotation curves, namely the slope of the linear region and thermal buckling threshold, are predicted. They are found in good agreement with experimental data. PMID:19413977

  5. Dimer packings with gaps and electrostatics

    PubMed Central

    Ciucu, Mihai

    2008-01-01

    Fisher and Stephenson conjectured in 1963 that the correlation function (defined by dimer packings) of two unit holes on the square lattice is rotationally invariant in the limit of large separation between the holes. We consider the same problem on the hexagonal lattice, extend it to an arbitrary finite collection of holes, and present an explicit conjectural answer. In recent work we managed to prove this conjecture in two fairly general cases. The quantity giving the answer can be regarded as the exponential of the negative of the two-dimensional electrostatic energy of a system of charges naturally associated with the holes. We further develop this analogy to electrostatics by presenting two different natural ways to define a field in our setup, and showing that both lead to the electric field, in the limit of large separations between the holes. For one of the fields, this is also stated as a limit shape theorem for random surfaces, with the continuum limit being a sum of helicoids. We conclude by explaining the relationship of our results to previous results in the physics literature on spin correlations in the Ising model.

  6. Spacecraft Electrostatic Radiation Shielding

    NASA Technical Reports Server (NTRS)

    2008-01-01

    This project analyzed the feasibility of placing an electrostatic field around a spacecraft to provide a shield against radiation. The concept was originally proposed in the 1960s and tested on a spacecraft by the Soviet Union in the 1970s. Such tests and analyses showed that this concept is not only feasible but operational. The problem though is that most of this work was aimed at protection from 10- to 100-MeV radiation. We now appreciate that the real problem is 1- to 2-GeV radiation. So, the question is one of scaling, in both energy and size. Can electrostatic shielding be made to work at these high energy levels and can it protect an entire vehicle? After significant analysis and consideration, an electrostatic shield configuration was proposed. The selected architecture was a torus, charged to a high negative voltage, surrounding the vehicle, and a set of positively charged spheres. Van de Graaff generators were proposed as the mechanism to move charge from the vehicle to the torus to generate the fields necessary to protect the spacecraft. This design minimized complexity, residual charge, and structural forces and resolved several concerns raised during the internal critical review. But, it still is not clear if such a system is costeffective or feasible, even though several studies have indicated usefulness for radiation protection at energies lower than that of the galactic cosmic rays. Constructing such a system will require power supplies that can generate voltages 10 times that of the state of the art. Of more concern is the difficulty of maintaining the proper net charge on the entire structure and ensuring that its interaction with solar wind will not cause rapid discharge. Yet, if these concerns can be resolved, such a scheme may provide significant radiation shielding to future vehicles, without the excessive weight or complexity of other active shielding techniques.

  7. Bridging implicit and explicit solvent approaches for membrane electrostatics.

    PubMed Central

    Lin, Jung-Hsin; Baker, Nathan A; McCammon, J Andrew

    2002-01-01

    Conformations of a zwitterionic bilayer were sampled from a molecular dynamics simulation and their electrostatic properties analyzed by solution of the Poisson equation. These traditionally implicit electrostatic calculations were performed in the presence of varying amounts of explicit solvent to assess the magnitude of error introduced by a uniform dielectric description of water surrounding the bilayer. It was observed that membrane dipole potential calculations in the presence of explicit water were significantly different than wholly implicit solvent calculations with the calculated dipole potential converging to a reasonable value when four or more hydration layers were included explicitly. PMID:12202363

  8. Micromachined, Electrostatically Deformable Reflectors

    NASA Technical Reports Server (NTRS)

    Bartman, Randall K.; Wang, Paul K. C.; Miller, Linda M.; Kenny, Thomas W.; Kaiser, William J.; Hadaegh, Fred Y.; Agronin, Michael L.

    1995-01-01

    Micromachined, closed-loop, electrostatically actuated reflectors (microCLEARs) provide relatively simple and inexpensive alternatives to large, complex, expensive adaptive optics used to control wavefronts of beams of light in astronomy and in experimental laser weapons. Micromachining used to make deformable mirror, supporting structure, and actuation circuitry. Development of microCLEARs may not only overcome some of disadvantages and limitations of older adaptive optics but may also satisfy demands of potential market for small, inexpensive deformable mirrors in electronically controlled film cameras, video cameras, and other commercial optoelectronic instruments.

  9. Electrostatically Driven Nanoballoon Actuator.

    PubMed

    Barzegar, Hamid Reza; Yan, Aiming; Coh, Sinisa; Gracia-Espino, Eduardo; Dunn, Gabriel; Wågberg, Thomas; Louie, Steven G; Cohen, Marvin L; Zettl, Alex

    2016-11-09

    We demonstrate an inflatable nanoballoon actuator based on geometrical transitions between the inflated (cylindrical) and collapsed (flattened) forms of a carbon nanotube. In situ transmission electron microscopy experiments employing a nanoelectromechanical manipulator show that a collapsed carbon nanotube can be reinflated by electrically charging the nanotube, thus realizing an electrostatically driven nanoballoon actuator. We find that the tube actuator can be reliably cycled with only modest control voltages (few volts) with no apparent wear or fatigue. A complementary theoretical analysis identifies critical parameters for nanotube nanoballoon actuation.

  10. PREFACE: Electrostatics 2015

    NASA Astrophysics Data System (ADS)

    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

  11. Energetics and structure in solvent: A dielectric continuum model of solvation combined with molecular mechanics, Ab Initio, and Semi-empirical molecular orbital treatments of the solute

    SciTech Connect

    Tawa, G.J.; Pratt, L.R.; Martin, R.L.

    1996-12-31

    We present a method for computing the electrostatic component of the solvation free energy, {Delta}G{sup el}, of a solute molecule in the presence of solvent modeled as a dielectric continuum. The method is based on an integral form of Poisson`s equation which is solved to obtain a distribution of induced polarization charge at the solute-solvent dielectric interface. The solution of Poisson`s equation is obtained by application of a boundary element procedure. The method is tested by comparing its predictions of {Delta}G{sup el} to exact values for several model problems. The method is then used in a variety of contexts to assess its qualitative prediction ability. It is first combined with a molecular mechanics treatment of the solute to evaluate the effects of aqueous solvent on the conformational equilibria of several small molecules of interest-these are N-methyl acetamide and alanine dipeptide. For both molecules dielectric continuum solvation predicts torsional free energies of solvation that are in accord with other more complete treatments of solvation. The method is then combined with ab initio and semi-empirical molecular orbital theory for the solute. Self consistent reaction field calculations (SCRF) are performed to evaluate the correlation is in general very good. Relative agreement with experiment is best for ions where electrostatics predominate and worst for non-polar neutral molecules were electrostatics are minor. Semi-empirical configuration interaction SCRF calculations are also performed in the presence of solvent in order to determine ground-to-excited state absorption energy shifts for formaldehyde and indole mine ground-to-excited state absorption energy shifts for formaldehyde and indole when placed in water. We find a rough correlation between transition energy shifts and the dipole moments of the initial and final states involved in the transition.

  12. Undamped electrostatic plasma waves

    SciTech Connect

    Valentini, F.; Perrone, D.; Veltri, P.; Califano, F.; Pegoraro, F.; Morrison, P. J.; O'Neil, T. M.

    2012-09-15

    Electrostatic waves in a collision-free unmagnetized plasma of electrons with fixed ions are investigated for electron equilibrium velocity distribution functions that deviate slightly from Maxwellian. Of interest are undamped waves that are the small amplitude limit of nonlinear excitations, such as electron acoustic waves (EAWs). A deviation consisting of a small plateau, a region with zero velocity derivative over a width that is a very small fraction of the electron thermal speed, is shown to give rise to new undamped modes, which here are named corner modes. The presence of the plateau turns off Landau damping and allows oscillations with phase speeds within the plateau. These undamped waves are obtained in a wide region of the (k,{omega}{sub R}) plane ({omega}{sub R} being the real part of the wave frequency and k the wavenumber), away from the well-known 'thumb curve' for Langmuir waves and EAWs based on the Maxwellian. Results of nonlinear Vlasov-Poisson simulations that corroborate the existence of these modes are described. It is also shown that deviations caused by fattening the tail of the distribution shift roots off of the thumb curve toward lower k-values and chopping the tail shifts them toward higher k-values. In addition, a rule of thumb is obtained for assessing how the existence of a plateau shifts roots off of the thumb curve. Suggestions are made for interpreting experimental observations of electrostatic waves, such as recent ones in nonneutral plasmas.

  13. Electrostatic Plasma Accelerator (EPA)

    NASA Technical Reports Server (NTRS)

    Brophy, John R.; Aston, Graeme

    1995-01-01

    The application of electric propulsion to communications satellites, however, has been limited to the use of hydrazine thrusters with electric heaters for thrust and specific impulse augmentation. These electrothermal thrusters operate at specific impulse levels of approximately 300 s with heater powers of about 500 W. Low power arcjets (1-3 kW) are currently being investigated as a way to increase specific impulse levels to approximately 500 s. Ion propulsion systems can easily produce specific impulses of 3000 s or greater, but have yet to be applied to communications satellites. The reasons most often given for not using ion propulsion systems are their high level of overall complexity, low thrust with long burn times, and the difficulty of integrating the propulsion system into existing commercial spacecraft busses. The Electrostatic Plasma Accelerator (EPA) is a thruster concept which promises specific impulse levels between low power arcjets and those of the ion engine while retaining the relative simplicity of the arcjet. The EPA thruster produces thrust through the electrostatic acceleration of a moderately dense plasma. No accelerating electrodes are used and the specific impulse is a direct function of the applied discharge voltage and the propellant atomic mass.

  14. Electrostatic Beneficiation of Coal

    SciTech Connect

    D. Lindquist; K. B. Tennal; M. K. Mazumder

    1998-10-29

    It was suggested in the proposal that small particles, due to low inertia, may not impact on the surfaces of the tribocharger. They would, thus, not receive charge and would not be beneficiated in the electrostatic separation. A milling process was proposed in which the small particles are stirred together with larger carrier beads producing the desired contact charge exchange. A force is necessary for removing the coal particles from the carrier beads. In copying machines electrostatic force is used to pull toner particles away horn iron carrier particles which are held back by magnetic force. Aerodynamic force is used in test instruments for measuring the charge to mass ratio on toners. A similar system of milling and removal is desired for use with the small coal particles. The carrier beads need to be made of copper rather than iron. This complicates the separation process since copper is non-magnetic. We are working on coating of iron beads with a layer of copper. Dr. Robert Engleken of Arkansas State University has supplied us with several test batches of copper-coated iron in the size range of -40 +70 mesh. ` We are currently testing whether the milling process used with the copper coated iron beads produces the desired charge on the coal particles.

  15. Dust continuum spectra from model HII regions

    NASA Technical Reports Server (NTRS)

    Aannestad, P. A.; Emery, R. J.

    1989-01-01

    The infrared spectrum emitted by nebular dust, heated by the ionizing stars in H II blisters and spherical H II regions, is calculated for various model parameters. Absorption of the non-ionizing radiation in a neutral layer is included. Heating by the Lyman alpha photon field is taken into account. The dust is composed of silicate and graphite grains, and evaporation of the grains in the inner region is considered. The models are presented with a view to interpretation of infrared observations of dusty H II regions and can be applied directly to the infrared astronomy satellite survey data. The continuum emission is compared with calculated fine structure line emission.

  16. Continuum Modeling of Facet Evolution

    NASA Astrophysics Data System (ADS)

    Kandel, Daniel

    2000-03-01

    Standard continuum models of surface dynamics are very useful for studying thin film evolution on the micron length scale. Unfortunately, they are inadequate below the roughening transition, since they do not appropriately describe faceting. Our goal is to propose a continuum approach which deals with facet dynamics in a physically accurate way. We studied in detail the dynamics of faceting in simple submicron surface structures [1], and proposed two approaches for the development of continuum models. First, we rigorously derived continuum kinetic models of the systems of interest, starting from step flow models. These models break down at singular points, which we identify as facet edges. The models are not applicable on facets, and the surface profile is obtained as a solution of the continuum model with boundary conditions at the singular points. Secondly, we showed [2] that if the existence of both steps and anti-steps in regions of small surface slope is taken into account, it is possible to construct continuum models that are valid even on facets. The solutions of both types of continuum models are in excellent agreement with step flow models. The resulting surface profiles are of relevance to experiments on decay of one dimensional periodic gratings. Our work points to a possible general continuum model for an accurate description of kinetics of crystalline surfaces below the roughening transition. [1] N. Israeli and D. Kandel, Phys. Rev. Lett. 80, 3300 (1998); N. Israeli and D. Kandel, Phys. Rev. B 60, 5946 (1999). [2] N. Israeli and D. Kandel, preprint.

  17. Electrostatics of solvated systems in periodic boundary conditions

    NASA Astrophysics Data System (ADS)

    Andreussi, Oliviero; Marzari, Nicola

    2014-12-01

    Continuum solvation methods can provide an accurate and inexpensive embedding of quantum simulations in liquid or complex dielectric environments. Notwithstanding a long history and manifold applications to isolated systems in open boundary conditions, their extension to materials simulations, typically entailing periodic boundary conditions, is very recent, and special care is needed to address correctly the electrostatic terms. We discuss here how periodic boundary corrections developed for systems in vacuum should be modified to take into account solvent effects, using as a general framework the self-consistent continuum solvation model developed within plane-wave density-functional theory [O. Andreussi et al., J. Chem. Phys. 136, 064102 (2012), 10.1063/1.3676407]. A comprehensive discussion of real- and reciprocal-space corrective approaches is presented, together with an assessment of their ability to remove electrostatic interactions between periodic replicas. Numerical results for zero- and two-dimensional charged systems highlight the effectiveness of the different suggestions, and underline the importance of a proper treatment of electrostatic interactions in first-principles studies of charged systems in solution.

  18. Continuum limbed robots for locomotion

    NASA Astrophysics Data System (ADS)

    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.

  19. The virial theorem for the polarizable continuum model

    SciTech Connect

    Cammi, R.

    2014-02-28

    The electronic virial theorem is extended to molecular systems within the framework of the Polarizable Continuum Model (PCM) to describe solvation effects. The theorem is given in the form of a relation involving the components of the energy (kinetic and potential) of a molecular solute and its electrostatic properties (potential and field) at the boundary of the cavity in the continuum medium. The virial theorem is also derived in the presence of the Pauli repulsion component of the solute-solvent interaction. Furthermore, it is shown that these forms of the PCM virial theorem may be related to the virial theorem of more simple systems as a molecule in the presence of fixed point charges, and as an atom in a spherical box with confining potential.

  20. ELECTROSTATIC MEMORY SYSTEM

    DOEpatents

    Chu, J.C.

    1958-09-23

    An improved electrostatic memory system is de scribed fer a digital computer wherein a plarality of storage tubes are adapted to operate in either of two possible modes. According to the present irvention, duplicate storage tubes are provided fur each denominational order of the several binary digits. A single discriminator system is provided between corresponding duplicate tubes to determine the character of the infurmation stored in each. If either tube produces the selected type signal, corresponding to binazy "1" in the preferred embodiment, a "1" is regenerated in both tubes. In one mode of operation each bit of information is stored in two corresponding tubes, while in the other mode of operation each bit is stored in only one tube in the conventional manner.

  1. Versatile electrostatic trap

    SciTech Connect

    Veldhoven, Jacqueline van; Bethlem, Hendrick L.; Schnell, Melanie; Meijer, Gerard

    2006-06-15

    A four electrode electrostatic trap geometry is demonstrated that can be used to combine a dipole, quadrupole, and hexapole field. A cold packet of {sup 15}ND{sub 3} molecules is confined in both a purely quadrupolar and hexapolar trapping field and additionally, a dipole field is added to a hexapole field to create either a double-well or a donut-shaped trapping field. The profile of the {sup 15}ND{sub 3} packet in each of these four trapping potentials is measured, and the dependence of the well-separation and barrier height of the double-well and donut potential on the hexapole and dipole term are discussed.

  2. MEMS electrostatic influence machines

    NASA Astrophysics Data System (ADS)

    Phu Le, Cuong; Halvorsen, Einar

    2016-11-01

    This paper analyses the possibility of MEMS electrostatic influence machines using electromechanical switches like the historical predecessors did two centuries ago. We find that a generator design relying entirely on standard silicon-on-insulator(SOI) micromachining is conceivable and analyze its performance by simulations. The concept appears preferable over comparable diode circuits due to its higher maximum energy, faster charging and low precharging voltage. A full electromechanical lumped-model including parasitic capacitances of the switches is built to capture the dynamic of the generator. Simulation results show that the output voltage can be exponentially bootstrapped from a very low precharging voltage so that otherwise inadequately small voltage differences or charge imbalances can be made useful.

  3. The wet solidus of silica: Predictions from the scaled particle theory and polarized continuum model

    NASA Astrophysics Data System (ADS)

    Ottonello, G.; Richet, P.; Vetuschi Zuccolini, M.

    2015-02-01

    We present an application of the Scaling Particle Theory (SPT) coupled with an ab initio assessment of the electronic, dispersive, and repulsive energy terms based on the Polarized Continuum Model (PCM) aimed at reproducing the observed solubility behavior of OH2 over the entire compositional range from pure molten silica to pure water and wide pressure and temperature regimes. It is shown that the solution energy is dominated by cavitation terms, mainly entropic in nature, which cause a large negative solution entropy and a consequent marked increase of gas phase fugacity with increasing temperatures. Besides, the solution enthalpy is negative and dominated by electrostatic terms which depict a pseudopotential well whose minimum occurs at a low water fraction (XH2O) of about 6 mol. %. The fine tuning of the solute-solvent interaction is achieved through very limited adjustments of the electrostatic scaling factor γel which, in pure water, is slightly higher than the nominal value (i.e., γel = 1.224 against 1.2), it attains its minimum at low H2O content (γel = 0.9958) and then rises again at infinite dilution (γel = 1.0945). The complex solution behavior is interpreted as due to the formation of energetically efficient hydrogen bonding when OH functionals are in appropriate amount and relative positioning with respect to the discrete OH2 molecules, reinforcing in this way the nominal solute-solvent inductive interaction. The interaction energy derived from the SPT-PCM calculations is then recast in terms of a sub-regular Redlich-Kister expansion of appropriate order whereas the thermodynamic properties of the H2O component at its standard state (1-molal solution referred to infinite dilution) are calculated from partial differentiation of the solution energy over the intensive variables.

  4. The wet solidus of silica: Predictions from the scaled particle theory and polarized continuum model

    SciTech Connect

    Ottonello, G. Vetuschi Zuccolini, M.; Richet, P.

    2015-02-07

    We present an application of the Scaling Particle Theory (SPT) coupled with an ab initio assessment of the electronic, dispersive, and repulsive energy terms based on the Polarized Continuum Model (PCM) aimed at reproducing the observed solubility behavior of OH{sub 2} over the entire compositional range from pure molten silica to pure water and wide pressure and temperature regimes. It is shown that the solution energy is dominated by cavitation terms, mainly entropic in nature, which cause a large negative solution entropy and a consequent marked increase of gas phase fugacity with increasing temperatures. Besides, the solution enthalpy is negative and dominated by electrostatic terms which depict a pseudopotential well whose minimum occurs at a low water fraction (X{sub H{sub 2O}}) of about 6 mol. %. The fine tuning of the solute-solvent interaction is achieved through very limited adjustments of the electrostatic scaling factor γ{sub el} which, in pure water, is slightly higher than the nominal value (i.e., γ{sub el}  =  1.224 against 1.2), it attains its minimum at low H{sub 2}O content (γ{sub el} = 0.9958) and then rises again at infinite dilution (γ{sub el}   =  1.0945). The complex solution behavior is interpreted as due to the formation of energetically efficient hydrogen bonding when OH functionals are in appropriate amount and relative positioning with respect to the discrete OH{sub 2} molecules, reinforcing in this way the nominal solute-solvent inductive interaction. The interaction energy derived from the SPT-PCM calculations is then recast in terms of a sub-regular Redlich-Kister expansion of appropriate order whereas the thermodynamic properties of the H{sub 2}O component at its standard state (1-molal solution referred to infinite dilution) are calculated from partial differentiation of the solution energy over the intensive variables.

  5. Relativistic Continuum Shell Model

    NASA Astrophysics Data System (ADS)

    Grineviciute, Janina; Halderson, Dean

    2011-04-01

    The R-matrix formalism of Lane and Thomas has been extended to the relativistic case so that the many-coupled channels problem may be solved for systems in which binary breakup channels satisfy a relative Dirac equation. The formalism was previously applied to the relativistic impulse approximation RIA and now we applied it to Quantum Hadrodynamics QHD in the continuum Tamm-Dancoff approximation TDA with the classical meson fields replaced by one-meson exchange potentials. None of the published QHD parameters provide a decent fit to the 15 N + p elastic cross section. The deficiency is also evident in inability of the QHD parameters with the one meson exchange potentials to reproduce the QHD single particle energies. Results with alternate parameters sets are presented. A. M. Lane and R. G. Thomas, R-Matrix Theory of Nuclear Reactions, Reviews of Modern Physics, 30 (1958) 257

  6. ABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutions

    PubMed Central

    Vitalis, Andreas; Pappu, Rohit V.

    2009-01-01

    A new implicit solvation model for use in Monte Carlo simulations of polypeptides is introduced. The model is termed ABSINTH for self-Assembly of Biomolecules Studied by an Implicit, Novel, and Tunable Hamiltonian. It is designed primarily for simulating conformational equilibria and oligomerization reactions of intrinsically disordered proteins in aqueous solutions. The paradigm for ABSINTH is conceptually similar to the EEF1 model of Lazaridis and Karplus (Proteins: Struct. Func. Genet., 1999, 35: 133-152). In ABSINTH, the transfer of a polypeptide solute from the gas phase into a continuum solvent is the sum of a direct mean field interaction (DMFI), and a term to model the screening of polar interactions. Polypeptide solutes are decomposed into a set of distinct solvation groups. The DMFI is a sum of contributions from each of the solvation groups, which are analogs of model compounds. Continuum-mediated screening of electrostatic interactions is achieved using a framework similar to the one used for the DMFI. Promising results are shown for a set of test cases. These include the calculation of NMR coupling constants for short peptides, the assessment of the thermal stability of two small proteins, reversible folding of both an alpha-helix and a beta-hairpin forming peptide, and the polymeric properties of intrinsically disordered polyglutamine peptides of varying lengths. The tests reveal that the computational expense for simulations with the ABSINTH implicit solvation model increase by a factor that is in the range of 2.5-5.0 with respect to gas-phase calculations. PMID:18506808

  7. Continuum lowering - A new perspective

    NASA Astrophysics Data System (ADS)

    Crowley, B. J. B.

    2014-12-01

    What is meant by continuum lowering and ionization potential depression (IPD) in a Coulomb system depends very much upon precisely what question is being asked. It is shown that equilibrium (equation of state) phenomena and non-equilibrium dynamical processes like photoionization are characterized by different values of the IPD. In the former, the ionization potential of an atom embedded in matter is the difference in the free energy of the many-body system between states of thermodynamic equilibrium differing by the ionization state of just one atom. Typically, this energy is less than that required to ionize the same atom in vacuo. Probably, the best known example of this is the IPD given by Stewart and Pyatt (SP). However, it is a common misconception that this formula should apply directly to the energy of a photon causing photoionization, since this is a local adiabatic process that occurs in the absence of a response from the surrounding plasma. To achieve the prescribed final equilibrium state, in general, additional energy, in the form of heat and work, is transferred between the atom and its surroundings. This additional relaxation energy is sufficient to explain the discrepancy between recent spectroscopic measurements of IPD in dense plasmas and the predictions of the SP formula. This paper provides a detailed account of an analytical approach, based on SP, to calculating thermodynamic and spectroscopic (adiabatic) IPDs in multicomponent Coulomb systems of arbitrary coupling strength with Te ≠ Ti. The ramifications for equilibrium Coulomb systems are examined in order to elucidate the roles of the various forms of the IPD and any possible connection with the plasma microfield. The formulation embodies an analytical equation of state (EoS) that is thermodynamically self-consistent, provided that the bound and free electrons are dynamically separable, meaning that the system is not undergoing pressure ionization. Apart from this restriction, the model is

  8. Teaching Electrostatics in University Courses

    ERIC Educational Resources Information Center

    Hughes, J. F.

    1974-01-01

    Describes an optional course on applied electrostatics that was offered to electrical engineers in their final year. Topics included the determination of electric fields, nature of the charging process, static electricity in liquids, solid state processes, charged particle applications, and electrostatic ignition. (GS)

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

    PubMed

    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.

  10. The Paranoid-Depressive Continuum

    ERIC Educational Resources Information Center

    Johnson, Betty J.

    1977-01-01

    Few investigators have attempted to lay a conceptual base for comparative studies of paranoia and depression within a single general framework. The paranoid-depressive continuum is an attempt to develop such a framework. (Author)

  11. Electrostatic Transport and Manipulation of Lunar Soil and Dust

    SciTech Connect

    Kawamoto, Hiroyuki

    2008-01-21

    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.

  12. Ash Dispersal in Planetary Atmospheres: Continuum vs. Non-continuum Effects

    NASA Astrophysics Data System (ADS)

    Fagents, S. A.; Baloga, S. M.; Glaze, L. S.

    2013-12-01

    The dispersal of ash from a volcanic vent on any given planet is dictated by particle properties (density, shape, and size distribution), the intensity of the eruptive source, and the characteristics of the planetary environment (atmospheric structure, wind field, and gravity) into which the ash is erupted. Relating observations of potential pyroclastic deposits to source locations and eruption conditions requires a detailed quantitative understanding of the settling rates of individual particles under changing ambient conditions. For atmospheres that are well described by continuum mechanics, the conventional Newtonian description of particle motion allows particle settling velocities to be related to particle characteristics via a drag coefficient. However, under rarefied atmospheric conditions (i.e., on Mars and at high altitude on Earth), non-continuum effects become important for ash-sized particles, and an equation of motion based on statistical mechanics is required for calculating particle motion. We have developed a rigorous new treatment of particle settling under variable atmospheric conditions and applied it to Earth and Mars. When non-continuum effects are important (as dictated by the mean free path of atmospheric gas relative to the particle size), fall velocities are greater than those calculated by continuum mechanics. When continuum conditions (i.e., higher atmospheric densities) are reached during descent, our model switches to a conventional formulation that determines the appropriate drag coefficient as the particle transits varying atmospheric properties. The variation of settling velocity with altitude allows computation of particle trajectories, fall durations and downwind dispersal. Our theoretical and numerical analyses show that several key, competing factors strongly influence the downwind trajectories of ash particles and the extents of the resulting deposits. These factors include: the shape of the particles (non-spherical particles

  13. Energetics of the Cleft Closing Transition and the Role of Electrostatic Interactions in Conformational Rearrangements of the Glutamate Receptor Ligand Binding Domain

    PubMed Central

    Mamonova, Tatyana; Yonkunas, Michael J.; Kurnikova, Maria G.

    2009-01-01

    The ionotropic glutamate receptors are localized in the pre- and postsynaptic membrane of neurons in the brain. Activation by the principal excitatory neurotransmitter glutamate allows the ligand binding domain to change conformation, communicating opening of the channel for ion conduction. The free energy of the GluR2 S1S2 ligand binding domain (S1S2) closure transition was computed using a combination of thermodynamic integration and umbrella sampling modeling methods. A path that involves lowering the charge on E705 was chosen to clarify the role of this binding site residue. A continuum electrostatic approach in S1S2 is used to show E705, located in the ligand binding cleft, stabilizes the closed conformation of S1S2. In the closed conformation, in the absence of a ligand, S1S2 is somewhat more closed than reported from X-ray structures. A semi-open conformation has been identified which is characterized by disruption of a single cross-cleft interaction and differs only slightly in energy from the fully closed S1S2. The fully open S1S2 conformation exhibits a wide energy well and shares structural similarity to the apo S1S2 crystal structure. Hybrid continuum electrostatics/MD calculations along the chosen closure transition pathway reveal solvation energies, as well as electrostatic interaction energies between two lobes of the protein increase the relative energetic difference between the open and the closed conformational states. By analyzing the role of several cross-cleft contacts as well as other binding site residues we demonstrate how S1S2 interactions facilitate formation of the closed conformation of the ligand binding domain. PMID:18823129

  14. Micromachined silicon electrostatic chuck

    DOEpatents

    Anderson, Robert A.; Seager, Carleton H.

    1996-01-01

    An electrostatic chuck is faced with a patterned silicon plate 11, created y micromachining a silicon wafer, which is attached to a metallic base plate 13. Direct electrical contact between the chuck face 15 (patterned silicon plate's surface) and the silicon wafer 17 it is intended to hold is prevented by a pattern of flat-topped silicon dioxide islands 19 that protrude less than 5 micrometers from the otherwise flat surface of the chuck face 15. The islands 19 may be formed in any shape. Islands may be about 10 micrometers in diameter or width and spaced about 100 micrometers apart. One or more concentric rings formed around the periphery of the area between the chuck face 15 and wafer 17 contain a low-pressure helium thermal-contact gas used to assist heat removal during plasma etching of a silicon wafer held by the chuck. The islands 19 are tall enough and close enough together to prevent silicon-to-silicon electrical contact in the space between the islands, and the islands occupy only a small fraction of the total area of the chuck face 15, typically 0.5 to 5 percent. The pattern of the islands 19, together with at least one hole 12 bored through the silicon veneer into the base plate, will provide sufficient gas-flow space to allow the distribution of the helium thermal-contact gas.

  15. Micromachined silicon electrostatic chuck

    DOEpatents

    Anderson, R.A.; Seager, C.H.

    1996-12-10

    An electrostatic chuck is faced with a patterned silicon plate, created by micromachining a silicon wafer, which is attached to a metallic base plate. Direct electrical contact between the chuck face (patterned silicon plate`s surface) and the silicon wafer it is intended to hold is prevented by a pattern of flat-topped silicon dioxide islands that protrude less than 5 micrometers from the otherwise flat surface of the chuck face. The islands may be formed in any shape. Islands may be about 10 micrometers in diameter or width and spaced about 100 micrometers apart. One or more concentric rings formed around the periphery of the area between the chuck face and wafer contain a low-pressure helium thermal-contact gas used to assist heat removal during plasma etching of a silicon wafer held by the chuck. The islands are tall enough and close enough together to prevent silicon-to-silicon electrical contact in the space between the islands, and the islands occupy only a small fraction of the total area of the chuck face, typically 0.5 to 5 percent. The pattern of the islands, together with at least one hole bored through the silicon veneer into the base plate, will provide sufficient gas-flow space to allow the distribution of the helium thermal-contact gas. 6 figs.

  16. Electrostatic drops in orbit

    NASA Astrophysics Data System (ADS)

    Rodriguez, Isabel J.; Schmidt, Erin; Weislogel, Mark M.; Pettit, Donald

    2016-11-01

    We present what we think are the first intentional electrostatic orbits in the near-weightless environment of a drop tower. Classical physics problems involving Coulombic forces in orbital mechanics have traditionally been confined to thought experiments due to practical terrestrial experimental limitations, namely, the preponderance of gravity. However, the use of a drop tower as an experimental platform can overcome this challenge for brief periods. We demonstrate methanol-water droplets in orbit around a variety of charged objects- some of which can be used to validate special cases of N-body systems. Footage collected via a high-speed camera is analyzed and orbital trajectories are compared with existing theoretical predictions. Droplets of diameters 0.5 to 2mm in a variety of obits are observed. Due to the repeatability of drop tower initial conditions and effective low-g environment, such experiments may be used to construct empirical analogues and confirm analyses toward the benefit of other fields including space and planetary science. NASA Cooperative Agreement NNX12A047A, Portland State LSAMP, Robert E. McNair Scholars Program.

  17. The Electrostatic Bell

    NASA Astrophysics Data System (ADS)

    Martrou, Guillaume; Leonetti, Marc

    2016-11-01

    An initially static fluid-fluid interface is known to become unstable under a strong electric field leading to jet instability, surface pattern and spout formation. Applying an electric field to an initial dripping mode accelerates the dripping rate and leads to a continuous jet mode. We show that those two different configurations, when applied to dielectric liquids, can lead to the same instability, the formation of an unexpected macroscopic fluid bell-shape of typical size few times the capillary length even if the needle is as small as 200 μm . The instability results from the competition between the dielectric and the gravity forces, reminiscent of the Taylor-Melcher mechanism. The study is performed on several fluids of various densities, permittivity and surface tension on a large range of electric field. We show that the transition is an imperfect subcritical bifurcation with its characteristic bottleneck effect (lag time). Finally, in the case of flow rate, we established a shape diagram with four domains corresponding to dripping, jetting, bridge and electrostatic bell.

  18. Electrostatic study of the proton pumping mechanism in bovine heart cytochrome C oxidase.

    PubMed

    Popović, Dragan M; Stuchebrukhov, Alexei A

    2004-02-18

    Cytochrome c oxidase (CcO) is the terminal enzyme of the cell respiratory chain in mitochondria and aerobic bacteria. It catalyzes the reduction of oxygen to water and utilizes the free energy of the reduction reaction for proton pumping across the inner-mitochondrial membrane, a process that results in a membrane electrochemical proton gradient. Although the structure of the enzyme has been solved for several organisms, the molecular mechanism of proton pumping remains unknown. In the present paper, continuum electrostatic calculations were employed to evaluate the electrostatic potential, energies, and protonation state of bovine heart cytochrome c oxidase for different redox states of the enzyme along its catalytic cycle. Three different computational models of the enzyme were employed to test the stability of the results. The energetics and pH dependence of the P-->F, F-->O, and O-->E steps of the cycle have been investigated. On the basis of electrostatic calculations, two possible schemes of redox-linked proton pumping are discussed. The first scheme involves His291 as a pump element, whereas the second scheme involves a group linked to propionate D of heme a(3). In both schemes, loading of the pump site is coupled to ET between the two hemes of the enzyme, while transfer of a chemical proton is accompanied by ejection of the pumped H(+). The two models, as well as the energetics results are compared with recent experimental kinetic data. The proton pumping across the membrane is an endergonic process, which requires a sufficient amount of energy to be provided by the chemical reaction in the active site. In our calculations, the conversion of OH(-) to H(2)O provides 520 meV of energy to displace pump protons from a loading site and overall about 635 meV for each electron passing through the system. Assuming that the two charges are translocated per electron against the membrane potential of 200 meV, the model predicts an overall efficiency of 63%.

  19. Wavelet formulation of the polarizable continuum model.

    PubMed

    Weijo, Ville; Randrianarivony, Maharavo; Harbrecht, Helmut; Frediani, Luca

    2010-05-01

    The first implementation of a wavelet discretization of the Integral Equation Formalism (IEF) for the Polarizable Continuum Model (PCM) is presented here. The method is based on the application of a general purpose wavelet solver on the cavity boundary to solve the integral equations of the IEF-PCM problem. Wavelet methods provide attractive properties for the solution of the electrostatic problem at the cavity boundary: the system matrix is highly sparse and iterative solution schemes can be applied efficiently; the accuracy of the solver can be increased systematically and arbitrarily; for a given system, discretization error accuracy is achieved at a computational expense that scales linearly with the number of unknowns. The scaling of the computational time with the number of atoms N is formally quadratic but a N(1.5) scaling has been observed in practice. The current bottleneck is the evaluation of the potential integrals at the cavity boundary which scales linearly with the system size. To reduce this overhead, interpolation of the potential integrals on the cavity surface has been successfully used.

  20. Explosion safety in industrial electrostatics

    NASA Astrophysics Data System (ADS)

    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.

  1. Computational Methods for Biomolecular Electrostatics

    PubMed Central

    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

  2. Electrostatic prepregging of thermoplastic matrices

    NASA Technical Reports Server (NTRS)

    Muzzy, John D.; Varughese, Babu; Thammongkol, Vivan; Tincher, Wayne

    1989-01-01

    Thermoplastic towpregs of PEEK/AS-4, PEEK/S-2 glass and LaRC-TPI/AS-4, produced by electrostatic deposition of charged and fluidized polymer powders on spread continuous fiber tows, are described. Processing parameters for combining PEEK 150 powder with unsized 3k AS-4 carbon fiber are presented. The experimental results for PEEK 150/AS-4 reveal that electrostatic fluidized bed coating may be an economically attractive process for producing towpreg.

  3. Calculated coupling of electron and proton transfer in the photosynthetic reaction center of Rhodopseudomonas viridis.

    PubMed Central

    Lancaster, C R; Michel, H; Honig, B; Gunner, M R

    1996-01-01

    Based on new Rhodopseudomonas (Rp.) viridis reaction center (RC) coordinates with a reliable structure of the secondary acceptor quinone (QB) site, a continuum dielectric model and finite difference technique have been used to identify clusters of electrostatically interacting ionizable residues. Twenty-three residues within a distance of 25 A from QB (QB cluster) have been shown to be strongly electrostatically coupled to QB, either directly or indirectly. An analogous cluster of 24 residues is found to interact with QA (QA cluster). Both clusters extend to the cytoplasmic surface in at least two directions. However, the QB cluster differs from the QA cluster in that it has a surplus of acidic residues, more strong electrostatic interactions, is less solvated, and experiences a strong positive electrostatic field arising from the polypeptide backbone. Consequently, upon reduction of QA or QB, it is the QB cluster, and not the QA cluster, which is responsible for substoichiometric proton uptake at neutral pH. The bulk of the changes in the QB cluster are calculated to be due to the protonation of a tightly coupled cluster of the three Glu residues (L212, H177, and M234) within the QB cluster. If the lifetime of the doubly reduced state QB2- is long enough, Asp M43 and Ser L223 are predicted to also become protonated. The calculated complex titration behavior of the strongly interacting residues of the QB cluster and the resulting electrostatic response to electron transfer may be a common feature in proton-transferring membrane protein complexes. Images FIGURE 2 p2482-a FIGURE 6 FIGURE 8 FIGURE 10 PMID:8744288

  4. Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions.

    PubMed

    Marenich, Aleksandr V; Cramer, Christopher J; Truhlar, Donald G

    2009-05-07

    We present a new continuum solvation model based on the quantum mechanical charge density of a solute molecule interacting with a continuum description of the solvent. The model is called SMD, where the "D" stands for "density" to denote that the full solute electron density is used without defining partial atomic charges. "Continuum" denotes that the solvent is not represented explicitly but rather as a dielectric medium with surface tension at the solute-solvent boundary. SMD is a universal solvation model, where "universal" denotes its applicability to any charged or uncharged solute in any solvent or liquid medium for which a few key descriptors are known (in particular, dielectric constant, refractive index, bulk surface tension, and acidity and basicity parameters). The model separates the observable solvation free energy into two main components. The first component is the bulk electrostatic contribution arising from a self-consistent reaction field treatment that involves the solution of the nonhomogeneous Poisson equation for electrostatics in terms of the integral-equation-formalism polarizable continuum model (IEF-PCM). The cavities for the bulk electrostatic calculation are defined by superpositions of nuclear-centered spheres. The second component is called the cavity-dispersion-solvent-structure term and is the contribution arising from short-range interactions between the solute and solvent molecules in the first solvation shell. This contribution is a sum of terms that are proportional (with geometry-dependent proportionality constants called atomic surface tensions) to the solvent-accessible surface areas of the individual atoms of the solute. The SMD model has been parametrized with a training set of 2821 solvation data including 112 aqueous ionic solvation free energies, 220 solvation free energies for 166 ions in acetonitrile, methanol, and dimethyl sulfoxide, 2346 solvation free energies for 318 neutral solutes in 91 solvents (90 nonaqueous

  5. Quantum Dynamics in Continuum for Proton Transport I: Basic Formulation

    PubMed Central

    Chen, Duan; Wei, Guo-Wei

    2012-01-01

    Proton transport is one of the most important and interesting phenomena in living cells. The present work proposes a multiscale/multiphysics model for the understanding of the molecular mechanism of proton transport in transmembrane proteins. We describe proton dynamics quantum mechanically via a density functional approach while implicitly model other solvent ions as a dielectric continuum to reduce the number of degrees of freedom. The densities of all other ions in the solvent are assumed to obey the Boltzmann distribution. The impact of protein molecular structure and its charge polarization on the proton transport is considered explicitly at the atomic level. We formulate a total free energy functional to put proton kinetic and potential energies as well as electrostatic energy of all ions on an equal footing. The variational principle is employed to derive nonlinear governing equations for the proton transport system. Generalized Poisson-Boltzmann equation and Kohn-Sham equation are obtained from the variational framework. Theoretical formulations for the proton density and proton conductance are constructed based on fundamental principles. The molecular surface of the channel protein is utilized to split the discrete protein domain and the continuum solvent domain, and facilitate the multiscale discrete/continuum/quantum descriptions. A number of mathematical algorithms, including the Dirichlet to Neumann mapping, matched interface and boundary method, Gummel iteration, and Krylov space techniques are utilized to implement the proposed model in a computationally efficient manner. The Gramicidin A (GA) channel is used to demonstrate the performance of the proposed proton transport model and validate the efficiency of proposed mathematical algorithms. The electrostatic characteristics of the GA channel is analyzed with a wide range of model parameters. The proton conductances are studied over a number of applied voltages and reference concentrations. A

  6. Quantum Dynamics in Continuum for Proton Transport I: Basic Formulation.

    PubMed

    Chen, Duan; Wei, Guo-Wei

    2013-01-01

    Proton transport is one of the most important and interesting phenomena in living cells. The present work proposes a multiscale/multiphysics model for the understanding of the molecular mechanism of proton transport in transmembrane proteins. We describe proton dynamics quantum mechanically via a density functional approach while implicitly model other solvent ions as a dielectric continuum to reduce the number of degrees of freedom. The densities of all other ions in the solvent are assumed to obey the Boltzmann distribution. The impact of protein molecular structure and its charge polarization on the proton transport is considered explicitly at the atomic level. We formulate a total free energy functional to put proton kinetic and potential energies as well as electrostatic energy of all ions on an equal footing. The variational principle is employed to derive nonlinear governing equations for the proton transport system. Generalized Poisson-Boltzmann equation and Kohn-Sham equation are obtained from the variational framework. Theoretical formulations for the proton density and proton conductance are constructed based on fundamental principles. The molecular surface of the channel protein is utilized to split the discrete protein domain and the continuum solvent domain, and facilitate the multiscale discrete/continuum/quantum descriptions. A number of mathematical algorithms, including the Dirichlet to Neumann mapping, matched interface and boundary method, Gummel iteration, and Krylov space techniques are utilized to implement the proposed model in a computationally efficient manner. The Gramicidin A (GA) channel is used to demonstrate the performance of the proposed proton transport model and validate the efficiency of proposed mathematical algorithms. The electrostatic characteristics of the GA channel is analyzed with a wide range of model parameters. The proton conductances are studied over a number of applied voltages and reference concentrations. A

  7. Continuum modeling of deformation and aggregation of red blood cells.

    PubMed

    Yoon, Daegeun; You, Donghyun

    2016-07-26

    In order to gain better understanding for rheology of an isolated red blood cell (RBC) and a group of multiple RBCs, new continuum models for describing mechanical properties of cellular structures of an RBC and inter-cellular interactions among multiple RBCs are developed. The viscous property of an RBC membrane, which characterizes dynamic behaviors of an RBC under stress loading and unloading processes, is determined using a generalized Maxwell model. The present model is capable of predicting stress relaxation and stress-strain hysteresis, of which prediction is not possible using the commonly used Kelvin-Voigt model. Nonlinear elasticity of an RBC is determined using the Yeoh hyperelastic material model in a framework of continuum mechanics using finite-element approximation. A novel method to model inter-cellular interactions among multiple adjacent RBCs is also developed. Unlike the previous modeling approaches for aggregation of RBCs, where interaction energy for aggregation is curve-fitted using a Morse-type potential function, the interaction energy is analytically determined. The present aggregation model, therefore, allows us to predict various effects of physical parameters such as the osmotic pressure, the thickness of a glycocalyx layer, the penetration depth, and the permittivity, on the depletion and electrostatic energy among RBCs. Simulations for elongation and recovery deformation of an RBC and for aggregation of multiple RBCs are conducted to evaluate the efficacy of the present continuum modeling methods.

  8. Lagrangian continuum dynamics in ALEGRA.

    SciTech Connect

    Wong, Michael K. W.; Love, Edward

    2007-12-01

    Alegra is an ALE (Arbitrary Lagrangian-Eulerian) multi-material finite element code that emphasizes large deformations and strong shock physics. The Lagrangian continuum dynamics package in Alegra uses a Galerkin finite element spatial discretization and an explicit central-difference stepping method in time. The goal of this report is to describe in detail the characteristics of this algorithm, including the conservation and stability properties. The details provided should help both researchers and analysts understand the underlying theory and numerical implementation of the Alegra continuum hydrodynamics algorithm.

  9. Submillimeter Continuum Observations of Comets

    NASA Technical Reports Server (NTRS)

    Jewitt, David

    1998-01-01

    The aim of this proposal was to study the submillimeter continuum emission from comets. The study was based mainly on the exploitation of the world's leading submillimeter telescope, the JCMT (James Clerk Maxwell Telescope) on Mauna Kea. Submillimeter wavelengths provide a unique view of cometary physics for one main reason. The cometary size distribution is such that the scattering cross-section is dominated by small dust grains, while the mass is dominated by the largest particles. Submillimeter continuum radiation samples cometary particles much larger than those sampled by more common observations at shorter (optical and infrared) wavelengths and therefore provides a nearly direct measure of the cometary dust mass.

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

    PubMed

    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.

  11. Engineering scale electrostatic enclosure demonstration

    SciTech Connect

    Meyer, L.C.

    1993-09-01

    This report presents results from an engineering scale electrostatic enclosure demonstration test. The electrostatic enclosure is part of an overall in-depth contamination control strategy for transuranic (TRU) waste recovery operations. TRU contaminants include small particles of plutonium compounds associated with defense-related waste recovery operations. Demonstration test items consisted of an outer Perma-con enclosure, an inner tent enclosure, and a ventilation system test section for testing electrostatic curtain devices. Three interchangeable test fixtures that could remove plutonium from the contaminated dust were tested in the test section. These were an electret filter, a CRT as an electrostatic field source, and an electrically charged parallel plate separator. Enclosure materials tested included polyethylene, anti-static construction fabric, and stainless steel. The soil size distribution was determined using an eight stage cascade impactor. Photographs of particles containing plutonium were obtained with a scanning electron microscope (SEM). The SEM also provided a second method of getting the size distribution. The amount of plutonium removed from the aerosol by the electrostatic devices was determined by radiochemistry from input and output aerosol samplers. The inner and outer enclosures performed adequately for plutonium handling operations and could be used for full scale operations.

  12. Parameter identification in continuum models

    NASA Technical Reports Server (NTRS)

    Banks, H. T.; Crowley, J. M.

    1983-01-01

    Approximation techniques for use in numerical schemes for estimating spatially varying coefficients in continuum models such as those for Euler-Bernoulli beams are discussed. The techniques are based on quintic spline state approximations and cubic spline parameter approximations. Both theoretical and numerical results are presented.

  13. Electrostatic interactions in charged nanoslits within an explicit solvent theory.

    PubMed

    Buyukdagli, Sahin

    2015-11-18

    Within a dipolar Poisson-Boltzmann theory including electrostatic correlations, we consider the effect of explicit solvent structure on solvent and ion partition confined to charged nanopores. We develop a relaxation scheme for the solution of this highly non-linear integro-differential equation for the electrostatic potential. The scheme is an extension of the approach previously introduced for simple planes (Buyukdagli and Blossey 2014 J. Chem. Phys. 140 234903) to nanoslit geometry. We show that the reduced dielectric response of solvent molecules at the membrane walls gives rise to an electric field significantly stronger than the field of the classical Poisson-Boltzmann equation. This peculiarity associated with non-local electrostatic interactions results in turn in an interfacial counterion adsorption layer absent in continuum theories. The observation of this enhanced counterion affinity in the very close vicinity of the interface may have important impacts on nanofluidic transport through charged nanopores. Our results indicate the quantitative inaccuracy of solvent implicit nanofiltration theories in predicting the ionic selectivity of membrane nanopores.

  14. GroPBS: Fast Solver for Implicit Electrostatics of Biomolecules

    PubMed Central

    Bertelshofer, Franziska; Sun, Liping; Greiner, Günther; Böckmann, Rainer A.

    2015-01-01

    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 also guide 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, needs to be carefully considered, e.g., in design studies on membrane proteins. PMID:26636074

  15. GroPBS: Fast Solver for Implicit Electrostatics of Biomolecules.

    PubMed

    Bertelshofer, Franziska; Sun, Liping; Greiner, Günther; Böckmann, Rainer A

    2015-01-01

    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 also guide 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, needs to be carefully considered, e.g., in design studies on membrane proteins.

  16. Electrostatic interactions in charged nanoslits within an explicit solvent theory

    NASA Astrophysics Data System (ADS)

    Buyukdagli, Sahin

    2015-11-01

    Within a dipolar Poisson-Boltzmann theory including electrostatic correlations, we consider the effect of explicit solvent structure on solvent and ion partition confined to charged nanopores. We develop a relaxation scheme for the solution of this highly non-linear integro-differential equation for the electrostatic potential. The scheme is an extension of the approach previously introduced for simple planes (Buyukdagli and Blossey 2014 J. Chem. Phys. 140 234903) to nanoslit geometry. We show that the reduced dielectric response of solvent molecules at the membrane walls gives rise to an electric field significantly stronger than the field of the classical Poisson-Boltzmann equation. This peculiarity associated with non-local electrostatic interactions results in turn in an interfacial counterion adsorption layer absent in continuum theories. The observation of this enhanced counterion affinity in the very close vicinity of the interface may have important impacts on nanofluidic transport through charged nanopores. Our results indicate the quantitative inaccuracy of solvent implicit nanofiltration theories in predicting the ionic selectivity of membrane nanopores.

  17. Capacity calculation of the electrotechnical scheme of discharge gap replacement of the ozonizer in the COMSOL environment

    NASA Astrophysics Data System (ADS)

    Isaev, Yu N.; Kolchanova, V. A.; Maltsev, A. P.; Aksenov, V. P.

    2017-02-01

    The investigation of electrostatic field distribution of ozonator electrode gap caused by inhomogeneous permittivity has been done. The paper presents calculation of electrostatic field energy of ozonator electrode gap. From the energy of electrostatic field distribution the information about electrode system capacity has been extracted. For calculation of the electrostatic field and capacity of electrode system the software integrated environment COMSOL has been used.

  18. Structure and electrostatic property of cytoplasmic domain of ZntB transporter.

    SciTech Connect

    Tan, K.; Sather, A.; Robertson, J. L.; Moy, S.; Roux, B.; Joachimiak, A.; Biosciences Division; Cornell Univ.; Univ. of Chicago

    2009-10-01

    ZntB is the distant homolog of CorA Mg{sup 2+} transporter within the metal ion transporter superfamily. It was early reported that the ZntB from Salmonella typhimurium facilitated efflux of Zn{sup 2+} and Cd{sup 2+}, but not Mg{sup 2+}. Here, we report the 1.90 {angstrom} crystal structure of the intracellular domain of ZntB from Vibrio parahemolyticus. The domain forms a funnel-shaped homopentamer that is similar to the full-length CorA from Thermatoga maritima, but differs from two previously reported dimeric structures of truncated CorA intracellular domains. However, no Zn{sup 2+} or Cd{sup 2+} binding sites were identified in the high-resolution structure. Instead, 25 well-defined Cl{sup -} ions were observed and some of these binding sites are highly conserved within the ZntB family. Continuum electrostatics calculations suggest that the central pore of the funnel is highly attractive for cations, especially divalents. The presence of the bound Cl{sup -} ions increases the stability of cations along the pore suggesting they could be important in enhancing cation transport.

  19. Structure and electrostatic property of cytoplasmic domain of ZntB transporter

    PubMed Central

    Tan, Kemin; Sather, Alicia; Robertson, Janice L; Moy, Shiu; Roux, Benoît; Joachimiak, Andrzej

    2009-01-01

    ZntB is the distant homolog of CorA Mg2+ transporter within the metal ion transporter superfamily. It was early reported that the ZntB from Salmonella typhimurium facilitated efflux of Zn2+ and Cd2+, but not Mg2+. Here, we report the 1.90 Å crystal structure of the intracellular domain of ZntB from Vibrio parahemolyticus. The domain forms a funnel-shaped homopentamer that is similar to the full-length CorA from Thermatoga maritima, but differs from two previously reported dimeric structures of truncated CorA intracellular domains. However, no Zn2+ or Cd2+ binding sites were identified in the high-resolution structure. Instead, 25 well-defined Cl− ions were observed and some of these binding sites are highly conserved within the ZntB family. Continuum electrostatics calculations suggest that the central pore of the funnel is highly attractive for cations, especially divalents. The presence of the bound Cl− ions increases the stability of cations along the pore suggesting they could be important in enhancing cation transport. PMID:19653298

  20. Diffuse Galactic low energy gamma ray continuum emission

    NASA Technical Reports Server (NTRS)

    Skibo, J. G.; Ramaty, R.

    1993-01-01

    We investigate the origin of diffuse low-energy Galactic gamma-ray continuum down to about 30 keV. We calculate gamma-ray emission via bremsstrahlung and inverse Compton scattering by propagating an unbroken electron power law injection spectrum and employing a Galactic emmissivity model derived from COSB observations. To maintain the low energy electron population capable of producing the observed continuum via bremsstrahlung, a total power input of 4 x 10 exp 41 erg/s is required. This exceeds the total power supplied to the nuclear cosmic rays by about an order of magnitude.

  1. FUV Continuum in Flare Kernels Observed by IRIS

    NASA Astrophysics Data System (ADS)

    Daw, Adrian N.; Kowalski, Adam; Allred, Joel C.; Cauzzi, Gianna

    2016-05-01

    Fits to Interface Region Imaging Spectrograph (IRIS) spectra observed from bright kernels during the impulsive phase of solar flares are providing long-sought constraints on the UV/white-light continuum emission. Results of fits of continua plus numerous atomic and molecular emission lines to IRIS far ultraviolet (FUV) spectra of bright kernels are presented. Constraints on beam energy and cross sectional area are provided by cotemporaneous RHESSI, FERMI, ROSA/DST, IRIS slit-jaw and SDO/AIA observations, allowing for comparison of the observed IRIS continuum to calculations of non-thermal electron beam heating using the RADYN radiative-hydrodynamic loop model.

  2. Electrostatic attraction between overall neutral surfaces.

    PubMed

    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.

  3. Electrostatically actuatable light modulating device

    DOEpatents

    Koehler, Dale R.

    1991-01-01

    The electrostatically actuatable light modulator utilizes an opaque substrate plate patterned with an array of aperture cells, the cells comprised of physically positionable dielectric shutters and electrostatic actuators. With incorporation of a light source and a viewing screen, a projection display system is effected. Inclusion of a color filter array aligned with the aperture cells accomplishes a color display. The system is realized in terms of a silicon based manufacturing technology allowing fabrication of a high resolution capability in a physically small device which with the utilization of included magnification optics allows both large and small projection displays.

  4. Polarizable multipolar electrostatics for cholesterol

    NASA Astrophysics Data System (ADS)

    Fletcher, Timothy L.; Popelier, Paul L. A.

    2016-08-01

    FFLUX is a novel force field under development for biomolecular modelling, and is based on topological atoms and the machine learning method kriging. Successful kriging models have been obtained for realistic electrostatics of amino acids, small peptides, and some carbohydrates but here, for the first time, we construct kriging models for a sizeable ligand of great importance, which is cholesterol. Cholesterol's mean total (internal) electrostatic energy prediction error amounts to 3.9 kJ mol-1, which pleasingly falls below the threshold of 1 kcal mol-1 often cited for accurate biomolecular modelling. We present a detailed analysis of the error distributions.

  5. Electrostatics at the molecular level

    NASA Astrophysics Data System (ADS)

    Zürcher, Ulrich

    2017-01-01

    In molecular systems, positive and negative charges are separated, making them ideal systems to examine electrostatic interactions. The attractive force between positive and negative charges is balanced by repulsive ‘forces’ that are quantum-mechanical in origin. We introduce an ‘effective’ potential energy that captures the repulsion; it allows us to obtain fairly accurate estimates of the bonding properties of molecular systems. We use units (e.g., kcal mol-1 for energy) that emphasize the relevance of electrostatics to macroscopic behavior.

  6. Fabrication of nanoscale electrostatic lenses

    NASA Astrophysics Data System (ADS)

    Sinno, I.; Sanz-Velasco, A.; Kang, S.; Jansen, H.; Olsson, E.; Enoksson, P.; Svensson, K.

    2010-09-01

    The fabrication of cylindrical multi-element electrostatic lenses at the nanoscale presents a challenge; they are high-aspect-ratio structures that should be rotationally symmetric, well aligned and freestanding, with smooth edges and flat, clean surfaces. In this paper, we present the fabrication results of a non-conventional process, which uses a combination of focused gallium ion-beam milling and hydrofluoric acid vapor etching. This process makes it possible to fabricate nanoscale electrostatic lenses down to 140 nm in aperture diameter and 4.2 µm in column length, with a superior control of the geometry as compared to conventional lithography-based techniques.

  7. Charge sniffer for electrostatics demonstrations

    NASA Astrophysics Data System (ADS)

    Dinca, Mihai P.

    2011-02-01

    An electronic electroscope with a special design for demonstrations and experiments on static electricity is described. It operates as an electric charge sniffer by detecting slightly charged objects when they are brought to the front of its sensing electrode. The sniffer has the advantage of combining high directional sensitivity with a logarithmic bar display. It allows for the identification of electric charge polarity during charge separation by friction, peeling, electrostatic induction, batteries, or secondary coils of power transformers. Other experiments in electrostatics, such as observing the electric field of an oscillating dipole and the distance dependence of the electric field generated by simple charge configurations, are also described.

  8. Homogenization of a Cauchy continuum towards a micromorphic continuum

    NASA Astrophysics Data System (ADS)

    Hütter, Geralf

    2017-02-01

    The micromorphic theory of Eringen and Mindlin, including special cases like strain gradient theory or Cosserat theory, is widely used to model size effects and localization phenomena. The heuristic construction of such theories based on thermodynamic considerations is well-established. However, the identification of corresponding constitutive laws and of the large number of respective constitutive parameters limits the practical application of such theories. In the present contribution, a closed procedure for the homogenization of a Cauchy continuum at the microscale towards a fully micromorphic continuum is derived including explicit definitions of all involved generalized macroscopic stress and deformation measures. The boundary value problem to be solved on the microscale is formulated either for using static or kinematic boundary conditions. The procedure is demonstrated with an example.

  9. Rabi-split states broadened by a continuum

    SciTech Connect

    Maialle, M. Z.; Degani, M. H.; Madureira, J. R.

    2013-12-04

    In this work we theoretically investigate a Λ-like three-level system. Our model consists of a onedimensional quantum well with a nearby continuum. The Λ level structure is formed by the ground state (a valence band state) and two excited states (both in conduction band), one being a localized and the other a quasi-bound state which is interacting with the continuum. An infrared (IR) field is used to drive the excited states into dressed states creating Autler-Townes doublets. We solve the semiconductor Bloch equation, in real space and in time domain, to follow the interband optical excitation dynamics. The optical absorption and the photocurrent spectra are calculated for different potential barriers separating the well and the continuum. We show how this affects the Autler-Townes doublets since this is a possible way of changing the relationship between the IR Rabi frequency and the dephasing rates.

  10. Electrostatic interactions in hirudin-thrombin binding.

    PubMed

    Sharp, K A

    1996-08-30

    Hirudin is a good anticoagulant owing to potent inhibition of the serine protease thrombin. An aspartate- and glutamate-rich portion of hirudin plays an important part in its tight binding to thrombin through a ladder of salt bridges, and these residues have previously been mutated to asparagine or glutamine. Detailed calculations of the electrostatic contribution to changes in binding from these mutations have been performed using the finite-difference Poisson-Boltzmann method which include charge--charge interactions, solvation interactions, the residual electrostatic interaction of mutant residues, pKa shifts, and ionic strength. Single mutant effects on binding energy were close to experimental values, except for the D55N mutant whose effect is overestimated, perhaps because of displacement of a bound chloride ion from the site where it binds. Multiple mutation values were generally overestimated. The effect of pKa shifts upon the binding is significant for one hirudin residue E58, but this appears to be due to a poor salt bridge with thrombin caused by crystal contacts. Electrostatic interaction between the acidic residues is unfavorable. However, analysis of experimental multiple mutation/single mutation data shows apparently negative interactions between these residues, from which it is concluded that structural changes can occur in the complex to relieve an unfavorable interaction when more than one acidic residue is mutated. In all cases, there is a loss in stability of the complex from mutations due to loss of favorable charge--charge interactions with thrombin, but this is largely compensated for by reduced unfavorable desolvation interactions, and by residual polar interactions in the Asn/Gln mutants.

  11. Resistivity Problems in Electrostatic Precipitation

    ERIC Educational Resources Information Center

    White, Harry J.

    1974-01-01

    The process of electrostatic precipitation has ever-increasing application in more efficient collection of fine particles from industrial air emissions. This article details a large number of new developments in the field. The emphasis is on high resistivity particles which are a common cause of poor precipitator performance. (LS)

  12. Defining protein electrostatic recognition processes

    NASA Astrophysics Data System (ADS)

    Getzoff, Elizabeth D.; Roberts, Victoria A.

    The objective is to elucidate the nature of electrostatic forces controlling protein recognition processes by using a tightly coupled computational and interactive computer graphics approach. The TURNIP program was developed to determine the most favorable precollision orientations for two molecules by systematic search of all orientations and evaluation of the resulting electrostatic interactions. TURNIP was applied to the transient interaction between two electron transfer metalloproteins, plastocyanin and cytochrome c. The results suggest that the productive electron-transfer complex involves interaction of the positive region of cytochrome c with the negative patch of plastocyanin, consistent with experimental data. Application of TURNIP to the formation of the stable complex between the HyHEL-5 antibody and its protein antigen lysozyme showed that long-distance electrostatic forces guide lysozyme toward the HyHEL-5 binding site, but do not fine tune its orientation. Determination of docked antigen/antibody complexes requires including steric as well as electrostatic interactions, as was done for the U10 mutant of the anti-phosphorylcholine antibody S107. The graphics program Flex, a convenient desktop workstation program for visualizing molecular dynamics and normal mode motions, was enhanced. Flex now has a user interface and was rewritten to use standard graphics libraries, so as to run on most desktop workstations.

  13. Electrostatic Precipitator (ESP) TRAINING MANUAL

    EPA Science Inventory

    The manual assists engineers in using a computer program, the ESPVI 4.0W, that models all elements of an electrostatic precipitator (ESP). The program is a product of the Electric Power Research Institute and runs in the Windows environment. Once an ESP is accurately modeled, the...

  14. Optimizing molecular electrostatic interactions: Binding affinity and specificity

    NASA Astrophysics Data System (ADS)

    Kangas, Erik

    The design of molecules that bind tightly and specifically to designated target molecules is an important goal in many fields of molecular science. While the shape of the molecule to be designed is a relatively well defined problem with an intuitive answer, determination of the distribution of electrostatic charge that it should have in order to possess high affinity and/or specificity for a target is a subtle problem involving a tradeoff between an unfavorable electrostatic desolvation penalty incurred due to the removal of solvent from the interacting surfaces of the reactants, and the generally favorable intermolecular interactions made in the bound state. In this thesis, a theoretical formalism based on a continuum electrostatic approximation is developed in which charge distributions leading to optimal affinity and/or high specificity may be obtained. Methods for obtaining these charge distributions are developed in detail and analytical solutions are obtained in several special cases (where the molecules are shaped as infinite membranes, spheres, and spheroids). Their existence and non-uniqueness are also shown, and it is proven that the resulting optimized electrostatic binding free energies are favorable (negative) in many cases of physical interest. Affinity and specificity optimization is then applied to the chorismate mutase family of enzymes, including the catalytic antibody 1F7. It is shown that affinity optimization can be used to suggest better molecular inhibitors and that specificity optimization can be used to help elucidate molecular function and possibly aid in the creation of improved haptens. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)

  15. Mathematical Modeling in Continuum Mechanics

    NASA Astrophysics Data System (ADS)

    Temam, Roger; Miranville, Alain

    2005-06-01

    Temam and Miranville present core topics within the general themes of fluid and solid mechanics. The brisk style allows the text to cover a wide range of topics including viscous flow, magnetohydrodynamics, atmospheric flows, shock equations, turbulence, nonlinear solid mechanics, solitons, and the nonlinear Schrödinger equation. This second edition will be a unique resource for those studying continuum mechanics at the advanced undergraduate and beginning graduate level whether in engineering, mathematics, physics or the applied sciences. Exercises and hints for solutions have been added to the majority of chapters, and the final part on solid mechanics has been substantially expanded. These additions have now made it appropriate for use as a textbook, but it also remains an ideal reference book for students and anyone interested in continuum mechanics.

  16. Electrostatic electron cyclotron harmonic instability near Ganymede

    NASA Astrophysics Data System (ADS)

    Tripathi, A. K.; Singhal, R. P.; Singh, K. P.; Singh, O. N.

    2014-08-01

    Jupiter's moon—Ganymede—is the largest satellite in our solar system. Galileo spacecraft made six close flybys to explore Ganymede. More information was acquired about particle population, magnetic field and plasma waves during these encounters. In this paper, our aim is to study the generation of electrostatic electron cyclotron harmonic (ECH) emissions in the vicinity of Ganymede using the observed particle data. The calculated ECH wave's growth rates are analyzed in the light of observations of plasma waves along the path of Galileo near Ganymede. Dispersion relation for electrostatic mode is solved to obtain the temporal growth rates. A new electron distribution function, fitted to distribution observed near Ganymede, is used in the calculations. A parametric study is performed to evaluate the effect of loss-cone angle and the ratio of plasma to gyro-frequency on growth rates. It is found that ECH waves growth rates generally decrease as the loss-cone angle is increased. However, the ratio plasma to gyro-frequency has almost no effect on the growth rates. These parameters vary considerably along the Galileo trajectory near Ganymede. This is the first study which relates the occurrence of ECH waves with the particle and magnetic field data in the vicinity of Ganymede. The study of ECH wave growth rate near Ganymede is important for the calculation of pitch angle scattering rates of low-energy electrons and their subsequent precipitation into the thin atmosphere of Ganymede producing ultraviolet emissions. Results of the present study may also be relevant for the upcoming JUNO and JUICE missions to Jupiter.

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

    PubMed

    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.

  18. Continuum representations of cellular solids

    NASA Astrophysics Data System (ADS)

    Neilsen, M. K.

    1993-09-01

    Cellular materials consist of interconnected struts or plates which form cells. The struts or plates are constructed from a variety of metals, polymers, ceramics, and wood products. Cellular materials are often used in impact limiters for shipping containers to protect the contents from accidental impact events. These materials exhibit a variety of complex behavior when subjected to crushing loads. This research focuses on the development of continuum representations of cellular solids that can be used in the finite element analysis of shipping container accidents. A significant portion of this work is the development of a new methodology to relate localized deformations to appropriate constitutive descriptions. This methodology provides the insight needed to select constitutive descriptions for cellular solids that capture the localized deformations that are observed experimentally. Constitutive relations are developed for two different cellular materials, aluminum honeycomb and polyurethane foam. These constitutive relations are based on plasticity and continuum damage theories. Plasticity is used to describe the permanent deformation exhibited by both aluminum honeycomb and polyurethane foam. Continuum damage is needed to capture the change in elastic parameters due to cracking of the polyurethane cell wall materials. The new constitutive description of polyurethane foam is implemented in both static and dynamic finite element codes, and analytical and numerical predictions are compared with available experimental data.

  19. Continuum representations of cellular solids

    SciTech Connect

    Neilsen, M.K.

    1993-09-01

    Cellular materials consist of interconnected struts or plates which form cells. The struts or plates are constructed from a variety of metals, polymers, ceramics and wood products. Cellular materials are often used in impact limiters for shipping containers to protect the contents from accidental impact events. These materials exhibit a variety of complex behavior when subjected to crushing loads. This research focuses on the development of continuum representations of cellular solids that can be used in the finite element analysis of shipping container accidents. A significant portion of this work is the development of a new methodology to relate localized deformations to appropriate constitutive descriptions. This methodology provides the insight needed to select constitutive descriptions for cellular solids that capture the localized deformations that are observed experimentally. Constitutive relations are developed for two different cellular materials, aluminum honeycomb and polyurethane foam. These constitutive relations are based on plasticity and continuum damage theories. Plasticity is used to describe the permanent deformation exhibited by both aluminum honeycomb and polyurethane foam. Continuum damage is needed to capture the change in elastic parameters due to cracking of the polyurethane cell wall materials. The new constitutive description of polyurethane foam is implemented in both static and dynamic finite element codes, and analytical and numerical predictions are compared with available experimental data.

  20. 77 FR 45367 - Continuum of Care Homeless Assistance Grant Application; Continuum of Care Application

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-31

    ... URBAN DEVELOPMENT Continuum of Care Homeless Assistance Grant Application; Continuum of Care Application... subject proposal. Pre-established communities, called Continuums of Care (CoC), will complete the Exhibit 1 of the Continuum of Care Homeless Assistance application which collects data about the...

  1. First-principles calculation of pKa for cocaine, nicotine, neurotransmitters, and anilines in aqueous solution.

    PubMed

    Lu, Haiting; Chen, Xi; Zhan, Chang-Guo

    2007-09-06

    The absolute pKa values of 24 representative amine compounds, including cocaine, nicotine, 10 neurotransmitters, and 12 anilines, in aqueous solution were calculated by performing first-principles electronic structure calculations that account for the solvent effects using four different solvation models, i.e., the surface and volume polarization for electrostatic interaction (SVPE) model, the standard polarizable continuum model (PCM), the integral equation formalism for the polarizable continuum model (IEFPCM), and the conductor-like screening solvation model (COSMO). Within the examined computational methods, the calculations using the SVPE model lead to the absolute pKa values with the smallest root-mean-square-deviation (rmsd) value (1.18). When the SVPE model was replaced by the PCM, IEFPCM, and COSMO, the rmsd value of the calculated absolute pKa values became 3.21, 2.72, and 3.08, respectively. All types of calculated pKa values linearly correlate with the experimental pKa values very well. With the empirical corrections using the linear correlation relationships, the theoretical pKa values are much closer to the corresponding experimental data and the rmsd values become 0.51-0.83. The smallest rmsd value (0.51) is also associated with the SVPE model. All of the results suggest that the first-principles electronic structure calculations using the SVPE model are a reliable approach to the pKa prediction for the amine compounds.

  2. Continuum-kinetic approach to sheath simulations

    NASA Astrophysics Data System (ADS)

    Cagas, Petr; Hakim, Ammar; Srinivasan, Bhuvana

    2016-10-01

    Simulations of sheaths are performed using a novel continuum-kinetic model with collisions including ionization/recombination. A discontinuous Galerkin method is used to directly solve the Boltzmann-Poisson system to obtain a particle distribution function. Direct discretization of the distribution function has advantages of being noise-free compared to particle-in-cell methods. The distribution function, which is available at each node of the configuration space, can be readily used to calculate the collision integrals in order to get ionization and recombination operators. Analytical models are used to obtain the cross-sections as a function of energy. Results will be presented incorporating surface physics with a classical sheath in Hall thruster-relevant geometry. This work was sponsored by the Air Force Office of Scientific Research under Grant Number FA9550-15-1-0193.

  3. Edge-relevant plasma simulations with the continuum code COGENT

    NASA Astrophysics Data System (ADS)

    Dorf, M.; Dorr, M.; Ghosh, D.; Hittinger, J.; Rognlien, T.; Cohen, R.; Lee, W.; Schwartz, P.

    2016-10-01

    We describe recent advances in cross-separatrix and other edge-relevant plasma simulations with COGENT, a continuum gyro-kinetic code being developed by the Edge Simulation Laboratory (ESL) collaboration. The distinguishing feature of the COGENT code is its high-order finite-volume discretization methods, which employ arbitrary mapped multiblock grid technology (nearly field-aligned on blocks) to handle the complexity of tokamak divertor geometry with high accuracy. This paper discusses the 4D (axisymmetric) electrostatic version of the code, and the presented topics include: (a) initial simulations with kinetic electrons and development of reduced fluid models; (b) development and application of implicit-explicit (IMEX) time integration schemes; and (c) conservative modeling of drift-waves and the universal instability. Work performed for USDOE, at LLNL under contract DE-AC52-07NA27344 and at LBNL under contract DE-AC02-05CH11231.

  4. Quantitative nanoscale electrostatics of viruses

    NASA Astrophysics Data System (ADS)

    Hernando-Pérez, M.; Cartagena-Rivera, A. X.; Lošdorfer Božič, A.; Carrillo, P. J. P.; San Martín, C.; Mateu, M. G.; Raman, A.; Podgornik, R.; de Pablo, P. J.

    2015-10-01

    Electrostatics is one of the fundamental driving forces of the interaction between biomolecules in solution. In particular, the recognition events between viruses and host cells are dominated by both specific and non-specific interactions and the electric charge of viral particles determines the electrostatic force component of the latter. Here we probe the charge of individual viruses in liquid milieu by measuring the electrostatic force between a viral particle and the Atomic Force Microscope tip. The force spectroscopy data of co-adsorbed φ29 bacteriophage proheads and mature virions, adenovirus and minute virus of mice capsids is utilized for obtaining the corresponding density of charge for each virus. The systematic differences of the density of charge between the viral particles are consistent with the theoretical predictions obtained from X-ray structural data. Our results show that the density of charge is a distinguishing characteristic of each virus, depending crucially on the nature of the viral capsid and the presence/absence of the genetic material.Electrostatics is one of the fundamental driving forces of the interaction between biomolecules in solution. In particular, the recognition events between viruses and host cells are dominated by both specific and non-specific interactions and the electric charge of viral particles determines the electrostatic force component of the latter. Here we probe the charge of individual viruses in liquid milieu by measuring the electrostatic force between a viral particle and the Atomic Force Microscope tip. The force spectroscopy data of co-adsorbed φ29 bacteriophage proheads and mature virions, adenovirus and minute virus of mice capsids is utilized for obtaining the corresponding density of charge for each virus. The systematic differences of the density of charge between the viral particles are consistent with the theoretical predictions obtained from X-ray structural data. Our results show that the density of

  5. The direct approach to gravitation and electrostatics method for periodic systems.

    PubMed

    Losilla, S A; Sundholm, D; Jusélius, J

    2010-01-14

    The direct approach to gravitation and electrostatics (DAGE) algorithm is an accurate, efficient, and flexible method for calculating electrostatic potentials. In this paper, we show that the algorithm can be easily extended to consider systems with many different kinds of periodicities, such as crystal lattices, surfaces, or wires. The accuracy and performance are nearly the same for periodic and aperiodic systems. The electrostatic potential for semiperiodic systems, namely defects in crystal lattices, can be obtained by combining periodic and aperiodic calculations. The method has been applied to an ionic model system mimicking NaCl, and to a corresponding covalent model system.

  6. Intermediate electrostatic field for the generalized elongation method.

    PubMed

    Liu, Kai; Korchowiec, Jacek; Aoki, Yuriko

    2015-05-18

    An intermediate electrostatic field is introduced to improve the accuracy of fragment-based quantum-chemical computational methods by including long-range polarizations of biomolecules. The point charge distribution of the intermediate field is generated by a charge sensitivity analysis that is parameterized for five different population analyses, namely, atoms-in-molecules, Hirshfeld, Mulliken, natural orbital, and Voronoi population analysis. Two model systems are chosen to demonstrate the performance of the generalized elongation method (ELG) combined with the intermediate electrostatic field. The calculations are performed for the STO-3G, 6-31G, and 6-31G(d) basis sets and compared with reference Hartree-Fock calculations. It is shown that the error in the total energy is reduced by one order of magnitude, independently of the population analyses used. This demonstrates the importance of long-range polarization in electronic-structure calculations by fragmentation techniques.

  7. Electrostatic effects on proton coupled electron transfer in oxomanganese complexes inspired by the oxygen-evolving complex of photosystem II.

    PubMed

    Amin, Muhamed; Vogt, Leslie; Vassiliev, Serguei; Rivalta, Ivan; Sultan, Mohammad M; Bruce, Doug; Brudvig, Gary W; Batista, Victor S; Gunner, M R

    2013-05-23

    The influence of electrostatic interactions on the free energy of proton coupled electron transfer in biomimetic oxomanganese complexes inspired by the oxygen-evolving complex (OEC) of photosystem II (PSII) are investigated. The reported study introduces an enhanced multiconformer continuum electrostatics (MCCE) model, parametrized at the density functional theory (DFT) level with a classical valence model for the oxomanganese core. The calculated pKa's and oxidation midpoint potentials (E(m)'s) match experimental values for eight complexes, indicating that purely electrostatic contributions account for most of the observed couplings between deprotonation and oxidation state transitions. We focus on pKa's of terminal water ligands in [Mn(II/III)(H2O)6](2+/3+) (1), [Mn(III)(P)(H2O)2](3-) (2, P = 5,10,15,20-tetrakis(2,6-dichloro-3-sulfonatophenyl)porphyrinato), [Mn2(IV,IV)(μ-O)2(terpy)2(H2O)2](4+) (3, terpy = 2,2':6',2″-terpyridine), and [Mn3(IV,IV,IV)(μ-O)4(phen)4(H2O)2](4+) (4, phen = 1,10-phenanthroline) and the pKa's of μ-oxo bridges and Mn E(m)'s in [Mn2(μ-O)2(bpy)4] (5, bpy = 2,2'-bipyridyl), [Mn2(μ-O)2(salpn)2] (6, salpn = N,N'-bis(salicylidene)-1,3-propanediamine), [Mn2(μ-O)2(3,5-di(Cl)-salpn)2] (7), and [Mn2(μ-O)2(3,5-di(NO2)-salpn)2] (8). The analysis of complexes 6-8 highlights the strong coupling between electron and proton transfers, with any Mn oxidation lowering the pKa of an oxo bridge by 10.5 ± 0.9 pH units. The model also accounts for changes in the E(m)'s by ligand substituents, such as found in complexes 6-8, due to the electron withdrawing Cl (7) and NO2 (8). The reported study provides the foundation for analysis of electrostatic effects in other oxomanganese complexes and metalloenzymes, where proton coupled electron transfer plays a fundamental role in redox-leveling mechanisms.

  8. Asteroid electrostatic instrumentation and modelling

    NASA Astrophysics Data System (ADS)

    Aplin, K. L.; Bowles, N. E.; Urbak, E.; Keane, D.; Sawyer, E. C.

    2011-06-01

    Asteroid surface material is expected to become photoelectrically charged, and is likely to be transported through electrostatic levitation. Understanding any movement of the surface material is relevant to proposed space missions to return samples to Earth for detailed isotopic analysis. Motivated by preparations for the Marco Polo sample return mission, we present electrostatic modelling for a real asteroid, Itokawa, for which detailed shape information is available, and verify that charging effects are likely to be significant at the terminator and at the edges of shadow regions for the Marco Polo baseline asteroid, 1999JU3. We also describe the Asteroid Charge Experiment electric field instrumentation intended for Marco Polo. Finally, we find that the differing asteroid and spacecraft potentials on landing could perturb sample collection for the short landing time of 20min that is currently planned.

  9. Electrostatic Gating of Ultrathin Films

    NASA Astrophysics Data System (ADS)

    Goldman, A. M.

    2014-07-01

    Electrostatic gating of ultrathin films can be used to modify electronic and magnetic properties of materials by effecting controlled alterations of carrier concentration while, in principle, not changing the level of disorder. As such, electrostatic gating can facilitate the development of novel devices and can serve as a means of exploring the fundamental properties of materials in a manner far simpler than is possible with the conventional approach of chemical doping. The entire phase diagram of a compound can be traversed by changing the gate voltage. In this review, we survey results involving conventional field effect devices as well as more recent progress, which has involved structures that rely on electrochemical configurations such as electric double-layer transistors. We emphasize progress involving thin films of oxide materials such as high-temperature superconductors, magnetic oxides, and oxides that undergo metal-insulator transitions.

  10. Closed loop electrostatic levitation system

    NASA Technical Reports Server (NTRS)

    Rhim, W. K.; Saffren, M. M.; Elleman, D. D. (Inventor)

    1985-01-01

    An electrostatic levitation system is described, which can closely control the position of objects of appreciable size. A plurality of electrodes surround the desired position of an electrostatically charged object, the position of the objects is monitored, and the voltages applied to the electrodes are varied to hold the object at a desired position. In one system, the object is suspended above a plate-like electrode which has a concave upper face to urge the object toward the vertical axis of the curved plate. An upper electrode that is also curved can be positioned above the object, to assure curvature of the field at any height above the lower plate. In another system, four spherical electrodes are positioned at the points of a tetrahedron, and the voltages applied to the electrodes are varied in accordance with the object position as detected by two sensors.

  11. Electrostatic interactions in molecular materials

    NASA Astrophysics Data System (ADS)

    Painelli, Anna; Terenziani, Francesca

    2004-03-01

    Non-additive collective behavior appears in molecular materials as a result of intermolecular interactions. We present a model for interacting polar and polarizable molecules that applies to different supramolecular architectures of donor-π-acceptor molecules. We follow a bottom-up modeling strategy: the detailed analysis of spectroscopic data of solvated molecules leads to the definition of a simple two-state model for the molecular units. Classical electrostatic interactions are then introduced to model molecular clusters. The molecular properties are strickingly affected by supramolecular interactions, as demonstrated by spectroscopic studies. Brand new phenomena, like phase transitions and multielectron transfer, with no counterpart at the molecular level are observed as direct consequences of electrostatic intermolecular interactions.

  12. Electrostatic Spraying With Conductive Liquids

    NASA Technical Reports Server (NTRS)

    Kosmo, Joseph J.; Dawn, Frederic S.; Erlandson, Robert E.; Atkins, Loren E.

    1989-01-01

    Thin, uniform polymer coatings applied in water base normally impossible to charge. Electrostatic sprayer modified so applies coatings suspended or dissolved in electrically conductive liquids. Nozzle and gun constructed of nonconductive molded plastic. Liquid passageway made long enough electrical leakage through it low. Coaxial hose for liquid built of polytetrafluoroethylene tube, insulating sleeve, and polyurethane jacket. Sprayer provided with insulated seal at gun-to-hose connection, nonconductive airhose, pressure tank electrically isolated from ground, and special nozzle electrode. Supply of atomizing air reduced so particle momentum controlled by electrostatic field more effectively. Developed to apply water-base polyurethane coating to woven, shaped polyester fabric. Coating provides pressure seal for fabric, which is part of spacesuit. Also useful for applying waterproof, decorative, or protective coatings to fabrics for use on Earth.

  13. Turbulence in electrostatic ion acoustic shocks

    NASA Technical Reports Server (NTRS)

    Means, R. W.; Coroniti, F. V.; Wong, A. Y.; White, R. B.

    1973-01-01

    Three types of collisionless electrostatic ion acoustic shocks are investigated using a double plasma (DP) device: (1) laminar shocks; (2) small amplitude turbulent shocks in which the turbulence is confined to be upstream of the shock potential jump; and (3) large amplitude turbulent shocks in which the wave turbulence occurs throughout the shock transition. The wave turbulence is generated by ions which are reflected from the shock potential; linear theory spatial growth increments agree with experimental values. The experimental relationship between the shock Mach number and the shock potential is shown to be inconsistent with theoretical shock models which assume that the electrons are isothermal. Theoretical calculations which assume a trapped electron equation of a state and a turbulently flattened velocity distrubution function for the reflected ions yields a Mach number vs potential relationship in agreement with experiment.

  14. Electrostatic generator/motor configurations

    DOEpatents

    Post, Richard F

    2014-02-04

    Electrostatic generators/motors designs are provided that generally may include a first cylindrical stator centered about a longitudinal axis; a second cylindrical stator centered about the axis, a first cylindrical rotor centered about the axis and located between the first cylindrical stator and the second cylindrical stator. The first cylindrical stator, the second cylindrical stator and the first cylindrical rotor may be concentrically aligned. A magnetic field having field lines about parallel with the longitudinal axis is provided.

  15. Electrostatic forces for personnel restraints

    NASA Technical Reports Server (NTRS)

    Ashby, N.; Ciciora, J.; Gardner, R.; Porter, K.

    1977-01-01

    The feasibility of utilizing electrostatic forces for personnel retention devices on exterior spacecraft surfaces was analyzed. The investigation covered: (1) determination of the state of the art; (2) analysis of potential adhesion surfaces; (3) safety considerations for personnel; (4) electromagnetic force field determination and its effect on spacecraft instrumentation; and (5) proposed advances to current technology based on documentation review, analyses, and experimental test data.

  16. Defining Protein Electrostatic Recognition Processes

    DTIC Science & Technology

    1992-01-01

    electrostatic Interactions, as we have done for the U10 mutant of the antl- phosphorylcholine antibody S107. We have enhanced the graphics program Fla, a...10486 9393-10486 phosphorylcholine -binding antibody S107, (Chign et al., 1989; Behar et al., 1989). This mutant antibody results from a single-site...mutation of Asp 101 to Ala, over 9 A distant from the antigen binding site, which results in a complete loss of phosphorylcholine binding activity. A

  17. Monitoring Mars for Electrostatic Disturbances

    NASA Technical Reports Server (NTRS)

    Compton, D.

    2011-01-01

    The DSN radio telescope DSS-13 was used to monitor Mars for electrostatic discharges from 17 February to 11 April, 2010, and from 19 April to 4 May, 2011, over a total of 72 sessions. Of these sessions, few showed noteworthy results and no outstanding electrostatic disturbances were observed on Mars from analyzing the kurtosis of radio emission from Mars. Electrostatic discharges on mars were originally detected in June of 2006 by Ruf et al. using DSS-13. he kurtosis (normalized fourth moment of the electrical field strength) is sensitive to non-thermal radiation. Two frequencies bands, either 2.4 and 8.4 GHz or 8.4 and 32 GHz were used. The non-thermal radiation spectrum should have peaks at the lowest three modes of the theoretical Schumann Resonances of Mars. The telescope was pointed away from Mars every 5 minutes for 45 seconds to confirm if Mars was indeed the sources of any events. It was shown that by including a down-link signal in one channel and by observing when the kurtosis changed as the telescope was pointed away from the source that the procedure can monitor Mars without the need of extra equipment monitoring a control source.

  18. KSC Electrostatic Discharge (ESD) Issues

    NASA Technical Reports Server (NTRS)

    Buhler, Charles

    2008-01-01

    Discussion of key electrostatic issues that have arisen during the past few years at KSC that the Electrostatics Laboratory has studied. The lab has studied in depth the Space Shuttle's Thermal Control System Blankets, the International Space Station Thermal Blanket, the Pan/Tilt Camera Blankets, the Kapton Purge Barrier Curtain, the Aclar Purge Barrier Curtain, the Thrust Vector Controller Blankets, the Tyvek Reaction Control System covers, the AID-PAK and FLU-9 pyro inflatable devices, the Velostat Solid Rocket Booster mats, and the SCAPE suits. In many cases these materials are insulating meaning that they might be a source of unsafe levels of electrostatic discharge (ESD). For each, the lab provided in-depth testing of each material within its current configuration to ensure that it does not cause an ESD concern that may violate the safety of the astronauts, the workers and equipment for NASA. For example the lab provides unique solutions and testing such as Spark Incendivity Testing that checks whether a material is capable of generating a spark strong enough to ignite a flammable gas. The lab makes recommendations to changes in specifications, procedures, and material if necessary. The lab also consults with a variety of non-safety related ESD issues for the agency.

  19. Aspects of electrostatics in BTZ geometries

    NASA Astrophysics Data System (ADS)

    Herrera, Y.; Hurovich, V.; Santillán, O.; Simeone, C.

    2015-10-01

    In the present paper the electrostatics of charges in nonrotating BTZ black hole and wormhole spacetimes is studied. Our attention is focused on the self-force of a point charge in the geometry, for which a regularization prescription based on the Haddamard Green function is employed. The differences between the self-force in both cases is a theoretical experiment for distinguishing both geometries, which otherwise are locally indistinguishable. This idea was applied before to four and higher-dimensional black holes by the present and other authors. However, the particularities of the BTZ geometry makes the analysis considerable more complicated than those. First, the BTZ spacetimes are not asymptotically flat but instead asymptotically AdS. In addition, the relative distance d (r ,r +1 ) between two particles located at a radius r and r +1 in the geometry tends to zero when r →∞. This behavior, which is radically different in a flat geometry, changes the analysis of the asymptotic conditions for the electrostatic field. The other problem is that there exist several regularization methods other than the one we are employing, and there does not exist a proof in three dimensions that they are equivalent. However, we focus on the Haddamard method and obtain an expression for the hypothetical self-force in series, and the resulting expansion is convergent to the real solution. We suspect that the convergence is not uniform, and furthermore there are no summation formulas at our disposal. It appears, for points that are far away from the black hole the calculation of the Haddamard self-force requires higher-order summation. These subtleties are carefully analyzed in the paper, and it is shown that they lead to severe problems when calculating the Haddamard self-force for asymptotic points in the geometry.

  20. Analogies between continuum dislocation theory, continuum mechanics and fluid mechanics

    NASA Astrophysics Data System (ADS)

    Silbermann, C. B.; Ihlemann, J.

    2017-03-01

    Continuum Dislocation Theory (CDT) relates gradients of plastic deformation in crystals with the presence of geometrically necessary dislocations. Interestingly, CDT shows striking analogies to other branches of continuum mechanics. The present contribution demonstrates this on two essential kinematical quantities which reflect tensorial dislocation properties: the (resultant) Burgers vector and the dislocation density tensor. First, the limiting process for the (resultant) Burgers vector from an integral to a local quantity is performed analogously to the limiting process from the force vector to the traction vector. By evaluating the balance of forces on a tetrahedral volume element, Cauchy found his famous formula relating traction vector and stress tensor. It is shown how this procedure may be adopted to a continuously dislocated tetrahedron. Here, the conservation of Burger’s vector implicates the introduction of the dislocation density tensor. Second, analogies between the plastic flow of a continuously dislocated solid and the liquid flow of a fluid are highlighted: the resultant Burgers vector of a dislocation ensemble plays a similar role as the (resultant) circulation of a vortex tube. Moreover, both vortices within flowing fluids and dislocations within deforming solids induce discontinuities in the velocity field and the plastic distortion field, respectively. Beyond the analogies, some peculiar properties of the dislocation density tensor are presented as well.

  1. Continuum Gyrokinetic Edge New Technology

    SciTech Connect

    Dorr, M. R.; Hittinger, J. A.; Dorf, M.; Cohen, R.; Ghosh, D.; Lee, W.; Reynolds, C.

    2016-05-02

    COGENT is a simulation code that models the plasma evolution in the edge region of a tokamak fusion reactor, from the open field line scrape-off layer, across the separatrix, and into the core. The model is based on the 4D gyrokinetic closure of the kinetic equations for a plasma coupled to an electrostatic potential field. The background magnetic field is prescribed either analytically or generated from experimental data, and the grid is aligned with magnetic flux surfaces. Multiple collision operator options are provided, from Krook to fully nonlinear Fokker-Planck.

  2. Roles Played by Electrostatic Waves in Producing Radio Emissions

    NASA Technical Reports Server (NTRS)

    Cairns, Iver H.

    2000-01-01

    Processes in which electromagnetic radiation is produced directly or indirectly via intermediate waves are reviewed. It is shown that strict theoretical constraints exist for electrons to produce nonthermal levels of radiation directly by the Cerenkov or cyclotron resonances. In contrast, indirect emission processes in which intermediary plasma waves are converted into radiation are often favored on general and specific grounds. Four classes of mechanisms involving the conversion of electrostatic waves into radiation are linear mode conversion, hybrid linear/nonlinear mechanisms, nonlinear wave-wave and wave-particle processes, and radiation from localized wave packets. These processes are reviewed theoretically and observational evidence summarized for their occurrence. Strong evidence exists that specific nonlinear wave processes and mode conversion can explain quantitatively phenomena involving type III solar radio bursts and ionospheric emissions. On the other hand, no convincing evidence exists that magnetospheric continuum radiation is produced by mode conversion instead of nonlinear wave processes. Further research on these processes is needed.

  3. Disease management: a continuum approach.

    PubMed

    Harvey, N; DePue, D M

    1997-06-01

    Disease management is a comprehensive, integrated approach to managing the health of populations through the use of disease-specific standards and protocols and population segmentation. It has been increasing in popularity among integrated delivery systems (IDSs) and payers alike as a way to respond to competitive pressures and to shift care delivery from inpatient to alternative care sites. To successfully implement disease-management programs, IDSs must develop an organizational mind-set that stresses information-driven, evidence-based standards of care that are adhered to across a tightly integrated continuum of care.

  4. Predicted continuum spectra of type II supernovae - LTE results

    NASA Technical Reports Server (NTRS)

    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.

  5. Discrete and Continuum Elastic Properties of Interfaces.

    NASA Astrophysics Data System (ADS)

    Alber, Elliott Solomon

    The microstructure of defects in solids, e.g. interfaces, is heterogeneous and, consequently, so are the elastic properties. The complete anisotropic fourth-order tensors of both the discrete and the effective elastic moduli are defined in the interfacial region. To examine the meaning of discrete elastic constants, (i) a piecewise-continuous medium is considered where individual phases occupy the Voronoi polyhedra and have the elastic moduli associated with individual atoms, and (ii) the relationship between natural vibrations of the discrete systems and continuum waves is explored. Questions of local energy changes and stability are addressed in terms of continuum properties of the moduli, particularly positive definiteness and strong ellipticity. Comparisons between the atomistic results (exact effective moduli) and those for the continuum analog (bounds) establish the validity of the definition of elastic properties for heterogeneous structures at atomic scales and lead to criteria to assess the stability of a given microstructure. Homogenization of interfacial properties gives heterogeneous transition zone (or interphase) model. Interface phenomena in macrosystems (composites) and microsystems (grain boundaries) is explained by inner layer conditions between homogeneous bulk regions. Dynamical membrane and spring models of the imperfect interfaces are shown to be limiting models (similar to Reuss and Voigt bounding approximations in multiphase composite mechanics) for asymptotic expansions of stress and strain fields, respectively. Asymptotic expansion of both fields (in terms of small parameter h -thickness of the layer) produces mixed-type, exact approximation of the first order in h. Derived models of imperfect interface are used for investigation of interface waves in anisotropic bicrystals and for comparison with corresponding acoustical modes in phonon spectra. Localized interface waves are explained as general inhomogeneous plane waves in subsonic

  6. Discrete and continuum elastic properties of interfaces

    NASA Astrophysics Data System (ADS)

    Alber, Elliott Solomon

    1993-06-01

    The microstructure of defects in solids, e.g. interfaces, is heterogeneous and, consequently, so are the elastic properties. The complete anisotropic fourth-order tensors of both the discrete and the effective elastic moduli are defined in the interfacial region. To examine the meaning of discrete elastic constants, (1) a piecewise-continuous medium is considered where individual phases occupy the Voronoi polyhedra and have the elastic moduli associated with individual atoms, and (2) the relationship between natural vibrations of the discrete systems and continuum waves is explored. Questions of local energy changes and stability are addressed in terms of continuum properties of the moduli, particularly positive definiteness and strong ellipticity. Comparisons between the atomistic results (exact effective moduli) and those for the continuum analog (bounds) establish the validity of the definition of elastic properties for heterogeneous structures at atomic scales and lead to criteria to assess the stability of a given microstructure. Homogenization of interfacial properties gives heterogeneous transition zone (or interphase) model. Interface phenomena in macrosystems (composites) and microsystems (grain boundaries) is explained by inner layer conditions between homogeneous bulk regions. Dynamical membrane and spring models of the imperfect interfaces are shown to be limiting models (similar to Reuss and Voigt bounding approximations in multiphase composite mechanics) for asymptotic expansions of stress and strain fields, respectively. Asymptotic expansion of both fields (in terms of small parameter h-thickness of the layer) produces mixed-type, exact approximation of the first order in h. Derived models of imperfect interface are used for investigation of interface waves in anisotropic bicrystals and for comparison with corresponding acoustical modes in phonon spectra. Localized interface waves are explained as general inhomogeneous plane waves in subsonic

  7. Exploring continuum structures with a pseudo-state basis

    SciTech Connect

    Lay, J. A.; Moro, A. M.; Arias, J. M.; Gomez-Camacho, J.

    2010-08-15

    The ability of a recently developed square-integrable discrete basis to represent the properties of the continuum of a two-body system is investigated. The basis is obtained performing a simple analytic local scale transformation to the harmonic oscillator basis. Scattering phase-shifts and the electric transition probabilities B(E1) and B(E2) have been evaluated for several potentials using the proposed basis. Both quantities are found to be in excellent agreement with the exact values calculated from the true scattering states. The basis has been applied to describe the projectile continuum in the {sup 6}He scattering by {sup 12}C and {sup 208}Pb targets at 240 MeV/nucleon and the {sup 11}Be scattering by {sup 12}C at 67 MeV/nucleon. The calculated breakup differential cross sections are found to be in very good agreement with the available experimental data for these reactions.

  8. Nonlocal models in continuum mechanics

    SciTech Connect

    Johnson, N.L.; Phan-Thien, N.

    1993-09-01

    The recent appearance of nonlocal methods is examined in the light of traditional continuum mechanics. A comparison of nonlocal approaches in the fields of solid and fluid mechanics reveals that no consistent definition of a nonlocal theory has been used. We suggest a definition based on the violation of the principle of local action in continuum mechanics. From the consideration of the implications of a nonlocal theory based on this definition, we conclude that constitutive relations with nonlocal terms can confuse the traditional separation of the roles between conservation laws and constitutive relations. The diversity of motivations for the nonlocal approaches are presented, resulting primarily from deficiencies in numerical solutions to practical problems. To illustrate these concepts, the history of nonlocal terms in the field of viscoelastic fluids is reviewed. A specific example of a viscoelastic constitutive relation that contains a stress diffusion term is applied to a simple shear flow and found not to be a physical description of any known fluid. We conclude by listing questions that should be asked of nonlocal approaches.

  9. 3D RISM theory with fast reciprocal-space electrostatics

    SciTech Connect

    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.

  10. Observation of weak HF electrostatic turbulence in the auroral ionosphere

    NASA Astrophysics Data System (ADS)

    Pottelette, R.; Illiano, J. M.

    1982-07-01

    A numerical calculation of the cross spectrum of random signals received by two small antennas that were immersed in a two-component magnetoplasma has been conducted, for the case of a plasma model consisting of a cool and a warm component. The data were compiled by the HF electrostatic wave detection experiment of the Porcupine F3 rocket. A linear calculation of the natural electrostatic emissions detected around the electron gyrofrequency three-halves harmonic and around the upper hybrid frequency shows that their amplitudes are above the plasma thermal noise level. It is noted that the low energy precipitating suprathermal electrons present are highly anisotropic and enhance the three-halves electron gyrofrequency noise, although the electron distribution function remains stable and the most intense emissions are observed around the upper hybrid frequency.

  11. Continuum estimates of rotational dielectric friction and polar solvation

    SciTech Connect

    Maroncelli, M.

    1997-01-01

    Dynamical solvation data recently obtained with the probe solute coumarin 153 are used to test the reliability of dielectric continuum models for estimating dielectric friction effects. In particular, the predictions of the Nee{endash}Zwanzig theory of rotational dielectric friction are examined in some detail. The analysis undertaken here uncovers an error made in virtually all previous applications of the Nee{endash}Zwanzig formalism. The error involves neglect of the solvent{close_quote}s electronic polarizability when calculating dielectric friction constants. In highly polar solvents the effect of this neglect is shown to be minor, so that the results of past studies should not be appreciably altered. However, in weakly polar and especially in nondipolar solvents, the proper inclusion of electronic polarizability terms is essential. The equivalence between the Nee{endash}Zwanzig theory of dielectric friction and more general continuum treatments of polar solvation dynamics is also demonstrated. This equivalence enables the use of solvation data to test the reliability of the Nee{endash}Zwanzig description of electrical interactions between a solute and solvent that form the core of this and related continuum theories of dielectric friction. Comparisons to experimental data show that, with the important exception of nondipolar solvents, such continuum treatments provide reasonably accurate ({plus_minus}40{percent}) predictors of time-dependent solvation and/or dielectric friction. {copyright} {ital 1997 American Institute of Physics.}

  12. Modes of interconnected lattice trusses using continuum models, part 1

    NASA Technical Reports Server (NTRS)

    Balakrishnan, A. V.

    1991-01-01

    This represents a continuing systematic attempt to explore the use of continuum models--in contrast to the Finite Element Models currently universally in use--to develop feedback control laws for stability enhancement of structures, particularly large structures, for deployment in space. We shall show that for the control objective, continuum models do offer unique advantages. It must be admitted of course that developing continuum models for arbitrary structures is no easy task. In this paper we take advantage of the special nature of current Large Space Structures--typified by the NASA-LaRC Evolutionary Model which will be our main concern--which consists of interconnected orthogonal lattice trusses each with identical bays. Using an equivalent one-dimensional Timoshenko beam model, we develop an almost complete continuum model for the evolutionary structure. We do this in stages, beginning only with the main bus as flexible and then going on to make all the appendages also flexible-except for the antenna structure. Based on these models we proceed to develop formulas for mode frequencies and shapes. These are shown to be the roots of the determinant of a matrix of small dimension compared with mode calculations using Finite Element Models, even though the matrix involves transcendental functions. The formulas allow us to study asymptotic properties of the modes and how they evolve as we increase the number of bodies which are treated as flexible. The asymptotics, in fact, become simpler.

  13. Continuum channel coupling of shape resonances in N2

    NASA Astrophysics Data System (ADS)

    Poliakoff, E. D.; Kakar, Sandeep; Rosenberg, R. A.

    1992-02-01

    We have measured vibrational branching ratios for 2σ-1u photoionization of N2 in an effort to elucidate fundamental aspects of continuum channel coupling. Calculations have shown that photoejection of a 2σu electron from N2 should be influenced by a shape resonance in the 3σg →ɛσu photoionization channel and that this continuum channel coupling can result in deviations from Franck-Condon behavior for the resulting N+2(B 2Σ+u) ion. In the present study, the N2 molecules are ionized by monochromatic synchrotron radiation (25continuum coupling between the 2σ-1u and 3σ-1g ionization channels. However, our results exhibit significant discrepancies with theory. The areas of agreement and disagreement suggest useful avenues of further study to clarify the nature of continuum channel coupling in molecular photoionization.

  14. THE SOLAR X-RAY CONTINUUM MEASURED BY RESIK

    SciTech Connect

    Phillips, K. J. H.; Sylwester, J.; Sylwester, B.; Kuznetsov, V. D. E-mail: js@cbk.pan.wroc.p E-mail: kvd@izmiran.r

    2010-03-01

    The solar X-ray continuum emission at five wavelengths between 3.495 A and 4.220 A for 19 flares in a 7-month period in 2002-2003 was observed by the RESIK (REntgenovsky Spektrometr s Izognutymi Kristalami) crystal spectrometer on CORONAS-F. In this wavelength region, free-free and free-bound emissions have comparable fluxes. With a pulse-height analyzer having settings close to optimal, the fluorescence background was removed so that RESIK measured true solar continuum in these bands with an uncertainty in the absolute calibration of +-20%. With an isothermal assumption, and temperature and emission measure derived from the ratio of the two GOES channels, the observed continuum emission normalized to an emission measure of 10{sup 48} cm{sup -3} was compared with theoretical continua using the CHIANTI atomic code. The accuracy of the RESIK measurements allows photospheric and coronal abundance sets, important for the free-bound continuum, to be discriminated. It is found that there is agreement to about 25% of the measured continua with those calculated from CHIANTI assuming coronal abundances in which Mg, Si, and Fe abundances are four times photospheric.

  15. Electrostatic particle collection in vacuum

    NASA Astrophysics Data System (ADS)

    Afshar-Mohajer, Nima; Damit, Brian; Wu, Chang-Yu; Sorloaica-Hickman, Nicoleta

    2011-09-01

    Lunar grains accumulate charges due to solar-based ionizing radiations, and the repelling action of like-charged particles causes the levitation of lunar dust. The lunar dust deposit on sensitive and costly surfaces of investigative equipment is a serious concern in lunar explorations. Inspired by electrostatic precipitators (ESPs), the Electrostatic Lunar Dust Collector (ELDC) was proposed for collecting already charged lunar dust particles to prevent the lunar dust threat. As the conditions for terrestrial counterparts are not valid in the lunar environment, equations developed for terrestrial devices yield incorrect predictions in lunar application. Hence, a mathematical model was developed for the ELDC operating in vacuum to determine its collection efficiency. The ratios of electrical energy over potential energy, kinetic energy over potential energy and the ratio of ELDC dimensions were identified to be the key dimensionless parameters. Sensitivity analyses of the relevant parameters showed that depending on ELDC orientation, smaller particles would be collected more easily at vertical orientation, whereas larger particles were easier to collect in a horizontal ELDC configuration. In the worst case scenario, the electrostatic field needed to be 10 times stronger in the vertical mode in order to adequately collect larger particles. The collection efficiency was very sensitive to surface potential of lunar dust and it reached the maximum when surface potential was between 30 and 120 V. Except for regions of the lunar day side with surface potential close to zero, providing 1 kV ( E = 20 kV m -1) with the ELDC was more than enough for collecting all the particles in the most critical orientation. The needed field strength was about 4000 times less than that for repelling 1-μm size particles already settled on the surfaces. The analysis shows that the ELDC offers a viable solution for lunar dust control due to its effectiveness, ease of cleaning and low voltage

  16. Electrostatic effects in collagen fibrillization

    NASA Astrophysics Data System (ADS)

    Morozova, Svetlana; Muthukumar, Murugappan

    2014-03-01

    Using light scattering and AFM techniques, we have measured the kinetics of fibrillization of collagen (pertinent to the vitreous of human eye) as a function of pH and ionic strength. At higher and lower pH, collagen triple-peptides remain stable in solution without fibrillization. At neutral pH, the fibrillization occurs and its growth kinetics is slowed upon either an increase in ionic strength or a decrease in temperature. We present a model, based on polymer crystallization theory, to describe the observed electrostatic nature of collagen assembly.

  17. Langevin-Poisson-EQT: A dipolar solvent based quasi-continuum approach for electric double layers

    NASA Astrophysics Data System (ADS)

    Mashayak, S. Y.; Aluru, N. R.

    2017-01-01

    Water is a highly polar solvent. As a result, electrostatic interactions of interfacial water molecules play a dominant role in determining the distribution of ions in electric double layers (EDLs). Near a surface, an inhomogeneous and anisotropic arrangement of water molecules gives rise to pronounced variations in the electrostatic and hydration energies of ions. Therefore, a detailed description of the structural and dielectric properties of water is important to study EDLs. However, most theoretical models ignore the molecular effects of water and treat water as a background continuum with a uniform dielectric permittivity. Explicit consideration of water polarization and hydration of ions is both theoretically and numerically challenging. In this work, we present an empirical potential-based quasi-continuum theory (EQT) for EDL, which incorporates the polarization and hydration effects of water explicitly. In EQT, water molecules are modeled as Langevin point dipoles and a point dipole based coarse-grained model for water is developed systematically. The space dependence of the dielectric permittivity of water is included in the Poisson equation to compute the electrostatic potential. In addition, to reproduce hydration of ions, ion-water coarse-grained potentials are developed. We demonstrate the EQT framework for EDL by simulating NaCl aqueous electrolyte confined inside slit-like capacitor channels at various ion concentrations and surface charge densities. We show that the ion and water density predictions from EQT agree well with the reference molecular dynamics simulations.

  18. Electrostatic attraction between ionic reverse micelles with dielectric discontinuity

    NASA Astrophysics Data System (ADS)

    Chen, Peilong

    2002-11-01

    We have calculated the thermally-averaged electrostatic attractive potential between two spherical ionic reverse micelles in a medium of a different dielectric constant. Specifically the attractions between the charge density fluctuations in one micelle and interface polarizations on the other are computed. For water-in-oil microemulsions, we find that these contributions completely overwhelm those from correlated fluctuations in charge densities between two micelles.

  19. Predictions for Electrostatic Dust Levitation about Bennu's Equator

    NASA Astrophysics Data System (ADS)

    Hartzell, C. M.; Zimmerman, M. I.

    2015-12-01

    Electrostatic dust levitation was first hypothesized to occur on the Moon due to observations of Lunar Horizon Glow and results from the Apollo 17 LEAM instrument. Due to their weaker gravitational acceleration and similar plasma environment, electrostatic dust motion was also hypothesized to occur on asteroids. There is still no conclusive evidence, however, that electrostatic levitation occurs on either asteroids or the Moon. The OSIRIS-REx mission will visit the asteroid Bennu in 2018-2019. We have numerically modeled the plasma environment around the equator of Bennu, with the asteroid assumed to have a circular equatorial cross section. Our plasma model presents a significant improvement over previous semi-analytical models as it can seamlessly capture the transition from day-side plasma sheath to night-side plasma wake. Using the plasma model and assuming a uniform density for gravity calculations, we identify the altitudes, longitudinal locations, and the associated grain sizes at which electrostatic levitation is expected to occur. Our predictions of dust levitation at Bennu will enable assessments of the observability of levitating dust during the OSIRIS-REx mission and guide any observations.

  20. Conductivity of continuum percolating systems

    NASA Astrophysics Data System (ADS)

    Stenull, Olaf; Janssen, Hans-Karl

    2001-11-01

    We study the conductivity of a class of disordered continuum systems represented by the Swiss-cheese model, where the conducting medium is the space between randomly placed spherical holes, near the percolation threshold. This model can be mapped onto a bond percolation model where the conductance σ of randomly occupied bonds is drawn from a probability distribution of the form σ-a. Employing the methods of renormalized field theory we show to arbitrary order in ɛ expansion that the critical conductivity exponent of the Swiss-cheese model is given by tSC(a)=(d-2)ν+max[φ,(1-a)-1], where d is the spatial dimension and ν and φ denote the critical exponents for the percolation correlation length and resistance, respectively. Our result confirms a conjecture that is based on the ``nodes, links, and blobs'' picture of percolation clusters.

  1. Bound states in the continuum

    NASA Astrophysics Data System (ADS)

    Hsu, Chia Wei; Zhen, Bo; Stone, A. Douglas; Joannopoulos, John D.; Soljačić, Marin

    2016-09-01

    Bound states in the continuum (BICs) are waves that remain localized even though they coexist with a continuous spectrum of radiating waves that can carry energy away. Their very existence defies conventional wisdom. Although BICs were first proposed in quantum mechanics, they are a general wave phenomenon and have since been identified in electromagnetic waves, acoustic waves in air, water waves and elastic waves in solids. These states have been studied in a wide range of material systems, such as piezoelectric materials, dielectric photonic crystals, optical waveguides and fibres, quantum dots, graphene and topological insulators. In this Review, we describe recent developments in this field with an emphasis on the physical mechanisms that lead to BICs across seemingly very different materials and types of waves. We also discuss experimental realizations, existing applications and directions for future work.

  2. Dementia: Continuum or Distinct Entity?

    PubMed Central

    Walters, Glenn D.

    2009-01-01

    The latent structure of dementia was examined in a group of 10,775 older adults with indicators derived from a neuropsychological test battery. Subjecting these data to taxometric analysis using mean above minus below a cut (MAMBAC), maximum covariance (MAXCOV), and latent mode factor analysis (L-Mode) produced results more consistent with dementia as a dimensional (lying along a continuum) than categorical (representing a distinct entity) construct. A second study conducted on a group of 2375 21-to-64-year olds produced similar results. These findings denote that dementia, as measured by deficits in episodic memory, attention/concentration, executive function, and language, differs quantitatively rather than qualitatively from the cognitive status of non-demented adults. The implications of these results for classification, assessment, etiology, and prevention are discussed. PMID:20677881

  3. Continuum Fitting HST QSO Spectra

    NASA Technical Reports Server (NTRS)

    Tytler, David; Oliversen, Ronald J. (Technical Monitor)

    2002-01-01

    The Principal Component Analysis (PCA) method which we are using to fit and describe QSO spectra relies upon the fact that QSO continuum are generally very smooth and simple except for emission and absorption lines. To see this we need high signal-to-noise (S/N) spectra of QSOs at low redshift which have relatively few absorption lines in the Lyman-a forest. We need a large number of such spectra to use as the basis set for the PCA analysis which will find the set of principal component spectra which describe the QSO family as a whole. We have found that too few HST spectra have the required S/N and hence we need to supplement them with ground based spectra of QSOs at higher redshift. We have many such spectra and we have been working to make them suitable for this analysis. We have concentrated on this topic since 12/15/01.

  4. Micropolar continuum in spatial description

    NASA Astrophysics Data System (ADS)

    Ivanova, Elena A.; Vilchevskaya, Elena N.

    2016-11-01

    Within the spatial description, it is customary to refer thermodynamic state quantities to an elementary volume fixed in space containing an ensemble of particles. During its evolution, the elementary volume is occupied by different particles, each having its own mass, tensor of inertia, angular and linear velocities. The aim of the present paper is to answer the question of how to determine the inertial and kinematic characteristics of the elementary volume. In order to model structural transformations due to the consolidation or defragmentation of particles or anisotropic changes, one should consider the fact that the tensor of inertia of the elementary volume may change. This means that an additional constitutive equation must be formulated. The paper suggests kinetic equations for the tensor of inertia of the elementary volume. It also discusses the specificity of the inelastic polar continuum description within the framework of the spatial description.

  5. Computational Methods in Continuum Mechanics

    DTIC Science & Technology

    1993-11-30

    ftruet11ft bwalch.Aq 0.4.oiqn 04ta tou.MtC’ gahimtc" n matod .nAfitang In@ data 01#04141. OAd co0noIDW~ng And tft@nq the ~OIWCI&Qn of 1,onjt~omt .nd~ml...AD-A27S 560 DTIC\\3\\Ul3 10 S ELECTE1 FEB 9 1994 I c I £ COMPUTATIONAL METHODS IN CONTINUUM MECHANICS By Bolindra N . Borah N.C. A&T State University...PAGE 0me No 0.704-0158 io (reorovtnq burden ’Of .t..i e’iortion of Information is estimted to ’Adoraw 1O4 .0 e~o- * n th.n I~c ot.. "o.vw.n. q

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

    NASA Astrophysics Data System (ADS)

    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.

  7. Electrostatic Tuning of Cellular Excitability

    PubMed Central

    Börjesson, Sara I.; Parkkari, Teija; Hammarström, Sven; Elinder, Fredrik

    2010-01-01

    Abstract Voltage-gated ion channels regulate the electric activity of excitable tissues, such as the heart and brain. Therefore, treatment for conditions of disturbed excitability is often based on drugs that target ion channels. In this study of a voltage-gated K channel, we propose what we believe to be a novel pharmacological mechanism for how to regulate channel activity. Charged lipophilic substances can tune channel opening, and consequently excitability, by an electrostatic interaction with the channel's voltage sensors. The direction of the effect depends on the charge of the substance. This was shown by three compounds sharing an arachidonyl backbone but bearing different charge: arachidonic acid, methyl arachidonate, and arachidonyl amine. Computer simulations of membrane excitability showed that small changes in the voltage dependence of Na and K channels have prominent impact on excitability and the tendency for repetitive firing. For instance, a shift in the voltage dependence of a K channel with −5 or +5 mV corresponds to a threefold increase or decrease in K channel density, respectively. We suggest that electrostatic tuning of ion channel activity constitutes a novel and powerful pharmacological approach with which to affect cellular excitability. PMID:20141752

  8. Breakdown mechanisms in electrostatic deflector

    NASA Astrophysics Data System (ADS)

    Re, M.; Cuttone, G.; Zappalà, E.; Passarello, S.

    2001-12-01

    The Electrostatic Beam Deflectors for the K800 Superconducting Cyclotron are the most critical elements of the beam extraction system. It has been carried out an accurate investigation from the microscopic point of view, leading to a better comprehension of the complex phenomena taking part in the breakdown process. The environmental conditions are high electric field (up to 130 kV/cm), high magnetic field (up to 5 T) in addition with high energy (70 MeV/u) and high power ion beam. It has been found that all the materials constituent the electrostatic deflector, and not only the electrodes, give an important contribute to the mechanism of breakdown that occurs in two main ways: insulator metalization and enhanced electrodes electron emission. These two effects are involved in a positive feedback process which amplifies the effects leading to a fast breakdown. These phenomena are here shown and some possible solutions are at the moment under test using several bulk (Mo, Ti, Cu) and coating materials (TiN, Diamond Like Carbon).

  9. Electrostatic charging of lunar dust

    SciTech Connect

    Walch, Bob; Horanyi, Mihaly; Robertson, Scott

    1998-10-21

    Transient dust clouds suspended above the lunar surface were indicated by the horizon glow observed by the Surveyor spacecrafts and the Lunar Ejecta and Meteorite Experiment (Apollo 17), for example. The theoretical models cannot fully explain these observations, but they all suggest that electrostatic charging of the lunar surface due to exposure to the solar wind plasma and UV radiation could result in levitation, transport and ejection of small grains. We report on our experimental studies of the electrostatic charging properties of an Apollo-17 soil sample and two lunar simulants MLS-1 and JSC-1. We have measured their charge after exposing individual grains to a beam of fast electrons with energies in the range of 20{<=}E{<=}90 eV. Our measurements indicate that the secondary electron emission yield of the Apollo-17 sample is intermediate between MLS-1 and JSC-1, closer to that of MLS-1. We will also discuss our plans to develop a laboratory lunar surface model, where time dependent illumination and plasma bombardment will closely emulate the conditions on the surface of the Moon.

  10. Microencapsulation and Electrostatic Processing Device

    NASA Technical Reports Server (NTRS)

    Morrison, Dennis R. (Inventor); Mosier, Benjamin (Inventor); Cassanto, John M. (Inventor)

    2001-01-01

    A microencapsulation and electrostatic processing (MEP) device is provided for forming microcapsules. In one embodiment, the device comprises a chamber having a filter which separates a first region in the chamber from a second region in the chamber. An aqueous solution is introduced into the first region through an inlet port, and a hydrocarbon/ polymer solution is introduced into the second region through another inlet port. The filter acts to stabilize the interface and suppress mixing between the two immiscible solutions as they are being introduced into their respective regions. After the solutions have been introduced and have become quiescent, the interface is gently separated from the filter. At this point, spontaneous formation of microcapsules at the interface may begin to occur, or some fluid motion may be provided to induce microcapsule formation. In any case, the fluid shear force at the interface is limited to less than 100 dynes/sq cm. This low-shear approach to microcapsule formation yields microcapsules with good sphericity and desirable size distribution. The MEP device is also capable of downstream processing of microcapsules, including rinsing, re-suspension in tertiary fluids, electrostatic deposition of ancillary coatings, and free-fluid electrophoretic separation of charged microcapsules.

  11. Stiffness Control of a Continuum Manipulator in Contact with a Soft Environment.

    PubMed

    Mahvash, Mohsen; Dupont, Pierre E

    2010-12-03

    Stiffness control of a continuum robot can prevent excessive contact forces during robot navigation inside delicate, uncertain and confined environments. Furthermore, it enables the selection of tip stiffnesses that match varying task requirements. This paper introduces a computationally-efficient approach to continuum-robot stiffness control that is based on writing the forward kinematic model as the product of two transformations. The first transformation calculates the non-contact kinematics of the robot and can be formulated based on the specific type of continuum robot under consideration. The second transformation calculates the tip deflection due to applied forces and is efficiently computed using the special Cosserat rod model. To implement a desired tip stiffness, the two transformations are used to solve for the actuator positions that deform the manipulator so as to generate the required tip force at the measured tip position. The efficacy of the proposed controller is demonstrated experimentally on a concentric-tube continuum robot.

  12. Molecular electrostatic potential as a graph.

    PubMed

    Daza, Edgar E; Maza, Julio; Torres, Raul

    2013-06-01

    We present several procedures to represent molecular electrostatic potential as a graph, based on the pattern of critical points and their neighborhood relations. This representation is used for the molecular electrostatic comparison, which is reduced to a comparison of tree-type graphs. Several methods to compare trees are also presented. The applications of this algorithm to compare and classify molecules through their electrostatic potential are illustrated.

  13. Electrostatic ion waves in non-Maxwellian pair-ion plasmas

    SciTech Connect

    Arshad, Kashif; Mahmood, S.

    2010-12-15

    The electrostatic ion waves are studied for non-Maxwellian or Lorentzian distributed unmagnetized pair-ion plasmas. The Vlasov equation is solved and damping rates are calculated for electrostatic waves in Lorentzian pair-ion plasmas. The damping rates of the electrostatic ion waves are studied for the equal and different ion temperatures of pair-ion species. It is found that the Landau damping rate of the ion plasma wave is increased in Lorentzian plasmas in comparison with Maxwellian pair-ion plasmas. The numerical results are also presented for illustration by taking into account the parameters reported in fullerene pair-ion plasma experiments.

  14. Electrostatic Channeling in P. falciparum DHFR-TS: Brownian Dynamics and Smoluchowski Modeling

    PubMed Central

    Metzger, Vincent T.; Eun, Changsun; Kekenes-Huskey, Peter M.; Huber, Gary; McCammon, J. Andrew

    2014-01-01

    We perform Brownian dynamics simulations and Smoluchowski continuum modeling of the bifunctional Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (P. falciparum DHFR-TS) with the objective of understanding the electrostatic channeling of dihydrofolate generated at the TS active site to the DHFR active site. The results of Brownian dynamics simulations and Smoluchowski continuum modeling suggest that compared to Leishmania major DHFR-TS, P. falciparum DHFR-TS has a lower but significant electrostatic-mediated channeling efficiency (∼15–25%) at physiological pH (7.0) and ionic strength (150 mM). We also find that removing the electric charges from key basic residues located between the DHFR and TS active sites significantly reduces the channeling efficiency of P. falciparum DHFR-TS. Although several protozoan DHFR-TS enzymes are known to have similar tertiary and quaternary structure, subtle differences in structure, active-site geometry, and charge distribution appear to influence both electrostatic-mediated and proximity-based substrate channeling. PMID:25418308

  15. Electrostatic atomization: Effect of electrode materials on electrostatic atomizer performance

    NASA Astrophysics Data System (ADS)

    Sankaran, Abhilash; Staszel, Christopher; Kashir, Babak; Perri, Anthony; Mashayek, Farzad; Yarin, Alexander

    2016-11-01

    Electrostatic atomization was studied experimentally with a pointed electrode in a converging nozzle. Experiments were carried out on poorly conductive canola oil where it was observed that electrode material may affect charge transfer. This points at the possible faradaic reactions that can occur at the surfaces of the electrodes. The supply voltage is applied to the sharp electrode and the grounded nozzle body constitutes the counter-electrode. The charge transfer is controlled by the electrochemical reactions on both the electrodes. The electrical performance study of the atomizer issuing a charged oil jet was conducted using three different nozzle body materials - brass, copper and stainless steel. Also, two sharp electrode materials - brass and stainless steel - were tested. The experimental results revealed that both the nozzle body material, as well as the sharp electrode material affected the spray and leak currents. Moreover, the effect of the sharp electrode material is quite significant. This research is supported by NSF Grant 1505276.

  16. Momentum correlation in the three-body Coulomb continuum problem

    NASA Astrophysics Data System (ADS)

    Zhang, Suimeng

    2000-09-01

    Following the work of Berakdar (1996 Phys. Rev. A 53 2316), momentum correlation in the three-body Coulomb continuum problem is considered by the introduction of effective Sommerfeld parameters for both the symmetric and the asymmetric geometry. The triple differential cross sections for electron impact ionization of atomic helium at incident energies of 50 eV in the asymmetric geometry are calculated. Results of this approach are compared with the absolute measurements, the results of the BBK model without modification, the convergent close-coupling calculations and the results of our earlier model.

  17. Gamma-ray strength at low energies using relativistic QRPA with exact coupling to the continuum

    NASA Astrophysics Data System (ADS)

    Daoutidis, I.; Goriely, S.

    2012-02-01

    Continuum-quasiparticle random-phase Approximation (CQRPA) within the relativistic point-coupling model with density-dependent coupling constants is applied to investigate collective excitations in spherical nuclei. In particular we study the impact of the exact continuum on the giant-dipole and pygmy resonance of several Sn isotopes as well as the radiative neutron capture rates of importance for astrophysical calculations.

  18. Turbulent fluid motion 3: Basic continuum equations

    NASA Technical Reports Server (NTRS)

    Deissler, Robert G.

    1991-01-01

    A derivation of the continuum equations used for the analysis of turbulence is given. These equations include the continuity equation, the Navier-Stokes equations, and the heat transfer or energy equation. An experimental justification for using a continuum approach for the study of turbulence is given.

  19. Novel Continuum Modeling of Crystal Surface Evolution

    NASA Astrophysics Data System (ADS)

    Kandel, Daniel

    2003-03-01

    Below the roughening temperature the evolution of crystal surfaces proceeds by the nucleation, flow and annihilation of discrete atomic steps. The appropriate mathematical model of the evolution of such surfaces is discrete in nature, and consists of coupled equations for the motion, nucelation and annihilation of steps. It is useful, however, to describe surface evolution in terms of continuum models. Such models are more amenable to analytical treatments and have enormous computational advantages over their discrete counterparts. Standard continuum models successfully describe the evolution of surfaces with smooth morphology, but completely fail when the surface has singularities such as facets. It is an interesting and important challenge to develop continuum descriptions of surfaces with singularities, since in many cases the singularities drive the evolution of the whole system. In the talk I will present a conceptually new approach to continuum modeling of surface evolution, termed Configurational Continuum [1], which is valid even in singular regions. The approach consists of a new definition of the continuum limit. It is equivalent to standard continuum for very smooth morphology, but is radically different from it in singular regions, where it becomes equivalent to the discrete models. The validity of configurational continuum will be demonstrated on several simple systems. [1] N. Israeli and D. Kandel, Phys. Rev. Lett. 88, 116103 (2002).

  20. Between algorithm and model: different Molecular Surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution.

    PubMed

    Decherchi, Sergio; Colmenares, José; Catalano, Chiara Eva; Spagnuolo, Michela; Alexov, Emil; Rocchia, Walter

    2013-01-01

    The definition of a molecular surface which is physically sound and computationally efficient is a very interesting and long standing problem in the implicit solvent continuum modeling of biomolecular systems as well as in the molecular graphics field. In this work, two molecular surfaces are evaluated with respect to their suitability for electrostatic computation as alternatives to the widely used Connolly-Richards surface: the blobby surface, an implicit Gaussian atom centered surface, and the skin surface. As figures of merit, we considered surface differentiability and surface area continuity with respect to atom positions, and the agreement with explicit solvent simulations. Geometric analysis seems to privilege the skin to the blobby surface, and points to an unexpected relationship between the non connectedness of the surface, caused by interstices in the solute volume, and the surface area dependence on atomic centers. In order to assess the ability to reproduce explicit solvent results, specific software tools have been developed to enable the use of the skin surface in Poisson-Boltzmann calculations with the DelPhi solver. Results indicate that the skin and Connolly surfaces have a comparable performance from this last point of view.

  1. Between algorithm and model: different Molecular Surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution

    PubMed Central

    Decherchi, Sergio; Colmenares, José; Catalano, Chiara Eva; Spagnuolo, Michela; Alexov, Emil; Rocchia, Walter

    2011-01-01

    The definition of a molecular surface which is physically sound and computationally efficient is a very interesting and long standing problem in the implicit solvent continuum modeling of biomolecular systems as well as in the molecular graphics field. In this work, two molecular surfaces are evaluated with respect to their suitability for electrostatic computation as alternatives to the widely used Connolly-Richards surface: the blobby surface, an implicit Gaussian atom centered surface, and the skin surface. As figures of merit, we considered surface differentiability and surface area continuity with respect to atom positions, and the agreement with explicit solvent simulations. Geometric analysis seems to privilege the skin to the blobby surface, and points to an unexpected relationship between the non connectedness of the surface, caused by interstices in the solute volume, and the surface area dependence on atomic centers. In order to assess the ability to reproduce explicit solvent results, specific software tools have been developed to enable the use of the skin surface in Poisson-Boltzmann calculations with the DelPhi solver. Results indicate that the skin and Connolly surfaces have a comparable performance from this last point of view. PMID:23519863

  2. Observational constraints on non-Lorentzian continuum effects in the near-infrared solar spectrum using ARM ARESE data.

    NASA Astrophysics Data System (ADS)

    Vogelmann, A. M.; Ramanathan, V.; Conant, W. C.; Hunter, W. E.

    1998-08-01

    Uncertainties exist in the magnitude of the water vapor continuum at solar wavelengths and many models do not include a solar continuum. The authors assess whether the neglect of the continuum in some models could explain a significant amount of the excess solar absorption found by several studies, in which the observed atmospheric solar absorption is significantly greater than that modelled. Towards this goal, the authors constrain the magnitude of the near-infrared water vapor continuum absorption using observations from the Atmospheric Radiation Measurement (ARM) Enhanced Short-wave Experiment (ARESE). Narrow-band irradiances measured by two independent Multifilter Rotating Shadowband Radiometers (MFRSRs) are used to infer the clear-sky transmission by water vapor in the 0.94 μm band. Over 16000 such observations are compared to non-continuum (i.e. a pure Lorentzian model) and continuum calculations using a correlated-k distribution model, which shows excellent agreement with a line-by-line model and uses coincident measurements of the pressure, temperature and water vapor profiles. Continuum calculations use the CKD super-Lorentzian formulation. The data suggest the need for a far wing continuum in the 0.94 μm band with an absorption that falls between that computed for pure Lorentzian lines and the CKD continuum.

  3. Electrostatic properties of aqueous interfaces probed by small solutes

    NASA Astrophysics Data System (ADS)

    Pohorille, Andrew; Wilson, Michael A.; Schweighofer, Karl

    1999-11-01

    The excess chemical potentials of methane and its four fluorinated derivatives across the water-hexane, water-octanol, water-glycerol 1-monooleate and water-1-palmitoyl 2-oleoyl sn-glycero 3-phosphatidylcholine (POPC) interfaces are calculated using the particle insertion method. In all cases, the polar species exhibit interfacial minima indicating that these molecules tend to accumulate in the interfacial region, while the non-polar molecules exhibit no such minimum. The excess chemical potentials are further partitioned into electrostatic and non-electrostatic terms. For polar molecules, the electrostatic term changes nearly linearly over the distance of approximately 10 Å in the interfacial region and appears to depend only weakly on the nature of the interface. Solute molecules are not oriented isotropically at the interface, but tend to align themselves with the excess electric field created by the anisotropic interfacial environment. Using dipoles in a cavity as models, it is further shown that, in the water-POPC system, the electrostatic term changes with the size of the dipole according to the predictions of linear response theory. This approximation does not work as well for the other interfacial systems investigated. This may be an artifact due to the neglect of long-range effects in those simulations. The non-electrostatic term, dominated by the reversible work of cavity formation, shows interfacially induced structure. In particular, it is responsible for a maximum of the excess chemical potential on the dense, water side of the water-POPC interface. The results of this study provide guidance to developing simple but accurate implicit models of interfacial systems.

  4. Lyman Continuum Emission Search at z 1 Using GALEX Imaging

    NASA Astrophysics Data System (ADS)

    Friedman, Peter G.; Small, T. A.; Deharveng, J. M.; Milliard, B.

    2007-12-01

    We present the status and results of a search for Lyman continuum emission from galaxies at z 1. We use GALEX data in the Extended Groth Strip. Our method is to stack FUV image flux at locations of DEEP2 redshift catalog galaxies in the redshift range 1 < z < 1.5. In this range, the GALEX FUV band (1350-1800 A) is sensitive only to rest wavelengths below 912 A. We normalize FUV flux to NUV flux and calculate the Lyman continuum emission escape fraction by fitting SED models to broad-band fluxes from ground-based surveys of the same galaxies. GALEX is a NASA Small Explorer mission with contributions from France and South Korea. This work uses data from the AEGIS collaboration, which is supported by grants from the National Science Foundation, NASA, and the Keck Observatory.

  5. GALEX Imaging Search for Lyman Continuum Emission at z 1

    NASA Astrophysics Data System (ADS)

    Friedman, Peter G.; Small, T. A.; Deharveng, J. M.; Milliard, B.

    2009-01-01

    We present the status and results of a search for Lyman continuum emission from galaxies at z 1. We use GALEX data in the Extended Groth Strip. Our method is to stack FUV image flux at locations of DEEP2 redshift catalog galaxies in the redshift range 1 < z < 1.5. In this range, the GALEX FUV band (1350-1800 A) is sensitive only to rest wavelengths below 912 A. We normalize FUV flux to NUV flux and calculate the Lyman continuum emission escape fraction by fitting SED models to broad-band fluxes from ground-based surveys of the same galaxies. GALEX is a NASA Small Explorer mission with contributions from France and South Korea. This work uses data from the AEGIS collaboration, which is supported by grants from the National Science Foundation, NASA, and the Keck Observatory.

  6. GALEX Imaging Search for Lyman Continuum Emission at z 1

    NASA Astrophysics Data System (ADS)

    Friedman, Peter G.; Small, T. A.; Deharveng, J. M.; Milliard, B.

    2010-01-01

    We present the status and results of a search for Lyman continuum emission from galaxies at z 1. We use GALEX data in the Extended Groth Strip. Our method is to stack FUV image flux at locations of DEEP2 redshift catalog galaxies in the redshift range 1 < z < 1.5. In this range, the GALEX FUV band (1350-1800 A) is sensitive only to rest wavelengths below 912 A. We normalize FUV flux to NUV flux and calculate the Lyman continuum emission escape fraction by fitting SED models to broad-band fluxes from ground-based surveys of the same galaxies. GALEX is a NASA Small Explorer mission with contributions from France and South Korea. This work uses data from the AEGIS collaboration, which is supported by grants from the National Science Foundation, NASA, and the Keck Observatory.

  7. Portable liquid collection electrostatic precipitator

    DOEpatents

    Carlson, Duane C.; DeGange, John J.; Halverson, Justin E.

    2005-10-18

    A portable liquid collection electrostatic collection precipitator for analyzing air is provided which is a relatively small, self-contained device. The device has a tubular collection electrode, a reservoir for a liquid, and a pump. The pump pumps the liquid into the collection electrode such that the liquid flows down the exterior of the collection electrode and is recirculated to the reservoir. An air intake is provided such that air to be analyzed flows through an ionization section to ionize analytes in the air, and then flows near the collection electrode where ionized analytes are collected. A portable power source is connected to the air intake and the collection electrode. Ionizable constituents in the air are ionized, attracted to the collection electrode, and precipitated in the liquid. The precipitator may also have an analyzer for the liquid and may have a transceiver allowing remote operation and data collection.

  8. Microencapsulation and Electrostatic Processing Method

    NASA Technical Reports Server (NTRS)

    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.

  9. Large Aperture Electrostatic Dust Detector

    SciTech Connect

    C.H. Skinner, R. Hensley, and A.L Roquemore

    2007-10-09

    Diagnosis and management of dust inventories generated in next-step magnetic fusion devices is necessary for their safe operation. A novel electrostatic dust detector, based on a fine grid of interlocking circuit traces biased to 30 or 50 ν has been developed for the detection of dust particles on remote surfaces in air and vacuum environments. Impinging dust particles create a temporary short circuit and the resulting current pulse is recorded by counting electronics. Up to 90% of the particles are ejected from the grid or vaporized suggesting the device may be useful for controlling dust inventories. We report measurements of the sensitivity of a large area (5x5 cm) detector to microgram quantities of dust particles and review its applications to contemporary tokamaks and ITER.

  10. NMR studies of electrostatic potential distribution around biologically important molecules.

    PubMed Central

    Likhtenshtein, G I; Adin, I; Novoselsky, A; Shames, A; Vaisbuch, I; Glaser, R

    1999-01-01

    A new experimental approach has been developed to study the distribution of local electrostatic potential around specific protons in biologically important molecules. The approach is the development of a method denoted as "spin label/spin probe," which was proposed by one of us (. Mol. Biol. 6:498-507). The proposed method is based upon the quantitative measurement of the contribution of differently charged nitroxide probes to the spin lattice relaxation rate (1/T1) of protons in the molecule of interest, followed by calculation of local electrostatic potential using the classical Debye equation. In parallel, the theoretical calculation of potential distribution with the use of the MacSpartan Plus 1.0 program has been performed. Application of the method to solutions of simple organic molecules (aliphatic and aromatic alcohols, aliphatic carboxylates (propionate anion), and protonated ethyl amine and imidazole) allowed us to estimate the effective potential around the molecules under investigation. These were found to be in good agreement with theoretically expected values. This technique was then applied to zwitterionic amino acids bearing neutral and charged side chains (glycine, lysine, histidine, and aspartic acid). The reliability of the general approach is proved by the data presented in this paper. Application of this new methodology can afford insight into the biochemical significance of electrostatic effects in biological systems. PMID:10388770

  11. Review on the modeling of electrostatic MEMS.

    PubMed

    Chuang, Wan-Chun; Lee, Hsin-Li; Chang, Pei-Zen; Hu, Yuh-Chung

    2010-01-01

    Electrostatic-driven microelectromechanical systems devices, in most cases, consist of couplings of such energy domains as electromechanics, optical electricity, thermoelectricity, and electromagnetism. Their nonlinear working state makes their analysis complex and complicated. This article introduces the physical model of pull-in voltage, dynamic characteristic analysis, air damping effect, reliability, numerical modeling method, and application of electrostatic-driven MEMS devices.

  12. Electrostatics experiments with sharp metal points

    NASA Astrophysics Data System (ADS)

    Ivanov, Dragia; Nikolov, Stefan

    2016-11-01

    In this paper we examine the phenomena that arise around an electrically charged sharp metal spike and present numerous experiments that can be used in the teaching of electrostatics. The experiments are quite spectacular and attention-grabbing while being relatively simple and easy to perform in any decently supplied physics education laboratory that is equipped with an electrostatic machine (like a Wimshurst machine).

  13. Preliminary tests of the electrostatic plasma accelerator

    NASA Technical Reports Server (NTRS)

    Aston, G.; Acker, T.

    1990-01-01

    This report describes the results of a program to verify an electrostatic plasma acceleration concept and to identify those parameters most important in optimizing an Electrostatic Plasma Accelerator (EPA) thruster based upon this thrust mechanism. Preliminary performance measurements of thrust, specific impulse and efficiency were obtained using a unique plasma exhaust momentum probe. Reliable EPA thruster operation was achieved using one power supply.

  14. Ionic electrostatic excitations along biological membranes

    NASA Astrophysics Data System (ADS)

    Moradi, Afshin

    2011-02-01

    A theoretical analysis of ionic electrostatic excitations of a charged biological membrane is presented within the framework of the fluid theory for surface ions inside and outside the cell, in conjunction with the Poisson's equation. General expressions of dispersion relations are obtained for electrostatic oscillations of intrinsic cellular with different shapes and symmetries.

  15. Electrostatics with Computer-Interfaced Charge Sensors

    ERIC Educational Resources Information Center

    Morse, Robert A.

    2006-01-01

    Computer interfaced electrostatic charge sensors allow both qualitative and quantitative measurements of electrostatic charge but are quite sensitive to charges accumulating on modern synthetic materials. They need to be used with care so that students can correctly interpret their measurements. This paper describes the operation of the sensors,…

  16. Lattice continuum and diffusional creep

    NASA Astrophysics Data System (ADS)

    Mesarovic, Sinisa Dj.

    2016-04-01

    Diffusional creep is characterized by growth/disappearance of lattice planes at the crystal boundaries that serve as sources/sinks of vacancies, and by diffusion of vacancies. The lattice continuum theory developed here represents a natural and intuitive framework for the analysis of diffusion in crystals and lattice growth/loss at the boundaries. The formulation includes the definition of the Lagrangian reference configuration for the newly created lattice, the transport theorem and the definition of the creep rate tensor for a polycrystal as a piecewise uniform, discontinuous field. The values associated with each crystalline grain are related to the normal diffusional flux at grain boundaries. The governing equations for Nabarro-Herring creep are derived with coupled diffusion and elasticity with compositional eigenstrain. Both, bulk diffusional dissipation and boundary dissipation accompanying vacancy nucleation and absorption, are considered, but the latter is found to be negligible. For periodic arrangements of grains, diffusion formally decouples from elasticity but at the cost of a complicated boundary condition. The equilibrium of deviatorically stressed polycrystals is impossible without inclusion of interface energies. The secondary creep rate estimates correspond to the standard Nabarro-Herring model, and the volumetric creep is small. The initial (primary) creep rate is estimated to be much larger than the secondary creep rate.

  17. Lattice continuum and diffusional creep

    PubMed Central

    2016-01-01

    Diffusional creep is characterized by growth/disappearance of lattice planes at the crystal boundaries that serve as sources/sinks of vacancies, and by diffusion of vacancies. The lattice continuum theory developed here represents a natural and intuitive framework for the analysis of diffusion in crystals and lattice growth/loss at the boundaries. The formulation includes the definition of the Lagrangian reference configuration for the newly created lattice, the transport theorem and the definition of the creep rate tensor for a polycrystal as a piecewise uniform, discontinuous field. The values associated with each crystalline grain are related to the normal diffusional flux at grain boundaries. The governing equations for Nabarro–Herring creep are derived with coupled diffusion and elasticity with compositional eigenstrain. Both, bulk diffusional dissipation and boundary dissipation accompanying vacancy nucleation and absorption, are considered, but the latter is found to be negligible. For periodic arrangements of grains, diffusion formally decouples from elasticity but at the cost of a complicated boundary condition. The equilibrium of deviatorically stressed polycrystals is impossible without inclusion of interface energies. The secondary creep rate estimates correspond to the standard Nabarro–Herring model, and the volumetric creep is small. The initial (primary) creep rate is estimated to be much larger than the secondary creep rate. PMID:27274696

  18. Optimization of the multi-electrode electrostatic sensor for velocity distribution measurement

    NASA Astrophysics Data System (ADS)

    Wang, Chao; Zhang, Wenbiao; Wu, Weiping

    2014-04-01

    Measuring the velocity distribution of dilute gas-solid two-phase flow is necessary for industrial process monitor and control. However, in order to get correct measurement of the velocity distribution, the effective correlation calculation by non-corresponding side electrode couples of the electrostatic sensor was needed. By introducing the principle of electrostatic correlation based velocity distribution measurement method, the importance of the effective correlation calculation by non-corresponding side electrode couples was emphasized in this paper. In order to ensure effective correlation calculation by non-corresponding side electrode couples was emphasized in this paper. In order to ensure effective correlation calculation by non-corresponding side electrode couples, effective correlation analysis of multi-electrode electrostatic sensor was carried out and effective correlation analysis method was proposed. According to this method, the structure of multi-electrode electrostatic sensor was optimized. Finally, experimental results show that correlation calculation of non-corresponding side electrode couples could be done effectively by the optimized multi-electrode electrostatic sensor. This result lays a foundation for further research on velocity distribution measurement.

  19. Atom-partitioned multipole expansions for electrostatic potential boundary conditions

    NASA Astrophysics Data System (ADS)

    Lee, M.; Leiter, K.; Eisner, C.; Knap, J.

    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.

  20. Flexural-Phonon Scattering Induced by Electrostatic Gating in Graphene

    NASA Astrophysics Data System (ADS)

    Gunst, Tue; Kaasbjerg, Kristen; Brandbyge, Mads

    2017-01-01

    Graphene has an extremely high carrier mobility partly due to its planar mirror symmetry inhibiting scattering by the highly occupied acoustic flexural phonons. Electrostatic gating of a graphene device can break the planar mirror symmetry, yielding a coupling mechanism to the flexural phonons. We examine the effect of the gate-induced one-phonon scattering on the mobility for several gate geometries and dielectric environments using first-principles calculations based on density functional theory and the Boltzmann equation. We demonstrate that this scattering mechanism can be a mobility-limiting factor, and show how the carrier density and temperature scaling of the mobility depends on the electrostatic environment. Our findings may explain the high deformation potential for in-plane acoustic phonons extracted from experiments and, furthermore, suggest a direct relation between device symmetry and resulting mobility.

  1. Atomistic simulations of liquid water using Lekner electrostatics

    NASA Astrophysics Data System (ADS)

    English, Niall J.; MacElroy, J. M. D.

    Equilibrium molecular dynamics simulations have been performed for liquid water using three different potential models in the NVT and NPT ensembles. The flexible SPC model, the rigid TIP4P model and the rigid/polarizable TIP4P-FQ potential were studied. The Lekner method was used to handle long range electrostatic interactions, and an efficient trivariate cubic spline interpolation method was devised for this purpose. A partitioning of the electrostatic interactions into medium and long range parts was performed, and the concomitant use of multiple timestep techniques led to substantially enhanced computation speeds. The simulations were carried out using 256 molecules in the NVT ensemble at 25°C and 997kgm-3 and in the NPT ensemble at 25°C and 1 bar. Various dynamic, structural, dielectric, rotational and thermodynamic properties were calculated, and it was found that the simulation methodologies performed satisfactorily vis-à-vis previous simulation results and experimental observations.

  2. Control of electrostatic damage to electronic circuits

    SciTech Connect

    Kirk, W.J. Jr.

    1980-03-01

    Static is caused by the flow of materials and people within an environment. The static voltages generated by these movements can degrade or destroy many solid state devices currently being used in sophisticated electronic equipment. Discharge of static voltages through these sensitive devices during assembly operations can lead to a nonfunctional assembly fabricated from parts which previously were acceptable or to later failure of an assembly which was functional after fabrication. Sources of electrostatic charges, equipment and methods for minimizing the generation of electrostatic voltages during the production, assembly and packaging of solid state electronic equipment, and the sensitivity of solid state devices to electrostatic damage are discussed. It is concluded that static awareness is the key to an effective electrostatic damage (ESD) control program, and that production facilities must incorporate electrostatic protection facilities, materials, and processes so that workers can concentrate on producing a high-quality product without having to be overly concerned about ESD procedures. (LCL)

  3. Electrostatic thin film chemical and biological sensor

    DOEpatents

    Prelas, Mark A.; Ghosh, Tushar K.; Tompson, Jr., Robert V.; Viswanath, Dabir; Loyalka, Sudarshan K.

    2010-01-19

    A chemical and biological agent sensor includes an electrostatic thin film supported by a substrate. The film includes an electrostatic charged surface to attract predetermined biological and chemical agents of interest. A charge collector associated with said electrostatic thin film collects charge associated with surface defects in the electrostatic film induced by the predetermined biological and chemical agents of interest. A preferred sensing system includes a charge based deep level transient spectroscopy system to read out charges from the film and match responses to data sets regarding the agents of interest. A method for sensing biological and chemical agents includes providing a thin sensing film having a predetermined electrostatic charge. The film is exposed to an environment suspected of containing the biological and chemical agents. Quantum surface effects on the film are measured. Biological and/or chemical agents can be detected, identified and quantified based on the measured quantum surface effects.

  4. Cosmology of Continuum Creation and Annihilation

    NASA Astrophysics Data System (ADS)

    Ierokomos, Nikiforos

    2011-11-01

    An extensive cosmology hypothesis is presented that was developed over decades and is based on the existence and evolution of the universe via Cosmic Symmetry Breaks (CSBs) or phases with our universe (Cosmos) describable by a Cosmology of Continuum Creation and Annihilation, or CCA Cosmology. The CCA cosmology hypothesis does not belong to a Standard Model Big Bang. This hypothesis not only describes the universe but also the realm of elementary particles and forces. It provides plausible answers to a large number of puzzles in Physics and Cosmology. These answers range from those that can be calculated and values checked by observations, such as: How much and what is dark energy? How much and what is dark matter? How much baryonic matter? How much and why is there a time-delay for GRB energetic photons? When (or did?) the universe started to accelerate? Are primordial galaxies smaller? Why are orbits non-Newtonian beyond an acceleration value, and other calculable parameters. Also, answers which are more fundamental in interpretation, such as: What is mass and gravity? How many families of elementary particles exist and why are there only three generations of each? Why did the universe start with such low entropy? Does the Cosmos violate the First or Second Law of Thermodynamics? Why is there an asymmetry of matter over antimatter in the universe and what is antimatter? These and other questions the CCA hypothesis is proposing to answer. This hypothesis requires minimum assumptions and can build a coherent theory that can arrive at today's complex universe with plausible evolutionary steps from one postulate and one particle. cosmogony, non-standard cosmology, dark energy, dark matter, new elementary particles, gravity, antimatter, accelerated universe.

  5. Slits, plates, and Poisson-Boltzmann theory in a local formulation of nonlocal electrostatics.

    PubMed

    Paillusson, Fabien; Blossey, Ralf

    2010-11-01

    Polar liquids like water carry a characteristic nanometric length scale, the correlation length of orientation polarizations. Continuum theories that can capture this feature commonly run under the name of "nonlocal" electrostatics since their dielectric response is characterized by a scale-dependent dielectric function ε(q), where q is the wave vector; the Poisson(-Boltzmann) equation then turns into an integro-differential equation. Recently, "local" formulations have been put forward for these theories and applied to water, solvated ions, and proteins. We review the local formalism and show how it can be applied to a structured liquid in slit and plate geometries, and solve the Poisson-Boltzmann theory for a charged plate in a structured solvent with counterions. Our results establish a coherent picture of the local version of nonlocal electrostatics and show its ease of use when compared to the original formulation.

  6. Quantum dynamics in continuum for proton transport--generalized correlation.

    PubMed

    Chen, Duan; Wei, Guo-Wei

    2012-04-07

    As a key process of many biological reactions such as biological energy transduction or human sensory systems, proton transport has attracted much research attention in biological, biophysical, and mathematical fields. A quantum dynamics in continuum framework has been proposed to study proton permeation through membrane proteins in our earlier work and the present work focuses on the generalized correlation of protons with their environment. Being complementary to electrostatic potentials, generalized correlations consist of proton-proton, proton-ion, proton-protein, and proton-water interactions. In our approach, protons are treated as quantum particles while other components of generalized correlations are described classically and in different levels of approximations upon simulation feasibility and difficulty. Specifically, the membrane protein is modeled as a group of discrete atoms, while ion densities are approximated by Boltzmann distributions, and water molecules are represented as a dielectric continuum. These proton-environment interactions are formulated as convolutions between number densities of species and their corresponding interaction kernels, in which parameters are obtained from experimental data. In the present formulation, generalized correlations are important components in the total Hamiltonian of protons, and thus is seamlessly embedded in the multiscale/multiphysics total variational model of the system. It takes care of non-electrostatic interactions, including the finite size effect, the geometry confinement induced channel barriers, dehydration and hydrogen bond effects, etc. The variational principle or the Euler-Lagrange equation is utilized to minimize the total energy functional, which includes the total Hamiltonian of protons, and obtain a new version of generalized Laplace-Beltrami equation, generalized Poisson-Boltzmann equation and generalized Kohn-Sham equation. A set of numerical algorithms, such as the matched interface and

  7. Quantum dynamics in continuum for proton transport—Generalized correlation

    NASA Astrophysics Data System (ADS)

    Chen, Duan; Wei, Guo-Wei

    2012-04-01

    As a key process of many biological reactions such as biological energy transduction or human sensory systems, proton transport has attracted much research attention in biological, biophysical, and mathematical fields. A quantum dynamics in continuum framework has been proposed to study proton permeation through membrane proteins in our earlier work and the present work focuses on the generalized correlation of protons with their environment. Being complementary to electrostatic potentials, generalized correlations consist of proton-proton, proton-ion, proton-protein, and proton-water interactions. In our approach, protons are treated as quantum particles while other components of generalized correlations are described classically and in different levels of approximations upon simulation feasibility and difficulty. Specifically, the membrane protein is modeled as a group of discrete atoms, while ion densities are approximated by Boltzmann distributions, and water molecules are represented as a dielectric continuum. These proton-environment interactions are formulated as convolutions between number densities of species and their corresponding interaction kernels, in which parameters are obtained from experimental data. In the present formulation, generalized correlations are important components in the total Hamiltonian of protons, and thus is seamlessly embedded in the multiscale/multiphysics total variational model of the system. It takes care of non-electrostatic interactions, including the finite size effect, the geometry confinement induced channel barriers, dehydration and hydrogen bond effects, etc. The variational principle or the Euler-Lagrange equation is utilized to minimize the total energy functional, which includes the total Hamiltonian of protons, and obtain a new version of generalized Laplace-Beltrami equation, generalized Poisson-Boltzmann equation and generalized Kohn-Sham equation. A set of numerical algorithms, such as the matched interface and

  8. Patch Finder Plus (PFplus): a web server for extracting and displaying positive electrostatic patches on protein surfaces.

    PubMed

    Shazman, Shula; Celniker, Gershon; Haber, Omer; Glaser, Fabian; Mandel-Gutfreund, Yael

    2007-07-01

    Positively charged electrostatic patches on protein surfaces are usually indicative of nucleic acid binding interfaces. Interestingly, many proteins which are not involved in nucleic acid binding possess large positive patches on their surface as well. In some cases, the positive patches on the protein are related to other functional properties of the protein family. PatchFinderPlus (PFplus) http://pfp.technion.ac.il is a web-based tool for extracting and displaying continuous electrostatic positive patches on protein surfaces. The input required for PFplus is either a four letter PDB code or a protein coordinate file in PDB format, provided by the user. PFplus computes the continuum electrostatics potential and extracts the largest positive patch for each protein chain in the PDB file. The server provides an output file in PDB format including a list of the patch residues. In addition, the largest positive patch is displayed on the server by a graphical viewer (Jmol), using a simple color coding.

  9. Continuum kinetic and multi-fluid simulations of classical sheaths

    NASA Astrophysics Data System (ADS)

    Cagas, P.; Hakim, A.; Juno, J.; Srinivasan, B.

    2017-02-01

    The kinetic study of plasma sheaths is critical, among other things, to understand the deposition of heat on walls, the effect of sputtering, and contamination of the plasma with detrimental impurities. The plasma sheath also provides a boundary condition and can often have a significant global impact on the bulk plasma. In this paper, kinetic studies of classical sheaths are performed with the continuum kinetic code, Gkeyll, which directly solves the Vlasov-Maxwell equations. The code uses a novel version of the finite-element discontinuous Galerkin scheme that conserves energy in the continuous-time limit. The fields are computed using Maxwell equations. Ionization and scattering collisions are included; however, surface effects are neglected. The aim of this work is to introduce the continuum kinetic method and compare its results with those obtained from an already established finite-volume multi-fluid model also implemented in Gkeyll. Novel boundary conditions on the fluids allow the sheath to form without specifying wall fluxes, so the fluids and fields adjust self-consistently at the wall. The work presented here demonstrates that the kinetic and fluid results are in agreement for the momentum flux, showing that in certain regimes, a multi-fluid model can be a useful approximation for simulating the plasma boundary. There are differences in the electrostatic potential between the fluid and kinetic results. Further, the direct solutions of the distribution function presented here highlight the non-Maxwellian distribution of electrons in the sheath, emphasizing the need for a kinetic model. The densities, velocities, and the potential show a good agreement between the kinetic and fluid results. However, kinetic physics is highlighted through higher moments such as parallel and perpendicular temperatures which provide significant differences from the fluid results in which the temperature is assumed to be isotropic. Besides decompression cooling, the heat flux

  10. Electrostatic comb drive for vertical actuation

    SciTech Connect

    Lee, A. P., LLNL

    1997-07-10

    The electrostatic comb finger drive has become an integral design for microsensor and microactuator applications. This paper reports on utilizing the levitation effect of comb fingers to design vertical-to-the-substrate actuation for interferometric applications. For typical polysilicon comb drives with 2 {micro}m gaps between the stationary and moving fingers, as well as between the microstructures and the substrate, the equilibrium position is nominally 1-2 {micro}m above the stationary comb fingers. This distance is ideal for many phase shifting interferometric applications. Theoretical calculations of the vertical actuation characteristics are compared with the experimental results, and a general design guideline is derived from these results. The suspension flexure stiffnesses, gravity forces, squeeze film damping, and comb finger thicknesses are parameters investigated which affect the displacement curve of the vertical microactuator. By designing a parallel plate capacitor between the suspended mass and the substrate, in situ position sensing can be used to control the vertical movement, providing a total feedback-controlled system. Fundamentals of various capacitive position sensing techniques are discussed. Experimental verification is carried out by a Zygo distance measurement interferometer.

  11. ELECTROSTATICALLY ENHANCED BARRIER FILTER COLLECTION

    SciTech Connect

    John Erjavec; Michael D. Mann; Ryan Z. Knutson; Michael L. Swanson; Michael E. Collings

    2003-06-01

    This work was performed through the University of North Dakota (UND) Chemical Engineering Department with assistance from UND's Energy & Environmental Research Center. This research was undertaken in response to the U.S. Department of Energy Federal Technology Center Program Solicitation No. DE-PS26-99FT40479, Support of Advanced Coal Research at U.S. Universities and Colleges. Specifically, this research was in support of the UCR Core Program and addressees Topic 1, Improved Hot-Gas Contaminant and Particulate Removal Techniques, introducing an advanced design for particulate removal. Integrated gasification combined cycle (IGCC) offers the potential for very high efficiency and clean electric generation. In IGCC, the product gas from the gasifier needs to be cleaned of particulate matter to avoid erosion and high-temperature corrosion difficulties arising with the turbine blades. Current methods involve cooling the gases to {approx}100 C to condense alkalis and remove sulfur and particulates using conventional scrubber technology. This ''cool'' gas is then directed to a turbine for electric generation. While IGCC has the potential to reach efficiencies of over 50%, the current need to cool the product gas for cleaning prior to firing it in a turbine is keeping IGCC from reaching its full potential. The objective of the current project was to develop a highly reliable particulate collector system that can meet the most stringent turbine requirements and emission standards, can operate at temperatures above 1500 F, is applicable for use with all U.S. coals, is compatible with various sorbent injection schemes for sulfur and alkali control, can be integrated into a variety of configurations for both pressurized gasification and combustion, increases allowable face velocity to reduce filter system capital cost, and is cost-competitive with existing technologies. The collector being developed is a new concept in particulate control called electrostatically enhanced

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

    NASA Astrophysics Data System (ADS)

    Kotsalis, E. M.; Walther, J. H.; Koumoutsakos, P.

    2007-07-01

    We present a control algorithm to eliminate spurious density fluctuations associated with the coupling of atomistic and continuum descriptions for dense liquids. A Schwartz domain decomposition algorithm is employed to couple molecular dynamics for the simulation of the atomistic system 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 of the method makes it suitable for any type of coupling between atomistic and continuum descriptions of dense fluids.

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

    PubMed

    Kotsalis, E M; Walther, J H; Koumoutsakos, P

    2007-07-01

    We present a control algorithm to eliminate spurious density fluctuations associated with the coupling of atomistic and continuum descriptions for dense liquids. A Schwartz domain decomposition algorithm is employed to couple molecular dynamics for the simulation of the atomistic system 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 of the method makes it suitable for any type of coupling between atomistic and continuum descriptions of dense fluids.

  14. Nonuniform elastic properties of macromolecules and effect of prestrain on their continuum nature.

    PubMed

    Aggarwal, Ankush; May, Eric R; Brooks, Charles L; Klug, William S

    2016-01-01

    Many experimental and theoretical methods have been developed to calculate the coarse-grained continuum elastic properties of macromolecules. However, all of those methods assume uniform elastic properties. Following the continuum mechanics framework, we present a systematic way of calculating the nonuniform effective elastic properties from atomic thermal fluctuations obtained from molecular dynamics simulation at any coarse-grained scale using a potential of the mean-force approach. We present the results for a mutant of Sesbania mosaic virus capsid, where we calculate the elastic moduli at different scales and observe an apparent problem with the chosen reference configuration in some cases. We present a possible explanation using an elastic network model, where inducing random prestrain results in a similar behavior. This phenomenon provides a novel insight into the continuum nature of macromolecules and defines the limits on details that the elasticity theory can capture. Further investigation into prestrains could elucidate important aspects of conformational dynamics of macromolecules.

  15. Modeling salt-mediated electrostatics of macromolecules: the discrete surface charge optimization algorithm and its application to the nucleosome.

    PubMed

    Beard, D A; Schlick, T

    2001-01-01

    Much progress has been achieved on quantitative assessment of electrostatic interactions on the all-atom level by molecular mechanics and dynamics, as well as on the macroscopic level by models of continuum solvation. Bridging of the two representations-an area of active research-is necessary for studying integrated functions of large systems of biological importance. Following perspectives of both discrete (N-body) interaction and continuum solvation, we present a new algorithm, DiSCO (Discrete Surface Charge Optimization), for economically describing the electrostatic field predicted by Poisson-Boltzmann theory using a discrete set of Debye-Hückel charges distributed on a virtual surface enclosing the macromolecule. The procedure in DiSCO relies on the linear behavior of the Poisson-Boltzmann equation in the far zone; thus contributions from a number of molecules may be superimposed, and the electrostatic potential, or equivalently the electrostatic field, may be quickly and efficiently approximated by the summation of contributions from the set of charges. The desired accuracy of this approximation is achieved by minimizing the difference between the Poisson-Boltzmann electrostatic field and that produced by the linearized Debye-Hückel approximation using our truncated Newton optimization package. DiSCO is applied here to describe the salt-dependent electrostatic environment of the nucleosome core particle in terms of several hundred surface charges. This representation forms the basis for modeling-by dynamic simulations (or Monte Carlo)-the folding of chromatin. DiSCO can be applied more generally to many macromolecular systems whose size and complexity warrant a model resolution between the all-atom and macroscopic levels.

  16. Electrostatic-free piezoresponse force microscopy

    NASA Astrophysics Data System (ADS)

    Kim, Sungho; Seol, Daehee; Lu, Xiaoli; Alexe, Marin; Kim, Yunseok

    2017-01-01

    Contact and non-contact based atomic force microscopy (AFM) approaches have been extensively utilized to explore various nanoscale surface properties. In most AFM-based measurements, a concurrent electrostatic effect between the AFM tip/cantilever and sample surface can occur. This electrostatic effect often hinders accurate measurements. Thus, it is very important to quantify as well as remove the impact of the electrostatic effect on AFM-based measurements. In this study, we examine the impact of the electrostatic effect on the electromechanical (EM) response in piezoresponse force microscopy as a model AFM mode. We quantitatively studied the effects of increasing the external electric field and reducing the spring constant of a cantilever. Further, we explored ways to minimize the electrostatic effect. The results provide broad guidelines for quantitatively analyzing the EM response as well as, eventually, for obtaining the electrostatic-free EM response. The conclusions can be applied to other AFM-based measurements that are subject to a strong electrostatic effect between the AFM tip/cantilever and sample surface, regardless of contact and non-contact modes.

  17. Intrinsic electrostatic effects in nanostructured ceramics

    SciTech Connect

    Uberuaga, Blas Pedro; Stanek, Chris R; Nerikar, Pankaj V

    2009-01-01

    Using empirical potentials, we have found that electrostatic dipoles can be created at grain boundaries formed from non-polar surfaces of fluorite-structured materials. In particular, the {Sigma}5(310)/[001] symmetric tilt grain boundary reconstructs to break the symmetry in the atomic structure at the boundary, forming the dipole. This dipole results in an abrupt change in electrostatic potential across the boundary. In multilayered ceramics composed of stacks of grain boundaries, the change in electrostatic potential at the boundary results in profound electrostatic effects within the crystalline layers, the nature of which depends on the electrostatic boundary conditions. For open-circuit boundary conditions, layers with either high or low electrostatic potential are formed. By contrast, for short-circuit boundary conditions, electric fields can be created within each layer, the strength of which then depends on the thickness of the layers. These electrostatic effects may have important consequences for the behavior of defects and dopants within these materials and offer the possibility of interesting technological applications.

  18. Electrostatic-free piezoresponse force microscopy

    PubMed Central

    Kim, Sungho; Seol, Daehee; Lu, Xiaoli; Alexe, Marin; Kim, Yunseok

    2017-01-01

    Contact and non-contact based atomic force microscopy (AFM) approaches have been extensively utilized to explore various nanoscale surface properties. In most AFM-based measurements, a concurrent electrostatic effect between the AFM tip/cantilever and sample surface can occur. This electrostatic effect often hinders accurate measurements. Thus, it is very important to quantify as well as remove the impact of the electrostatic effect on AFM-based measurements. In this study, we examine the impact of the electrostatic effect on the electromechanical (EM) response in piezoresponse force microscopy as a model AFM mode. We quantitatively studied the effects of increasing the external electric field and reducing the spring constant of a cantilever. Further, we explored ways to minimize the electrostatic effect. The results provide broad guidelines for quantitatively analyzing the EM response as well as, eventually, for obtaining the electrostatic-free EM response. The conclusions can be applied to other AFM-based measurements that are subject to a strong electrostatic effect between the AFM tip/cantilever and sample surface, regardless of contact and non-contact modes. PMID:28139715

  19. Emission of the third continuum of argon excited by a pulsed volume discharge

    SciTech Connect

    Lissovski, A. A.; Treshchalov, A. B.

    2009-12-15

    This paper presents the results of the observation of the third continuum band at 190 nm in a pulsed volume discharge at an argon pressure of 0.17-2 bar. The spatial-time kinetics of ultraviolet-visible photorecombination continuum and the third continuum of argon were measured and analyzed for the high- and low-current excitation regimes. Time-resolved imaging experiments with an intensified charge coupled device camera have shown that the second continuum of argon at 127 nm, Ar* lines and photorecombination continuum had a uniform distribution across the positive column of the discharge. However, the third continuum and Ar{sup +}* lines were emitted exclusively from the negative glow zone. This indicates to the existence of runaway electrons, accelerated in the electric field of the cathode layer and retarded in the negative glow zone. These electrons can achieve the energy of the cathode fall potential (130-250 eV). The radiative decay of the Ar{sub 2}{sup 2+} ions, created from Ar{sup 2+} precursors, is modeled. A good agreement has been achieved between the calculated and measured kinetics of the third continuum at different pressures, which supports the assignment of this continuum to the emission of Ar{sub 2}{sup 2+} ions. In contrast to the third continuum, the origin of the afterglow emission bands at 190 and 260 nm are connected with carbon-containing contaminants, accumulated inside the discharge chamber. These bands were disappeared during the gas circulation through the getter purifier.

  20. Periodic amplitude variations in Jovian continuum radiation

    NASA Technical Reports Server (NTRS)

    Kurth, W. S.; Gurnett, D. A.; Scarf, F. L.

    1986-01-01

    An analysis of periodic variations in the amplitude of continuum radiation near 3 kHz trapped in the Jovian magnetosphere shows structure with periods near both five and ten hours. Contrary to a plausible initial idea, the continuum amplitudes are not organized by position of the observer relative to the dense plasma sheet. Instead, there seem to be preferred orientations of system III longitude with respect to the direction to the sun which account for the peaks. This implies a clock-like modulation of the continuum radiation intensity as opposed to a searchlight effect. The importance of the dipole longitude-solar wind alignment to the amplitude of the continuum radiation implies the source region of the radiation is near the magnetopause and may indirectly tie the generation of the radio waves to the clocklike modulation of energetic electron fluxes from Jupiter.

  1. The infrared continuum spectrum of x ray illuminated molecular gas

    NASA Technical Reports Server (NTRS)

    Voit, G. Mark

    1990-01-01

    In starburst galaxies, active galaxies, and the mysterious ultraluminous infrared galaxies, x rays are likely to interact with molecular gas and dust, thereby inducing infrared emission. X ray heated thermal dust will emit the IR continuum, and x ray photoelectrons will excite an IR emission-line spectrum. Here, researchers model the IR continuum emission characteristic of some selected x ray spectral fluxes, in particular the x ray bremsstrahlung characteristic of supernova and stellar wind bubble shocks in dense media and the power law spectra characteristic of active galactic nuclei. These models are part of a larger project to determine the complete IR spectra, lines plus continuum, of x ray sources embedded in molecular gas. They modeled the thermal emission from grains by calculating a grain temperature/size/composition distribution function, f(T,a,Comp.), which accounts for temperature fluctuations by averaging over all grain thermal histories. In determining the grain thermal distribution, researchers account for both direct grain heating (by x ray absorption and subsequent electron energy deposition) and indirect grain heating (by absorption of the UV emission stimulated by non-thermal photo- and Auger electrons in the gas phase). We let the grain size distribution be proportional to a(exp -3.5), and they consider two types of grain composition: graphites, which we assume to be pure carbon, and silicates, which contain all other depleted heavy elements. They derive the grain composition distribution function from solar abundances and interstellar depletion data.

  2. DNA/chitosan electrostatic complex.

    PubMed

    Bravo-Anaya, Lourdes Mónica; Soltero, J F Armando; Rinaudo, Marguerite

    2016-07-01

    Up to now, chitosan and DNA have been investigated for gene delivery due to chitosan advantages. It is recognized that chitosan is a biocompatible and biodegradable non-viral vector that does not produce immunological reactions, contrary to viral vectors. Chitosan has also been used and studied for its ability to protect DNA against nuclease degradation and to transfect DNA into several kinds of cells. In this work, high molecular weight DNA is compacted with chitosan. DNA-chitosan complex stoichiometry, net charge, dimensions, conformation and thermal stability are determined and discussed. The influence of external salt and chitosan molecular weight on the stoichiometry is also discussed. The isoelectric point of the complexes was found to be directly related to the protonation degree of chitosan. It is clearly demonstrated that the net charge of DNA-chitosan complex can be expressed in terms of the ratio [NH3(+)]/[P(-)], showing that the electrostatic interactions between DNA and chitosan are the main phenomena taking place in the solution. Compaction of DNA long chain complexed with low molar mass chitosan gives nanoparticles with an average radius around 150nm. Stable nanoparticles are obtained for a partial neutralization of phosphate ionic sites (i.e.: [NH3(+)]/[P(-)] fraction between 0.35 and 0.80).

  3. Noise scaling in continuum percolating films

    NASA Astrophysics Data System (ADS)

    Garfunkel, G. A.; Weissman, M. B.

    1985-07-01

    Measurements of the scaling of 1/f noise magnitude versus resistance were made in metal films as the metal was removed by sandblasting. This procedure gives an approximate experimental realization of a Swiss-cheese continuum-percolation model, for which theory indicates some scaling properties very different from lattice percolation. The ratio of the resistance and noise exponents was in strong disagreement with lattice-percolation predictions and agreed approximately with simple continuum predictions.

  4. Geometric continuum regularization of quantum field theory

    SciTech Connect

    Halpern, M.B. . Dept. of Physics)

    1989-11-08

    An overview of the continuum regularization program is given. The program is traced from its roots in stochastic quantization, with emphasis on the examples of regularized gauge theory, the regularized general nonlinear sigma model and regularized quantum gravity. In its coordinate-invariant form, the regularization is seen as entirely geometric: only the supermetric on field deformations is regularized, and the prescription provides universal nonperturbative invariant continuum regularization across all quantum field theory. 54 refs.

  5. Terahertz Atmospheric Attenuation and Continuum Effects

    DTIC Science & Technology

    2013-05-01

    4 . TITLE AND SUBTITLE Terahertz atmospheric attenuation and continuum effects 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6...As stated previously, each dataset had 6 transmission scans, one for each path length. A total of 4 relative humidity levels were studied, 17.89...continuum absorption and instrumentation distortion (blue). All plots are 15.23Torr of water vapor and 746.77Torr or air. 4 RESULTS The

  6. Water vapour foreign-continuum absorption in near-infrared windows from laboratory measurements.

    PubMed

    Ptashnik, Igor V; McPheat, Robert A; Shine, Keith P; Smith, Kevin M; Williams, R Gary

    2012-06-13

    For a long time, it has been believed that atmospheric absorption of radiation within wavelength regions of relatively high infrared transmittance (so-called 'windows') was dominated by the water vapour self-continuum, that is, spectrally smooth absorption caused by H(2)O--H(2)O pair interaction. Absorption due to the foreign continuum (i.e. caused mostly by H(2)O--N(2) bimolecular absorption in the Earth's atmosphere) was considered to be negligible in the windows. We report new retrievals of the water vapour foreign continuum from high-resolution laboratory measurements at temperatures between 350 and 430 K in four near-infrared windows between 1.1 and 5 μm (9000-2000 cm(-1)). Our results indicate that the foreign continuum in these windows has a very weak temperature dependence and is typically between one and two orders of magnitude stronger than that given in representations of the continuum currently used in many climate and weather prediction models. This indicates that absorption owing to the foreign continuum may be comparable to the self-continuum under atmospheric conditions in the investigated windows. The calculated global-average clear-sky atmospheric absorption of solar radiation is increased by approximately 0.46 W m(-2) (or 0.6% of the total clear-sky absorption) by using these new measurements when compared with calculations applying the widely used MTCKD (Mlawer-Tobin-Clough-Kneizys-Davies) foreign-continuum model.

  7. Electrostatic Stabilization Of Growing Protein Crystals

    NASA Technical Reports Server (NTRS)

    Shlichta, Paul J.

    1991-01-01

    Proposed technique produces large crystals in compact, economical apparatus. Report presents concept for supporting protein crystals during growth in microgravity. Yields crystals larger and more-nearly perfect than those grown on Earth. Combines best features of sandwich-drop and electrostatic-levitation methods of support. Drop of protein solution inserted between pair of glass or plastic plates, as in sandwich-drop-support method. Electrostatically charged ring confines drop laterally and shapes it, as in electrostatic technique. Apparatus also made to accommodate several drops simultaneously between same pair of supporting plates. Drops can be inserted and crystals removed through ducts in plates.

  8. Electrostatically Driven Granular Media: Phase Transitions, Patterns and Vortices

    NASA Astrophysics Data System (ADS)

    Aranson, Igor

    2003-03-01

    Large ensembles of small particles display fascinating collective behavior when they acquire an electric charge and respond to competing long-range electromagnetic and short-range contact forces. Many industrial technologies face the challenge of assembling and separating such single- or multi-component micro and nano- size ensembles. The dynamics of conducting microparticles in strong electric field in the air or in deep vacuum was studied in Refs. [1,2]. Phase transitions and clustering instability of the electrostatically driven granular gas were found. A continuum model for the phase separation and coarsening in was formulated in terms of a Ginzburg-Landau equation subject to conservation of the total number of grains. In the regime of well-developed clusters, the continuum model is used to derive "sharp-interface" equations that govern the dynamics of the interphase boundary. The situation is remarkably different when the cell is filled with poorly conducting liquid (toluene-ethanol mixute). We have found that metallic particles form a rich variety of phases not observed in the air-filled cell. These phases include static precipitates: honeycombs lattices and Wigner crystals; and novel dynamic condensates: toroidal vortices and pulsating rings. The observed phenomena are attributed to interaction between particles and electro-hydrodynamic flows produced by the action of the electric field on ionic charges in the bulk of liquid. 1. I.S. Aranson, D. Blair, V.A. Kalatsky, G.W. Crabtree, W.-K. Kwok, V.M. Vinokur, and U.Welp, Phys. Rev. Lett. 84, 3306 (2000) 2. I.S. Aranson, B. Meerson, P.V. Sasorov, and V.M. Vinokur, Phys. Rev. Lett. 88, 204301 (2002)

  9. Quantum mechanics/molecular mechanics restrained electrostatic potential fitting.

    PubMed

    Burger, Steven K; Schofield, Jeremy; Ayers, Paul W

    2013-12-05

    We present a quantum mechanics/molecular mechanics (QM/MM) method to evaluate the partial charges of amino acid residues for use in MM potentials based on their protein environment. For each residue of interest, the nearby residues are included in the QM system while the rest of the protein is treated at the MM level of theory. After a short structural optimization, the partial charges of the central residue are fit to the electrostatic potential using the restrained electrostatic potential (RESP) method. The resulting charges and electrostatic potential account for the individual environment of the residue, although they lack the transferable nature of library partial charges. To evaluate the quality of the QM/MM RESP charges, thermodynamic integration is used to measure the pKa shift of the aspartic acid residues in three different proteins, turkey egg lysozyme, beta-cryptogein, and Thioredoxin. Compared to the AMBER ff99SB library values, the QM/MM RESP charges show better agreement between the calculated and experimental pK(a) values for almost all of the residues considered.

  10. Cyclophilin A catalyzes proline isomerization by an electrostatic handle mechanism

    SciTech Connect

    Camilloni, Carlo; Sahakyan, Aleksander B.; Holliday, Michael; Isern, Nancy G.; Zhang, Fengli; Eisenmesser, Elan Z.; Vendruscolo, Michele

    2014-07-15

    Proline isomerization is a ubiquitous process that plays a key role in the folding of proteins and in the regulation of their functions1-3. Different families of enzymes, known as peptidyl-prolyl isomerases (PPIases), catalyse this reaction, which involves the interconversion between the cis and trans isomers of the Nterminal amide bond of the amino acid proline2,3. A complete description of the mechanisms by which these enzymes function, however, has remained elusive. Here, we show that cyclophilin A, one of the most common PPIases4, provides a catalytic environment that acts on the substrate through an electrostatic lever mechanism. In this mechanism, the electrostatic field in the catalytic site turns the electric dipole associated with the carboxylic group of the amino acid preceding the proline in the substrate, thus causing the rotation of the peptide bond between the two residues. This mechanism resulted from the analysis of an ensemble of conformations populated by cyclophilin A during the enzymatic reaction using a combination of NMR measurements, molecular dynamics simulations and density functional theory calculations. We anticipate that this approach will be helpful in elucidating whether the electrostatic lever mechanism that we describe is common to other PPIases, and more generally to characterise other enzymatic processes.

  11. Design of a novel electrostatic ion storage ring at KACST

    NASA Astrophysics Data System (ADS)

    El Ghazaly, M. O. A.; Alshammari, S. M.; Welsch, C. P.; Alharbi, H. H.

    2013-05-01

    A new electrostatic storage ring for beams at energies up to 30 keV·q is currently under development at the National Centre for Mathematics and Physics (NCMP), King Abdulaziz City for Science and Technology (KACST). The ring design is based on the existing electrostatic storage rings, but stretches significantly beyond them in that it shall form the core of a unique flexible experimental facility at KACST. The lattice of this ring has been designed in a way that enables the use of state-of-the-art experimental methods to study electron-ion, laser-ion, and ion-neutral beams interactions. The lattice design also allows for a future upgrade of the ring to a double storage ring structure that would enable ion-ion beam interactions to be performed. In this paper, we present the design of this ring with a focus on beam dynamics calculations for the 7° single-bend racetrack layout. The study is principally based on the SIMION8 program. We complemented this study further by using purpose-written routine and MAD-X simulation code. An in-depth investigation into beam stability under consideration of non-linear field components in the electrostatic optical elements, is presented. Finally, different working points and stability regions are discussed.

  12. Analytical and numerical investigations into hemisphere-shaped electrostatic sensors.

    PubMed

    Lin, Jun; Chen, Zhong-Sheng; Hu, Zheng; Yang, Yong-Min; Tang, Xin

    2014-07-31

    Electrostatic sensors have been widely used in many applications due to their advantages of low cost and robustness. Their spatial sensitivity and time-frequency characteristics are two important performance parameters. In this paper, an analytical model of the induced charge on a novel hemisphere-shaped electrostatic sensor was presented to investigate its accurate sensing characteristics. Firstly a Poisson model was built for electric fields produced by charged particles. Then the spatial sensitivity and time-frequency response functions were directly derived by the Green function. Finally, numerical calculations were done to validate the theoretical results. The results demonstrate that the hemisphere-shaped sensors have highly 3D-symmetrical spatial sensitivity expressed in terms of elementary function, and the spatial sensitivity is higher and less homogeneous near the hemispherical surface and vice versa. Additionally, the whole monitoring system, consisting of an electrostatic probe and a signal conditioner circuit, acts as a band-pass filter. The time-frequency characteristics depend strongly on the spatial position and velocity of the charged particle, the radius of the probe as well as the equivalent resistance and capacitance of the circuit.

  13. Electrostatic interaction of two charged macroparticles in an equilibrium plasma

    NASA Astrophysics Data System (ADS)

    Filippov, A. V.; Pal', A. F.; Starostin, A. N.

    2015-11-01

    This article is a critical review of publications devoted to studying the electrostatic interaction of two charged macroparticles in an equilibrium plasma. It is shown from an analysis of the force of interaction based on the Maxwell stress tensor that two macroparticles with identical charges in the Poisson-Boltzmann model always repel each other both in isothermal and nonisothermal plasmas. At distances between macroparticles for which the Boltzmann exponents can be linearized, the interaction between macroparticles is completely described by the Debye-Hückel model. The correction to free energy due to the electrostatic interaction in the system of two macroparticles is determined by integrating the correction to the internal energy and by direct calculation of the correction for entropy. It is shown that the free energy coincides with the Yukawa potential. The coincidence of the interaction energy obtained by integrating the force of interaction with the free energy leads to the conclusion about the potential nature of the force of interaction between two macroparticles in an equilibrium plasma. The effect of the outer boundary on the electrostatic interaction force is analyzed; it is shown that the type of interaction depends on the choice of the boundary conditions at the outer boundary. It is also shown that the accumulation of space charge near the outer boundary can lead to the attraction of similarly charged particles at distances comparable with the radius of the outer boundary.

  14. Electrostatic-undulatory theory of plectonemically supercoiled DNA.

    PubMed Central

    Ubbink, J; Odijk, T

    1999-01-01

    We present an analytical calculation of the electrostatic interaction in a plectonemic supercoil within the Poisson-Boltzmann approximation. Undulations of the supercoil strands arising from thermal motion couple nonlinearly with the electrostatic interaction, giving rise to a strong enhancement of the bare interaction. In the limit of fairly tight winding, the free energy of a plectonemic supercoil may be split into an elastic contribution containing the bending and torsional energies and an electrostatic-undulatory free energy. The total free energy of the supercoil is minimized according to an iterative scheme, which utilizes the special symmetry inherent in the usual elastic free energy of the plectoneme. The superhelical radius, opening angle, and undulation amplitudes in the radius and pitch are obtained as a function of the specific linking difference and the concentration of monovalent salt. Our results compare favorably with the experimental values for these parameters of Boles et al. (1990. J. Mol. Biol. 213:931-951). In particular, we confirm the experimental observation that the writhe is a virtually constant fraction of the excess linking number over a wide range of superhelical densities. Another important prediction is the ionic strength dependence of the plectonemic parameters, which is in reasonable agreement with the results from computer simulations. PMID:10233067

  15. Analytical and Numerical Investigations into Hemisphere-Shaped Electrostatic Sensors

    PubMed Central

    Lin, Jun; Chen, Zhong-Sheng; Hu, Zheng; Yang, Yong-Min; Tang, Xin

    2014-01-01

    Electrostatic sensors have been widely used in many applications due to their advantages of low cost and robustness. Their spatial sensitivity and time-frequency characteristics are two important performance parameters. In this paper, an analytical model of the induced charge on a novel hemisphere-shaped electrostatic sensor was presented to investigate its accurate sensing characteristics. Firstly a Poisson model was built for electric fields produced by charged particles. Then the spatial sensitivity and time-frequency response functions were directly derived by the Green function. Finally, numerical calculations were done to validate the theoretical results. The results demonstrate that the hemisphere-shaped sensors have highly 3D-symmetrical spatial sensitivity expressed in terms of elementary function, and the spatial sensitivity is higher and less homogeneous near the hemispherical surface and vice versa. Additionally, the whole monitoring system, consisting of an electrostatic probe and a signal conditioner circuit, acts as a band-pass filter. The time-frequency characteristics depend strongly on the spatial position and velocity of the charged particle, the radius of the probe as well as the equivalent resistance and capacitance of the circuit. PMID:25090419

  16. Electrostatic interaction of two charged macroparticles in an equilibrium plasma

    SciTech Connect

    Filippov, A. V. Pal’, A. F.; Starostin, A. N.

    2015-11-15

    This article is a critical review of publications devoted to studying the electrostatic interaction of two charged macroparticles in an equilibrium plasma. It is shown from an analysis of the force of interaction based on the Maxwell stress tensor that two macroparticles with identical charges in the Poisson–Boltzmann model always repel each other both in isothermal and nonisothermal plasmas. At distances between macroparticles for which the Boltzmann exponents can be linearized, the interaction between macroparticles is completely described by the Debye–Hückel model. The correction to free energy due to the electrostatic interaction in the system of two macroparticles is determined by integrating the correction to the internal energy and by direct calculation of the correction for entropy. It is shown that the free energy coincides with the Yukawa potential. The coincidence of the interaction energy obtained by integrating the force of interaction with the free energy leads to the conclusion about the potential nature of the force of interaction between two macroparticles in an equilibrium plasma. The effect of the outer boundary on the electrostatic interaction force is analyzed; it is shown that the type of interaction depends on the choice of the boundary conditions at the outer boundary. It is also shown that the accumulation of space charge near the outer boundary can lead to the attraction of similarly charged particles at distances comparable with the radius of the outer boundary.

  17. Theory of the water vapor continuum and validations

    NASA Astrophysics Data System (ADS)

    Tipping, R. H.; Ma, Q.

    A far-wing line shape theory based on the binary collision and quasistatic approximations that is applicable for both the low- and high-frequency wings of the vibration-rotational bands has been developed. This theory has been applied in order to calculate the frequency and temperature dependence of the continuous absorption coefficient for frequencies up to 10,000 cm -1 for pure H 2O and for H 2ON 2 mixtures. The calculations were made assuming an interaction potential consisting of an isotropic Lennard-Jones part with two parameters that are consistent with values obtained from other data, and the leading long-range anisotropic part, together with the measured line strengths and transition frequencies. The results, obtained without the introduction of adjustable parameters, compare well with the existing laboratory data, both in magnitude and in temperature dependence. This leads us to the conclusion that the water continuum can be explained in terms of far-wing absorption. Current work in progress to extend the theory and to validate the theoretically calculated continuum will be discussed briefly.

  18. Theory of the water vapor continuum and validations

    NASA Technical Reports Server (NTRS)

    Tipping, Richard H.; Ma, Q.

    1995-01-01

    A far-wing line shape theory based on the binary collision and quasistatic approximations that is applicable for both the low- and high-frequency wings of the vibration-rotational bands has been developed. This theory has been applied in order to calculate the frequency and temperature dependence of the continuous absorption coefficient for frequencies up to 10,000 cm(exp -1) for pure H2O and for H2O-N2 mixtures. The calculations were made assuming an interaction potential consisting of an isotropic Lennard-Jones part with two parameters that are consistent with values obtained from other data, and the leading long-range anisotropic part, together with the measured line strengths and transition frequencies. The results, obtained without the introduction of adjustable parameters, compare well with the existing laboratory data, both in magnitude and in temperature dependence. This leads us to the conclusion that the water continuum can be explained in terms of far-wing absorption. Current work in progress to extend the theory and to validate the theoretically calculated continuum will be discussed briefly.

  19. Monitoring by Control Technique - Electrostatic Precipitators

    EPA Pesticide Factsheets

    Stationary source emissions monitoring is required to demonstrate that a source is meeting the requirements in Federal or state rules. This page is about electrostatic precipitator control techniques used to reduce pollutant emissions.

  20. The Electrocardiogram as an Example of Electrostatics

    ERIC Educational Resources Information Center

    Hobbie, Russell K.

    1973-01-01

    Develops a simplified electrostatic model of the heart with conduction within the torso neglected to relate electrocardiogram patterns to the charge distribution within the myocardium. Suggests its application to explanation of Coulomb's law in general physics. (CC)

  1. Nonlinear electrostatic drift Kelvin-Helmholtz instability

    NASA Technical Reports Server (NTRS)

    Sharma, Avadhesh C.; Srivastava, Krishna M.

    1993-01-01

    Nonlinear analysis of electrostatic drift Kelvin-Helmholtz instability is performed. It is shown that the analysis leads to the propagation of the weakly nonlinear dispersive waves, and the nonlinear behavior is governed by the nonlinear Burger's equation.

  2. NEW APPROACHES: A novel Kelvin Electrostatic Generator

    NASA Astrophysics Data System (ADS)

    Hill, M.; Jacobs, D. J.

    1997-01-01

    A form of the Kelvin Electrostatic Generator, made from readily available components, is described and an explanation given of how it works. The device described can generate 10 - 12 mm long sparks in air.

  3. Electrostatic discharge control for STDN stations

    NASA Technical Reports Server (NTRS)

    Mckiernan, J.

    1983-01-01

    This manual defines the requirements and control methods necessary to control the effect of electrostatic discharges that damage or destroy electronic equipment components. Test procedures for measuring the effectiveness of the control are included.

  4. Electrostatic processing of polymers and polymer composites

    NASA Astrophysics Data System (ADS)

    Sanders, Elliot Howard

    2005-11-01

    Polymers are a broad class of molecules whose use in modern life is undeniable ranging from automobile parts to pharmaceuticals. One method applicable to polymer material production is known as electrostatic processing which includes electrospraying, used to produce films or microparticles, and electrospinning, which can be used to produce fibers or non-woven materials. Electrostatic processing typically results in products with droplet or fiber diameters on the micron or nanometer scale. We have sought to develop novel polymeric materials and composites using electrostatic processing. The end uses of these materials were diverse, and included controlled release of drugs, microencapsulation of proteins and enzymes, provision of molecular cues for directed cell growth, hydronium ion transport, and electrically conductive polymer and catalytically active composites. We have successfully demonstrated that electrostatic processing can be used to produce a wide variety of functionally active polymer based materials with significant commercial, medical, and scientific potential.

  5. Electrostatic correlations near charged planar surfaces

    PubMed Central

    Deng, Mingge; Em Karniadakis, George

    2014-01-01

    Electrostatic correlation effects near charged planar surfaces immersed in a symmetric electrolytes solution are systematically studied by numerically solving the nonlinear six-dimensional electrostatic self-consistent equations. We compare our numerical results with widely accepted mean-field (MF) theory results, and find that the MF theory remains quantitatively accurate only in weakly charged regimes, whereas in strongly charged regimes, the MF predictions deviate drastically due to the electrostatic correlation effects. We also observe a first-order like phase-transition corresponding to the counterion condensation phenomenon in strongly charged regimes, and compute the phase diagram numerically within a wide parameter range. Finally, we investigate the interactions between two likely-charged planar surfaces, which repulse each other as MF theory predicts in weakly charged regimes. However, our results show that they attract each other above a certain distance in strongly charged regimes due to significant electrostatic correlations. PMID:25194382

  6. Electrostatic Beneficiation of Lunar Simulant

    NASA Technical Reports Server (NTRS)

    Trigwell, Steve; Captain, James; Captain, Janine; Arens, Ellen; Quinn, Jacqueline; Calle, Carlos

    2006-01-01

    Electrostatic beneficiation of lunar regolith is a method allowing refinement of specific minerals in the material for processing on the moon. The use of tribocharging the regolith prior to separation was investigated on the lunar simulant MLS-I by passing the dust through static mixers constructed from different materials; aluminum, copper, stainless steel, and polytetrafluoroethylene (PTFE). The amount of charge acquired by the simulant was dependent upon the difference in the work function of the dust and the charging material. XPS and SEM were used to characterize the simulant after it was sieved into five size fractions (> 100 pm, 75-100 pm, 50- 75 pm, 50-25 pm, and < 25 pm), where very little difference in surface composition was observed between the sizes. Samples of the smallest (< 25 pm) and largest (> 100 pm) size fractions were beneficiated through a charge separator using the aluminum (charged the simulant negatively) and PTFE (charged positively) mixers. The mass fractions of the separated simulant revealed that for the larger particle size, significant unipolar charging was observed for both mixers, whereas for the smaller particle sizes, more bipolar charging was observed, probably due to the finer simulant adhering to the inside of the mixers shielding the dust from the charging material. Subsequent XPS analysis of the beneficiated fractions showed the larger particle size fraction having some species differentiation, but very little difference for the smaller.size. Although MLS-1 was made to have similar chemistry to actual lunar dust, its mineralogy is quite different. On-going experiments are using NASA JSC-1 lunar simulant. A vacuum chamber has been constructed, and future experiments are planned in a simulated lunar environment.

  7. Miniature Bipolar Electrostatic Ion Thruster

    NASA Technical Reports Server (NTRS)

    Hartley, Frank T.

    2006-01-01

    The figure presents a concept of a bipolar miniature electrostatic ion thruster for maneuvering a small spacecraft. The ionization device in the proposed thruster would be a 0.1-micron-thick dielectric membrane with metal electrodes on both sides. Small conical holes would be micromachined through the membrane and electrodes. An electric potential of the order of a volt applied between the membrane electrodes would give rise to an electric field of the order of several mega-volts per meter in the submicron gap between the electrodes. An electric field of this magnitude would be sufficient to ionize all the molecules that enter the holes. In a thruster-based on this concept, one or more propellant gases would be introduced into such a membrane ionizer. Unlike in larger prior ion thrusters, all of the propellant molecules would be ionized. This thruster would be capable of bipolar operation. There would be two accelerator grids - one located forward and one located aft of the membrane ionizer. In one mode of operation, which one could denote the forward mode, positive ions leaving the ionizer on the backside would be accelerated to high momentum by an electric field between the ionizer and an accelerator grid. Electrons leaving the ionizer on the front side would be ejected into free space by a smaller accelerating field. The equality of the ion and electron currents would eliminate the need for an additional electron- or ion-emitting device to keep the spacecraft charge-neutral. In another mode of operation, which could denote the reverse mode, the polarities of the voltages applied to the accelerator grids and to the electrodes of the membrane ionizer would be the reverse of those of the forward mode. The reversal of electric fields would cause the ion and electrons to be ejected in the reverse of their forward mode directions, thereby giving rise to thrust in the direction opposite that of the forward mode.

  8. Electrostatic camera system functional design study

    NASA Technical Reports Server (NTRS)

    Botticelli, R. A.; Cook, F. J.; Moore, R. F.

    1972-01-01

    A functional design study for an electrostatic camera system for application to planetary missions is presented. The electrostatic camera can produce and store a large number of pictures and provide for transmission of the stored information at arbitrary times after exposure. Preliminary configuration drawings and circuit diagrams for the system are illustrated. The camera system's size, weight, power consumption, and performance are characterized. Tradeoffs between system weight, power, and storage capacity are identified.

  9. Miniature Electrostatic Ion Thruster With Magnet

    NASA Technical Reports Server (NTRS)

    Hartley, Frank T.

    2006-01-01

    A miniature electrostatic ion thruster is proposed that, with one exception, would be based on the same principles as those of the device described in the previous article, "Miniature Bipolar Electrostatic Ion Thruster". The exceptional feature of this thruster would be that, in addition to using electric fields for linear acceleration of ions and electrons, it would use a magnetic field to rotationally accelerate slow electrons into the ion stream to neutralize the ions.

  10. Electrostatic Levitation Furnace for the ISS

    NASA Technical Reports Server (NTRS)

    Murakami, Keiji; Koshikawa, Naokiyo; Shibasaki, Kohichi; Ishikawa, Takehiko; Okada, Junpei; Takada, Tetsuya; Arai, Tatsuya; Fujino, Naoki; Yamaura, Yukiko

    2012-01-01

    JAXA (Japan Aerospace Exploration Agency) has just started the development of Electrostatic Levitation Furnace to be launched in 2014 for the ISS. This furnace can control the sample position with electrostatic force and heat it above 2000 degree Celsius using semiconductor laser from four different directions. The announcement of Opportunity will be issued soon for this furnace. In this paper, we will show the specifications of this furnace and also the development schedule

  11. High-energy capacitance electrostatic micromotors

    NASA Astrophysics Data System (ADS)

    Baginsky, I. L.; Kostsov, E. G.

    2003-03-01

    The design and parameters of a new electrostatic micromotor with high energy output are described. The motor is created by means of microelectronic technology. Its operation is based on the electromechanic energy conversion during the electrostatic rolling of the metallic films (petals) on the ferroelectric film surface. The mathematical simulation of the main characteristics of the rolling process is carried out. The experimentally measured parameters of the petal step micromotors are shown. The motor operation and its efficiency are investigated.

  12. Semiclassical calculations of observable cross sections in breakup reactions

    SciTech Connect

    Marta, H. D.; Canto, L. F.; Donangelo, R.

    2008-09-15

    We develop a semiclassical procedure to calculate breakup reaction products' angular and energy distributions in the laboratory frame of reference. The effects of the Coulomb and nuclear interaction potentials on the classical trajectories, as well as bound-bound, bound-continuum, and continuum-continuum couplings, are included. As an example we consider the {sup 8}B+{sup 58}Ni system at E{sub lab}=26 MeV and find very good agreement with the available experimental data.

  13. A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers.

    PubMed

    Cooper, Christopher D; Bardhan, Jaydeep P; Barba, L A

    2014-03-01

    The continuum theory applied to biomolecular electrostatics leads to an implicit-solvent model governed by the Poisson-Boltzmann equation. Solvers relying on a boundary integral representation typically do not consider features like solvent-filled cavities or ion-exclusion (Stern) layers, due to the added difficulty of treating multiple boundary surfaces. This has hindered meaningful comparisons with volume-based methods, and the effects on accuracy of including these features has remained unknown. This work presents a solver called PyGBe that uses a boundary-element formulation and can handle multiple interacting surfaces. It was used to study the effects of solvent-filled cavities and Stern layers on the accuracy of calculating solvation energy and binding energy of proteins, using the well-known apbs finite-difference code for comparison. The results suggest that if required accuracy for an application allows errors larger than about 2% in solvation energy, then the simpler, single-surface model can be used. When calculating binding energies, the need for a multi-surface model is problem-dependent, becoming more critical when ligand and receptor are of comparable size. Comparing with the apbs solver, the boundary-element solver is faster when the accuracy requirements are higher. The cross-over point for the PyGBe code is in the order of 1-2% error, when running on one gpu card (nvidia Tesla C2075), compared with apbs running on six Intel Xeon cpu cores. PyGBe achieves algorithmic acceleration of the boundary element method using a treecode, and hardware acceleration using gpus via PyCuda from a user-visible code that is all Python. The code is open-source under MIT license.

  14. Numerical Investigation of Two-Phase Flows With Charged Droplets in Electrostatic Field

    NASA Technical Reports Server (NTRS)

    Kim, Sang-Wook

    1996-01-01

    A numerical method to solve two-phase turbulent flows with charged droplets in an electrostatic field is presented. The ensemble-averaged Navier-Stokes equations and the electrostatic potential equation are solved using a finite volume method. The transitional turbulence field is described using multiple-time-scale turbulence equations. The equations of motion of droplets are solved using a Lagrangian particle tracking scheme, and the inter-phase momentum exchange is described by the Particle-In-Cell scheme. The electrostatic force caused by an applied electrical potential is calculated using the electrostatic field obtained by solving a Laplacian equation and the force exerted by charged droplets is calculated using the Coulombic force equation. The method is applied to solve electro-hydrodynamic sprays. The calculated droplet velocity distributions for droplet dispersions occurring in a stagnant surrounding are in good agreement with the measured data. For droplet dispersions occurring in a two-phase flow, the droplet trajectories are influenced by aerodynamic forces, the Coulombic force, and the applied electrostatic potential field.

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

    SciTech Connect

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

    1999-10-21

    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.

  16. Retinal Photoisomerization in Rhodopsin: Electrostatic and Steric Catalysis

    SciTech Connect

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

    2007-12-26

    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 {beta}-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, {beta}-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.

  17. Electrostatic adhesion of multiple non-uniformly charged dielectric particles

    NASA Astrophysics Data System (ADS)

    Kemp, B. A.; Whitney, J. G.

    2013-01-01

    Charged particle adhesion measurements can be as much as one order of magnitude higher than theoretical calculations. This discrepancy has ignited a debate as to the nature of the physics occurring with microscopic particle adhesion. Attempts to bring calculations closer to measured results have produced models that include multiple particle interactions, dielectric polarization, and non-uniform charge. Individually, each of these models can only produce a 2× to 5× enhancement in predicted adhesion force over simple Coulombic attraction. In this correspondence, an analytical model of electrostatic particle forces is developed, which allows for independent assignment of dielectric constant and non-uniform surface charge distribution to an arbitrary number of particles. Because the model can include an image plane, it is ideal for electrostatic adhesion calculations. Application to a monolayer of printed toner particles predicts nearly an order of magnitude increase in adhesion force over Coulombic attraction. These results are the first analytical results to place predictions of charged particle adhesion on the same order of magnitude with measurements.

  18. Linear and nonlinear interactions of an electron beam with oblique whistler and electrostatic waves in the magnetosphere

    NASA Astrophysics Data System (ADS)

    Zhang, Y. L.; Matsumoto, H.; Omura, Y.

    1993-12-01

    Both linear and nonlinear interactions between oblique whistler, electrostatic, quasi-upper hybrid mode waves and an electron beam are studied by linear analyses and electromagnetic particle simulations. In addition to a background cold plasma, we assumed a hot electron beam drifting along a static magnetic field. Growth rates of the oblique whistler, oblique electrostatic, and quasi-upper hybrid instabilities were first calculated. We found that there are four kinds of unstable mode waves for parallel and oblique propagations. They are the electromagnetic whistler mode wave (WW1), the electrostatic whistler mode wave (WW2), the electrostatic mode wave (ESW), and the quasi-upper hybrid mode wave (UHW). A possible mechanism is proposed to explain the satellite observations of whistler mode chorus and accompanied electrostatic waves, whose amplitudes are sometimes modulated at the chorus frequency.

  19. A computational approach to continuum damping of Alfven waves in two and three-dimensional geometry

    SciTech Connect

    Koenies, Axel; Kleiber, Ralf

    2012-12-15

    While the usual way of calculating continuum damping of global Alfven modes is the introduction of a small artificial resistivity, we present a computational approach to the problem based on a suitable path of integration in the complex plane. This approach is implemented by the Riccati shooting method and it is shown that it can be transferred to the Galerkin method used in three-dimensional ideal magneto-hydrodynamics (MHD) codes. The new approach turns out to be less expensive with respect to resolution and computation time than the usual one. We present an application to large aspect ratio tokamak and stellarator equilibria retaining a few Fourier harmonics only and calculate eigenfunctions and continuum damping rates. These may serve as an input for kinetic MHD hybrid models making it possible to bypass the problem of having singularities on the path of integration on one hand and considering continuum damping on the other.

  20. Core excitations in (d,p) reactions including transitions to continuum levels

    NASA Astrophysics Data System (ADS)

    Makoto, Tanifuji; Osamu, Mikoshiba; Tokuo, Terasawa

    1982-11-01

    Effects of core excitations in (d, p) reactions are investigated for 12C(d, p) 13C ∗ reactions in the CCBA framework, where couplings of channels are considered for the ground and first-excited levels of 12C in the initial state and for the bound {1}/{2}+and{5}/{2}+ levels and low-lying continuum levels of 13C in the final state, where a discretization is introduced for the continuum region. In the transitions to the continuum levels, matrix elements are calculated by the use of scattering-state wave functions for the final neutron. Theoretical cross sections and vector analyzing powers are compared with experimental data, where significant contributions of core-excitation processes are identified, particularly in the transition to the {5}/{2}+II level of 13C. Spectra of emitted protons are calculated and compared with the measured ones. Adequate agreement between theory and experiment is found throughout the present investigation.

  1. Microstructural and continuum evolution modeling of sintering.

    SciTech Connect

    Braginsky, Michael V.; Olevsky, Eugene A.; Johnson, D. Lynn; Tikare, Veena; Garino, Terry J.; Arguello, Jose Guadalupe, Jr.

    2003-12-01

    deformation during. The continuum portion is based on a finite element formulation that allows 3D components to be modeled using SNL's nonlinear large-deformation finite element code, JAS3D. This tool provides a capability to model sintering of complex three-dimensional components. The model was verified by comparing to simulations results published in the literature. The model was validated using experimental results from various laboratory experiments performed by Garino. In addition, the mesoscale simulations were used to study anisotropic shrinkage in aligned, elongated powder compacts. Anisotropic shrinkage occurred in all compacts with aligned, elongated particles. However, the direction of higher shrinkage was in some cases along the direction of elongation and in other cases in the perpendicular direction depending on the details of the powder compact. In compacts of simple-packed, mono-sized, elongated particles, shrinkage was higher in the direction of elongation. In compacts of close-packed, mono-sized, elongated particles and of elongated particles with a size and shape distribution, the shrinkage was lower in the direction of elongation. We also explored the concept of a sintering stress tensor rather than the traditional sintering stress scalar concept for the case of anisotropic shrinkage. A thermodynamic treatment of this is presented. A method to calculate the sintering stress tensor is also presented. A user-friendly code that can simulate microstructural evolution during sintering in 2D and in 3D was developed. This code can run on most UNIX platforms and has a motif-based GUI. The microstructural evolution is shown as the code is running and many of the microstructural features, such as grain size, pore size, the average grain boundary length (in 2D) and area (in 3D), etc. are measured and recorded as a function of time. The overall density as the function of time is also recorded.

  2. Determination of Near-IR Water Vapor Self Continuum from Observations

    NASA Astrophysics Data System (ADS)

    Mlawer, Eli; Gombos, Daniel; Alvarado, Matthew; Cady-Pereira, Karen; Payne, Vivienne; Chase, Alison; Michalsky, Joseph

    2014-06-01

    There is still significant uncertainty in the strength of water vapor continuum absorption in the windows between near-infrared water vapor bands. Many radiation codes obtain their water vapor continuum absorption coefficients from the MT CKD continuum model, which derives its near-infrared values from a water vapor line-shape function that has been constrained by continuum measurements in other spectral regions. A number of recent laboratory studies have shown that the strength of the near-IR self continuum in the MT CKD model is too low, but these laboratory studies disagree with each other by more than an order of magnitude. At the high end of the range of measured strengths, the self continuum absorbs a significant amount of solar radiation, so it is crucial that other observational studies are performed to establish the actual strength of this absorption source. We describe here an analysis of measurements from a solar FTS in Lamont, OK, part of the Total Carbon Column Observing Network (TCCON). Thirteen periods on individual days in 2012 were identified as being reasonably stable with respect to aerosol optical depth and precipitable water vapor. For each period, the FTS measurements, coincident measurements from a Normal Incidence Multi-Filter Radiometer (NIMFR) at the DOE ARM site, and calculations from the Line-By-Line Radiative Transfer Model (LBLRTM) were used to obtain aerosol optical depths in window regions from 8000-20000 cm-1, which were then extended to lower wavenumbers through a generalized Angstrom relationship. In windows between 4000-7000 cm-1, these aerosol optical depths, and the LBLRTM optical depths without any self continuum, were subtracted from FTS-derived total optical depths. The self continuum absorption coefficients that were derived from this procedure were at the low end of the recent laboratory studies, but higher than the current version of MT CKD. The implications of the results of this study with respect to the absorption of

  3. FT-IR spectroscopy combined with DFT calculation to explore solvent effects of vinyl acetate.

    PubMed

    Chen, Yi; Zhang, Hui; Liu, Qing

    2014-05-21

    The infrared vibration frequencies of vinyl acetate (VAc) in 18 different solvents were theoretically computed at Density Function Theory (DFT) B3LYP/6-311G(*) level based on Polarizable Continuum Model (PCM) and experimentally recorded by FT-IR spectroscopy. The solvent-induced long-range bulk electrostatic solvation free energies of VAc (ΔGelec) were calculated by the SMD model. The C=O stretching vibration frequencies of VAc were utilized as a measure of the chemical reactivities of the CC group in VAc. The calculated and experimental C=O stretching vibration frequencies of VAc (νcal(C=O) and νexp(C=O)) were correlated with empirical solvent parameters including the KBM equation, the Swain equation and the linear solvation energy relationships (LSER). Through ab initio calculation, assignments of the two C=O absorption bands of VAc in alcohol solvents were achieved. The PCM, SMD and ab initio calculation offered supporting evidence to explain the FT-IR experimental observations from differing aspects.

  4. FT-IR spectroscopy combined with DFT calculation to explore solvent effects of vinyl acetate

    NASA Astrophysics Data System (ADS)

    Chen, Yi; Zhang, Hui; Liu, Qing

    The infrared vibration frequencies of vinyl acetate (VAc) in 18 different solvents were theoretically computed at Density Function Theory (DFT) B3LYP/6-311G* level based on Polarizable Continuum Model (PCM) and experimentally recorded by FT-IR spectroscopy. The solvent-induced long-range bulk electrostatic solvation free energies of VAc (ΔGelec) were calculated by the SMD model. The Cdbnd O stretching vibration frequencies of VAc were utilized as a measure of the chemical reactivities of the Cdbnd C group in VAc. The calculated and experimental Cdbnd O stretching vibration frequencies of VAc (νcal(Cdbnd O) and νexp(Cdbnd O)) were correlated with empirical solvent parameters including the KBM equation, the Swain equation and the linear solvation energy relationships (LSER). Through ab initio calculation, assignments of the two Cdbnd O absorption bands of VAc in alcohol solvents were achieved. The PCM, SMD and ab initio calculation offered supporting evidence to explain the FT-IR experimental observations from differing aspects.

  5. Computation of molecular electrostatics with boundary element methods.

    PubMed Central

    Liang, J; Subramaniam, S

    1997-01-01

    In continuum approaches to molecular electrostatics, the boundary element method (BEM) can provide accurate solutions to the Poisson-Boltzmann equation. However, the numerical aspects of this method pose significant problems. We describe our approach, applying an alpha shape-based method to generate a high-quality mesh, which represents the shape and topology of the molecule precisely. We also describe an analytical method for mapping points from the planar mesh to their exact locations on the surface of the molecule. We demonstrate that derivative boundary integral formulation has numerical advantages over the nonderivative formulation: the well-conditioned influence matrix can be maintained without deterioration of the condition number when the number of the mesh elements scales up. Singular integrand kernels are characteristics of the BEM. Their accurate integration is an important issue. We describe variable transformations that allow accurate numerical integration. The latter is the only plausible integral evaluation method when using curve-shaped boundary elements. Images FIGURE 3 FIGURE 5 FIGURE 6 FIGURE 7 FIGURE 8 PMID:9336178

  6. Stiffness Control of Surgical Continuum Manipulators

    PubMed Central

    Mahvash, Mohsen; Dupont, Pierre E.

    2013-01-01

    This paper introduces the first stiffness controller for continuum robots. The control law is based on an accurate approximation of a continuum robot’s coupled kinematic and static force model. To implement a desired tip stiffness, the controller drives the actuators to positions corresponding to a deflected robot configuration that produces the required tip force for the measured tip position. This approach provides several important advantages. First, it enables the use of robot deflection sensing as a means to both sense and control tip forces. Second, it enables stiffness control to be implemented by modification of existing continuum robot position controllers. The proposed controller is demonstrated experimentally in the context of a concentric tube robot. Results show that the stiffness controller achieves the desired stiffness in steady state, provides good dynamic performance, and exhibits stability during contact transitions. PMID:24273466

  7. Stiffness Control of Surgical Continuum Manipulators.

    PubMed

    Mahvash, Mohsen; Dupont, Pierre E

    2011-04-01

    This paper introduces the first stiffness controller for continuum robots. The control law is based on an accurate approximation of a continuum robot's coupled kinematic and static force model. To implement a desired tip stiffness, the controller drives the actuators to positions corresponding to a deflected robot configuration that produces the required tip force for the measured tip position. This approach provides several important advantages. First, it enables the use of robot deflection sensing as a means to both sense and control tip forces. Second, it enables stiffness control to be implemented by modification of existing continuum robot position controllers. The proposed controller is demonstrated experimentally in the context of a concentric tube robot. Results show that the stiffness controller achieves the desired stiffness in steady state, provides good dynamic performance, and exhibits stability during contact transitions.

  8. Defining and testing a granular continuum element

    SciTech Connect

    Rycroft, Chris H.; Kamrin, Ken; Bazant, Martin Z.

    2007-12-03

    Continuum mechanics relies on the fundamental notion of amesoscopic volume "element" in which properties averaged over discreteparticles obey deterministic relationships. Recent work on granularmaterials suggests a continuum law may be inapplicable, revealinginhomogeneities at the particle level, such as force chains and slow cagebreaking. Here, we analyze large-scale Discrete-Element Method (DEM)simulations of different granular flows and show that a "granularelement" can indeed be defined at the scale of dynamical correlations,roughly three to five particle diameters. Its rheology is rather subtle,combining liquid-like dependence on deformation rate and solid-likedependence on strain. Our results confirm some aspects of classicalplasticity theory (e.g., coaxiality of stress and deformation rate),while contradicting others (i.e., incipient yield), and can guide thedevelopment of more realistic continuum models.

  9. The matching of electrostatic extrema: A useful method in drug design? A study of phosphodiesterase III inhibitors

    NASA Astrophysics Data System (ADS)

    Apaya, Robert P.; Lucchese, Baldo; Price, Sarah L.; Vinter, J. G.

    1995-02-01

    Ligands which bind to a specific protein binding site are often expected to have a similar electrostatic environment which complements that of the binding site. One method of assessing molecular electrostatic similarity is to examine the possible overlay of the maxima and minima in the electrostatic potential outside the molecules and thereby match the regions where strong electrostatic interactions, including hydrogen bonds, with the residues of the binding site may be possible. This approach is validated with accurate calculations of the electrostatic potential, derived from a distributed multipole analysis of an ab initio charge density of the molecule, so that the effects of lone pair and π-electron density are correctly included. We have applied this method to the phosphodiesterase (PDE) III substrate adenosine-3',5'-cyclic monophosphate (cAMP) and a range of nonspecific and specific PDE III inhibitors. Despite the structural variation between cAMP and the inhibitors, it is possible to match three or four extrema to produce relative orientations in which the inhibitors are sufficiently sterically and electrostatically similar to the natural substrate to account for their affinity for PDE III. This matching of extrema is more apparent using the accurate electrostatic models than it was when this approach was first applied, using semiempirical point charge models. These results reinforce the hypothesis of electrostatic similarity and give weight to the technique of extrema matching as a useful tool in drug design.

  10. Orion Aerodynamics for Hypersonic Free Molecular to Continuum Conditions

    NASA Technical Reports Server (NTRS)

    Moss, James N.; Greene, Francis A.; Boyles, Katie A.

    2006-01-01

    Numerical simulations are performed for the Orion Crew Module, previously known as the Crew Exploration Vehicle (CEV) Command Module, to characterize its aerodynamics during the high altitude portion of its reentry into the Earth's atmosphere, that is, from free molecular to continuum hypersonic conditions. The focus is on flow conditions similar to those that the Orion Crew Module would experience during a return from the International Space Station. The bulk of the calculations are performed with two direct simulation Monte Carlo (DSMC) codes, and these data are anchored with results from both free molecular and Navier-Stokes calculations. Results for aerodynamic forces and moments are presented that demonstrate their sensitivity to rarefaction, that is, for free molecular to continuum conditions (Knudsen numbers of 111 to 0.0003). Also included are aerodynamic data as a function of angle of attack for different levels of rarefaction and results that demonstrate the aerodynamic sensitivity of the Orion CM to a range of reentry velocities (7.6 to 15 km/s).

  11. Modeling angiogenesis: A discrete to continuum description

    NASA Astrophysics Data System (ADS)

    Pillay, Samara; Byrne, Helen M.; Maini, Philip K.

    2017-01-01

    Angiogenesis is the process by which new blood vessels develop from existing vasculature. During angiogenesis, endothelial tip cells migrate via diffusion and chemotaxis, loops form via tip-to-tip and tip-to-sprout anastomosis, new tip cells are produced via branching, and a vessel network forms as endothelial cells follow the paths of tip cells. The latter process is known as the snail trail. We use a mean-field approximation to systematically derive a continuum model from a two-dimensional lattice-based cellular automaton model of angiogenesis in the corneal assay, based on the snail-trail process. From the two-dimensional continuum model, we derive a one-dimensional model which represents angiogenesis in two dimensions. By comparing the discrete and one-dimensional continuum models, we determine how individual cell behavior manifests at the macroscale. In contrast to the phenomenological continuum models in the literature, we find that endothelial cell creation due to tip cell movement (vessel formation via the snail trail) manifests as a source term of tip cells on the macroscale. Further, we find that phenomenological continuum models, which assume that endothelial cell creation is proportional to the flux of tip cells in the direction of increasing chemoattractant concentration, qualitatively capture vessel formation in two dimensions, but must be modified to accurately represent vessel formation. Additionally, we find that anastomosis imposes restrictions on cell density, which, if violated, leads to ill-posedness in our continuum model. We also deduce that self-loops should be excluded when tip-to-sprout anastomosis is active in the discrete model to ensure propagation of the vascular front.

  12. Influence of a channel-forming peptide on energy barriers to ion permeation, viewed from a continuum dielectric perspective.

    PubMed Central

    Partenskii, M B; Dorman, V; Jordan, P C

    1994-01-01

    The continuum three-dielectric model for an aqueous ion channel pore-forming peptide-membrane system is extended to account for the finite length of the channel. We focus on the electrostatic influence that a channel-forming peptide may exert on energy barriers to ion permeation. The nonlinear dielectric behavior of channel water caused by dielectric saturation in the presence of an ion is explicitly modeled by assigning channel water a mean dielectric constant much less than that of bulk water. An exact solution of the continuum problem is formulated by approximating the dielectric behavior of bulk water, assigning it a dielectric constant of infinity. The validity of this approximation is verified by comparison with a Poisson-Boltzmann description of the electrolyte. The formal equivalence of high ionic strength and high electrolyte dielectric constant is demonstrated. We estimate limits on the reduction of the electrostatic free energy caused by ionic interaction with the channel-forming peptide. We find that even assigning this region an epsilon of 100, its influence is insufficient to lower permeation free energy barriers to values consistent with observed channel conductances. We provide estimates of the effective dielectric constant of this highly polarizable region, by comparing energy barriers computed using the continuum approach with those found from a semi-microscopic analysis of a simplified model of a gramicidin-like charge distribution. Possible ways of improving both models are discussed. PMID:7529581

  13. A Comparative Study of Transferable Aspherical Pseudoatom Databank and Classical Force Fields for Predicting Electrostatic Interactions in Molecular Dimers

    PubMed Central

    2015-01-01

    Accurate and fast evaluation of electrostatic interactions in molecular systems is one of the most challenging tasks in the rapidly advancing field of macromolecular chemistry and drug design. Electrostatic interactions are of crucial importance in biological systems. They are well represented by quantum mechanical methods; however, such calculations are computationally expensive. In this study, we have evaluated the University of Buffalo Pseudoatom Databank (UBDB)1,2 approach for approximation of electrostatic properties of macromolecules and their complexes. We selected the S663 and JSCH-20054 data sets (208 molecular complexes in total) for this study. These complexes represent a wide range of chemical and biological systems for which hydrogen bonding, electrostatic, and van der Waals interactions play important roles. Reference electrostatic energies were obtained directly from wave functions at the B3LYP/aug-cc-pVTZ level of theory using the SAPT (Symmetry-Adapted Perturbation Theory) scheme for calculation of electrostatic contributions to total intermolecular interaction energies. Electrostatic energies calculated on the basis of the UBDB were compared with corresponding reference results. Results were also compared with energies computed using a point charge model from popular force fields (AM1-BCC and RESP used in AMBER and CGenFF from CHARMM family). The energy trends are quite consistent (R2 ≈ 0.98) for the UBDB method as compared to the AMBER5 and CHARMM force field methods6(R2 ≈ 0.93 on average). The RSMEs do not exceed 3.2 kcal mol–1 for the UBDB and are in the range of 3.7–7.6 kcal mol–1 for the point charge models. We also investigated the discrepancies in electrostatic potentials and magnitudes of dipole moments among the tested methods. This study shows that estimation of electrostatic interaction energies using the UBDB databank is accurate and reasonably fast when compared to other known methods, which opens potential new applications

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

    NASA Astrophysics Data System (ADS)

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

    2017-04-01

    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.

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

    PubMed

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

    2015-02-17

    . Complementary molecular dynamics simulations in conjunction with mixed quantum mechanical/molecular mechanical calculations accurately reproduced the vibrational frequency shifts in these probes and provided atomic-level insight into the residues influencing these changes. Our findings indicate that conformational and electrostatic changes are intimately related and functionally essential. This approach can be readily extended to the study of other enzyme systems to identify more general trends in the relationship between conformational fluctuations and electrostatic interactions. These results are relevant to researchers seeking to design novel enzymes as well as those seeking to develop therapeutic agents that function as enzyme inhibitors.

  16. Electrostatic effects on hyaluronic acid configuration

    NASA Astrophysics Data System (ADS)

    Berezney, John; Saleh, Omar

    2015-03-01

    In systems of polyelectrolytes, such as solutions of charged biopolymers, the electrostatic repulsion between charged monomers plays a dominant role in determining the molecular conformation. Altering the ionic strength of the solvent thus affects the structure of such a polymer. Capturing this electrostatically-driven structural dependence is important for understanding many biological systems. Here, we use single molecule manipulation experiments to collect force-extension behavior on hyaluronic acid (HA), a polyanion which is a major component of the extracellular matrix in all vertebrates. By measuring HA elasticity in a variety of salt conditions, we are able to directly assess the contribution of electrostatics to the chain's self-avoidance and local stiffness. Similar to recent results from our group on single-stranded nucleic acids, our data indicate that HA behaves as a swollen chain of electrostatic blobs, with blob size proportional to the solution Debye length. Our data indicate that the chain structure within the blob is not worm-like, likely due to long-range electrostatic interactions. We discuss potential models of this effect.

  17. Relativistic mean field calculations in neutron-rich nuclei

    SciTech Connect

    Gangopadhyay, G.; Bhattacharya, Madhubrata; Roy, Subinit

    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.

  18. Study on electrostatic resonance of nanoprisms with sharp corners

    NASA Astrophysics Data System (ADS)

    Chan, Wai Soen; Ng, Ka Ki; Yu, Kin Wah

    2015-03-01

    We have studied the electrostatic resonance of metal nanoprisms with sharp corners numerically. We consider an infinite metal cylinder with polygonal base, e.g. square. The incident electric field lies in the plane of cross-section of the cylinder. Yu and co-workers proposed Green's function formalism (GFF) to numerically calculate the electric potential and field distribution in plasmonic systems. We will adopt the scheme to demonstrate the effect of sharp corners, particularly on the effect of electrostatic resonance spectrum, as in the spectral analysis proposed by Bergman and Milton. Hetherington and Thorpe investigated the conductivity of a sheet containing dilute inclusion with sharp corners, they made use of a conformal mapping approach to calculate the conductivity from circular inclusions. Helsing, McPhedran and Milton also investigated the optical properties of a metamaterial lattice with inclusions having sharp corners. We study the possibility of improving numerical accuracy by combining the conformal mapping approach and GFF. We may extend similar approach to investigate the properties of plasmonic systems, for examples nanoboties and nanostars.

  19. Continuum theory of polymer crystallization.

    PubMed

    Kundagrami, Arindam; Muthukumar, M

    2007-04-14

    We present a kinetic model of crystal growth of polymers of finite molecular weight. Experiments help to classify polymer crystallization broadly into two kinetic regimes. One is observed in melts or in high molar mass polymer solutions and is dominated by nucleation control with G approximately exp(1/TDeltaT), where G is the growth rate and DeltaT is the supercooling. The other is observed in low molar mass solutions (as well as for small molecules) and is diffusion controlled with G approximately DeltaT, for small DeltaT. Our model unifies these two regimes in a single formalism. The model accounts for the accumulation of polymer chains near the growth front and invokes an entropic barrier theory to recover both limits of nucleation and diffusion control. The basic theory applies to both melts and solutions, and we numerically calculate the growth details of a single crystal in a dilute solution. The effects of molecular weight and concentration are also determined considering conventional polymer dynamics. Our theory shows that entropic considerations, in addition to the traditional energetic arguments, can capture general trends of a vast range of phenomenology. Unifying ideas on crystallization from small molecules and from flexible polymer chains emerge from our theory.

  20. Arbitrary order permanent Cartesian multipolar electrostatic interactions

    NASA Astrophysics Data System (ADS)

    Boateng, H. A.; Todorov, I. T.

    2015-01-01

    Recently, there has been a concerted effort to implement advanced classical potential energy surfaces by adding higher order multipoles to fixed point charge electrostatics in a bid to increase the accuracy of simulations of condensed phase systems. One major hurdle is the unwieldy nature of the expressions which in part has limited developers mostly to including only dipoles and quadrupoles. In this paper, we present a generalization of the Cartesian formulation of electrostatic multipolar interactions that enables the specification of an arbitrary order of multipoles. Specifically, we derive formulas for arbitrary order implementation of the particle mesh Ewald method and give a closed form formula for the stress tensor in the reciprocal space. In addition, we provide recurrence relations for common electrostatic potentials employed in molecular simulations, which allows for the generalization to arbitrary order and guarantees a computational cost that scales as O(p3) for Cartesian multipole interactions of order p.

  1. A Multiscale Morphing Continuum Description for Turbulence

    NASA Astrophysics Data System (ADS)

    Chen, James; Wonnell, Louis

    2015-11-01

    Turbulence is a flow physics phenomena invlolving multiple length scales. The popular Navier- Stokes equations only possess one length/time scale. Therefore, extremely fine mesh is needed for DNS attempting to resolve the small scale motion, which comes with a burden of excessive computational cost. For practical application with complex geometries, the research society rely on RANS and LES, which requre turbulence model or subgrid scale (SGS) model for closure problems. Different models not only lead to different results but usually are invalidated on solid physical grounds, such as objectivity and entropy principle.The Morphing Continuum Theory (MCT) is a high-order continuum theory formulated under the framework of thermalmechanics for physics phenomena involving microstructure. In this study, a theoretical perspective for the multiscale nature of the Morphing Continuum Theory is connected with the multiscale nature of turbulence physics. The kinematics, balance laws, constitutive equations and a Morphing Continuum description of turbulence are introduced. The equations were numerically implemented for a zero pressure gradient flat plate. The simulations are compate with the laminar, transitional and turbulence cases.

  2. Parental Involvement to Parental Engagement: A Continuum

    ERIC Educational Resources Information Center

    Goodall, Janet; Montgomery, Caroline

    2014-01-01

    Based on the literature of the field, this article traces a continuum between parental involvement with schools, and parental engagement with children's learning. The article seeks to shed light on an area of confusion; previous research has shown that different stakeholder groups understand "parental engagement" in different ways.…

  3. Language Attitudes in a Creole Continuum.

    ERIC Educational Resources Information Center

    Rickford, John R.

    The standard view of language attitudes in a creole continuum is that the creole is considered bad and the standard language is considered good. This standard view fits with the theory of decreolization by which such continua are thought to have come about. A study was carried out in Guyana in an effort to overcome the perceived limitations of the…

  4. Some Continuum Aspects of Data Assimilation

    NASA Technical Reports Server (NTRS)

    Cohn, Stephen E.; Menard, Richard

    1999-01-01

    A long-sought goal in data assimilation is to build more fully the time dimension into the data assimilation process. Truly four-dimensional data assimilation requires evolving second-moment information, namely the estimation error covariance, along with the state estimate itself. The continuum evolution equations for the estimation error covariance constitute a system of partial differential equations in six space dimensions, forced by a model error covariance and by the observations themselves. The high dimensionality of this system poses a difficult computational problem. Numerous methods have been proposed for approximate, discrete solution of this system of equations. Four-dimensional variational schemes solve these equations indirectly, while schemes based on Kalman filtering solve the equations more directly, usually on a small subspace of the full six-dimensional space. In both cases, most proposed solution methods are not derived from the continuum covariance evolution equations themselves. Instead, most methods simply inherit the discretization used for evolving the state estimate, either in the form of a discrete tangent linear model or, in the case of ensemble schemes, in the form of a fully nonlinear discrete model. In this lecture we show that solutions of the continuum covariance evolution equations possess simple properties that are not readily satisfied upon discretization of the equations. we give numerical examples illustrating that "inherited" discretizations sometimes fail to produce meaningfully accurate solutions. Finally, we suggest alternative discretization methods that may yield more faithful approximate solutions of the continuum problem.

  5. Radio continuum from FU Orionis stars

    SciTech Connect

    Rodriguez, L.F.; Hartmann, L.W.; Chavira, E. Harvard-Smithsonian Center for Astrophysics, Cambridge, MA Instituto Nacional de Astrofisica, Optica y Electronica, Puebla )

    1990-12-01

    Using the very large array a sensitive search is conducted for 3.6-cm continuum emission toward four FU Orionis objects: FU Ori, V1515 Cyg, V1057 Cyg, and Elias 1-12. V1057 Cyg and Elias 1-12 at the level of about 0.1 mJy is detected. The association of radio continuum emission with these FU Ori objects strengthens a possible relation between FU Ori stars and objects like L 1551 IRS 5 and Z CMa that are also sources of radio continuum emission and have been proposed as post-FU Ori objects. Whether the radio continuum emission is caused by free-free emission from ionized ejecta or if it is optically thin emission from a dusty disk is discussed. It was determined that, in the archives of the Tonantzintla Observatory, a plate taken in 1957 does not show Elias 1-12. This result significantly narrows the time range for the epoch of the outburst of this source to between 1957 and 1965. 38 refs.

  6. A Hybrid approach to molecular continuum processes combiningGaussian basis functions and the discrete variable representation

    SciTech Connect

    Rescigno, Thomas N.; Horner, Daniel A.; Yip, Frank L.; McCurdy,C. William

    2005-08-29

    Gaussian basis functions, routinely employed in molecular electronic structure calculations, can be combined with numerical grid-based functions in a discrete variable representation to provide an efficient method for computing molecular continuum wave functions. This approach, combined with exterior complex scaling, obviates the need for slowly convergent single-center expansions, and allows one to study a variety of electron-molecule collision problems. The method is illustrated by computation of various bound and continuum properties of H2+.

  7. Analytical theory of the shear Alfvén continuum in the presence of a magnetic island

    SciTech Connect

    Cook, C. R. Hegna, C. C.

    2015-04-15

    The effect of a magnetic island chain on the shear Alfvén continuum is calculated analytically. Using a WKB approximation of the linearized ideal MHD equations, the island is shown to cause an upshift in the continuum accumulation point frequency. This minimum of the frequency spectrum is shifted from the rational surface to the island separatrix. The structure of the eigenmodes is also presented.

  8. Continuum modeling of large lattice structures: Status and projections

    NASA Technical Reports Server (NTRS)

    Noor, Ahmed K.; Mikulas, Martin M., Jr.

    1988-01-01

    The status and some recent developments of continuum modeling for large repetitive lattice structures are summarized. Discussion focuses on a number of aspects including definition of an effective substitute continuum; characterization of the continuum model; and the different approaches for generating the properties of the continuum, namely, the constitutive matrix, the matrix of mass densities, and the matrix of thermal coefficients. Also, a simple approach is presented for generating the continuum properties. The approach can be used to generate analytic and/or numerical values of the continuum properties.

  9. Electrostatic Precipitation in Nearly Pure Gaseous Nitrogen

    NASA Technical Reports Server (NTRS)

    Buhler, Charles; Calle, Carlos; Clements, Sid; Cox, Bobby; Ritz, Mindy

    2008-01-01

    Electrostatic precipitation was performed in a nearly pure gaseous nitrogen system as a possible remedy for black dust contaminant from high pressure 6000 psi lines at the NASA Kennedy Space Center. The results of a prototype electrostatic precipitator that was built and tested using nitrogen gas at standard atmospheric pressures is presented. High voltage pulsed waveforms are generated using a rotating spark gap system at 30 Hz. A unique dust delivery system utilizing the Venturi effect was devised that supplies a given amount of dust per unit time for testing purposes.

  10. Electrostatic patch potentials in Casimir force measurements

    NASA Astrophysics Data System (ADS)

    Garrett, Joseph; Somers, David; Munday, Jeremy

    2015-03-01

    Measurements of the Casimir force require the elimination of the electrostatic force between interacting surfaces. The force can be minimized by applying a potential to one of the two surfaces. However, electrostatic patch potentials remain and contribute an additional force which can obscure the Casimir force signal. We will discuss recent measurements of patch potentials made with Heterodyne Amplitude-Modulated Kelvin Probe Force Microscopy that suggest patches could be responsible for >1% of the signal in some Casimir force measurements, and thus make the distinction between different theoretical models of the Casimir force (e.g. a Drude-model or a plasma-model for the dielectric response) difficult to discern.

  11. Electrostatic supersolitons in three-species plasmas

    SciTech Connect

    Verheest, Frank; Hellberg, Manfred A.; Kourakis, Ioannis

    2013-01-15

    Superficially, electrostatic potential profiles of supersolitons look like those of traditional solitons. However, their electric field profiles are markedly different, having additional extrema on the wings of the standard bipolar structure. This new concept was recently pointed out in the literature for a plasma model with five species. Here, it is shown that electrostatic supersolitons are not an artefact of exotic, complicated plasma models, but can exist even in three-species plasmas and are likely to occur in space plasmas. Further, a methodology is given to delineate their existence domains in a systematic fashion by determining the specific limiting factors.

  12. Kelvin transformation and inverse multipoles in electrostatics

    NASA Astrophysics Data System (ADS)

    Amaral, R. L. P. G.; Ventura, O. S.; Lemos, N. A.

    2017-03-01

    The inversion in the sphere or Kelvin transformation, which exchanges the radial coordinate for its inverse, is used as a guide to relate distinct electrostatic problems with dual features. The exact solution of some nontrivial problems are obtained through the mapping from simple highly symmetric systems. In particular, the concept of multipole expansion is revisited from a point of view opposed to the usual one: the sources are distributed in a region far from the origin while the electrostatic potential is described at points close to it.

  13. Fabrication of Electrostatically Actuated Microshutters Arrays

    NASA Technical Reports Server (NTRS)

    Oh, L.; Li, M.; Kelly, D.; Kutyrev, A.; Moseley, S.

    2016-01-01

    A new fabrication process has been developed to actuate microshutter arrays (MSA) electrostatically at NASA Goddard Space Flight Center. The microshutters, made with silicon nitride membranes with a pixel size of 100 x 200 sq microns, rotate on torsion bars. The microshutters are actuated, latched, and addressed electrostatically by applying voltages on the electrodes the front and back sides of the microshutters. The atomic layer deposition (ALD) of aluminum oxide was used to insulate electrodes on the back side of walls; the insulation can withstand over 100 V. The ALD aluminum oxide is dry etched, and then the microshutters are released in vapor HF.

  14. Inherently tunable electrostatic assembly of membrane proteins.

    PubMed

    Liang, Hongjun; Whited, Gregg; Nguyen, Chi; Okerlund, Adam; Stucky, Galen D

    2008-01-01

    Membrane proteins are a class of nanoscopic entities that control the matter, energy, and information transport across cellular boundaries. Electrostatic interactions are shown to direct the rapid co-assembly of proteorhodopsin (PR) and lipids into long-range crystalline arrays. The roles of inherent charge variations on lipid membranes and PR variants with different compositions are examined by tuning recombinant PR variants with different extramembrane domain sizes and charged amino acid substitutions, lipid membrane compositions, and lipid-to-PR stoichiometric ratios. Rational control of this predominantly electrostatic assembly for PR crystallization is demonstrated, and the same principles should be applicable to the assembly and crystallization of other integral membrane proteins.

  15. Dr. Jan Rogers with Electrostatic Levitator

    NASA Technical Reports Server (NTRS)

    1998-01-01

    Dr. Jan Rogers, project scientist for the Electrostatic Levitator (ESL) at NASA's Marshall Space Flight Center(MSFC). The ESL uses static electricity to suspend an obejct (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 sciences program.

  16. Observations of Continuum Depression in Warm Dense Matter with X-Ray Thomson Scattering

    NASA Astrophysics Data System (ADS)

    Fletcher, L. B.; Kritcher, A. L.; Pak, A.; Ma, T.; Döppner, T.; Fortmann, C.; Divol, L.; Jones, O. S.; Landen, O. L.; Scott, H. A.; Vorberger, J.; Chapman, D. A.; Gericke, D. O.; Mattern, B. A.; Seidler, G. T.; Gregori, G.; Falcone, R. W.; Glenzer, S. H.

    2014-04-01

    Detailed measurements of the electron densities, temperatures, and ionization states of compressed CH shells approaching pressures of 50 Mbar are achieved with spectrally resolved x-ray scattering. Laser-produced 9 keV x-rays probe the plasma during the transient state of three-shock coalescence. High signal-to-noise x-ray scattering spectra show direct evidence of continuum depression in highly degenerate warm dense matter states with electron densities ne>1024 cm-3. The measured densities and temperatures agree well with radiation-hydrodynamic modeling when accounting for continuum lowering in calculations that employ detailed configuration accounting.

  17. 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

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

    (+)-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 Δ E, 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.

  18. Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory

    NASA Astrophysics Data System (ADS)

    Wang, Hao; Yang, Weitao

    2016-06-01

    We developed a new method to calculate the atomic polarizabilities by fitting to the electrostatic potentials (ESPs) obtained from quantum mechanical (QM) calculations within the linear response theory. This parallels the conventional approach of fitting atomic charges based on electrostatic potentials from the electron density. Our ESP fitting is combined with the induced dipole model under the perturbation of uniform external electric fields of all orientations. QM calculations for the linear response to the external electric fields are used as input, fully consistent with the induced dipole model, which itself is a linear response model. The orientation of the uniform external electric fields is integrated in all directions. The integration of orientation and QM linear response calculations together makes the fitting results independent of the orientations and magnitudes of the uniform external electric fields applied. Another advantage of our method is that QM calculation is only needed once, in contrast to the conventional approach, where many QM calculations are needed for many different applied electric fields. The molecular polarizabilities obtained from our method show comparable accuracy with those from fitting directly to the experimental or theoretical molecular polarizabilities. Since ESP is directly fitted, atomic polarizabilities obtained from our method are expected to reproduce the electrostatic interactions better. Our method was used to calculate both transferable atomic polarizabilities for polarizable molecular mechanics' force fields and nontransferable molecule-specific atomic polarizabilities.

  19. Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory.

    PubMed

    Wang, Hao; Yang, Weitao

    2016-06-14

    We developed a new method to calculate the atomic polarizabilities by fitting to the electrostatic potentials (ESPs) obtained from quantum mechanical (QM) calculations within the linear response theory. This parallels the conventional approach of fitting atomic charges based on electrostatic potentials from the electron density. Our ESP fitting is combined with the induced dipole model under the perturbation of uniform external electric fields of all orientations. QM calculations for the linear response to the external electric fields are used as input, fully consistent with the induced dipole model, which itself is a linear response model. The orientation of the uniform external electric fields is integrated in all directions. The integration of orientation and QM linear response calculations together makes the fitting results independent of the orientations and magnitudes of the uniform external electric fields applied. Another advantage of our method is that QM calculation is only needed once, in contrast to the conventional approach, where many QM calculations are needed for many different applied electric fields. The molecular polarizabilities obtained from our method show comparable accuracy with those from fitting directly to the experimental or theoretical molecular polarizabilities. Since ESP is directly fitted, atomic polarizabilities obtained from our method are expected to reproduce the electrostatic interactions better. Our method was used to calculate both transferable atomic polarizabilities for polarizable molecular mechanics' force fields and nontransferable molecule-specific atomic polarizabilities.

  20. Deppdb--DNA electrostatic potential properties database: electrostatic properties of genome DNA.

    PubMed

    Osypov, Alexander A; Krutinin, Gleb G; Kamzolova, Svetlana G

    2010-06-01

    The electrostatic properties of genome DNA influence its interactions with different proteins, in particular, the regulation of transcription by RNA-polymerases. DEPPDB--DNA Electrostatic Potential Properties Database--was developed to hold and provide all available information on the electrostatic properties of genome DNA combined with its sequence and annotation of biological and structural properties of genome elements and whole genomes. Genomes in DEPPDB are organized on a taxonomical basis. Currently, the database contains all the completely sequenced bacterial and viral genomes according to NCBI RefSeq. General properties of the genome DNA electrostatic potential profile and principles of its formation are revealed. This potential correlates with the GC content but does not correspond to it exactly and strongly depends on both the sequence arrangement and its context (flanking regions). Analysis of the promoter regions for bacterial and viral RNA polymerases revealed a correspondence between the scale of these proteins' physical properties and electrostatic profile patterns. We also discovered a direct correlation between the potential value and the binding frequency of RNA polymerase to DNA, supporting the idea of the role of electrostatics in these interactions. This matches a pronounced tendency of the promoter regions to possess higher values of the electrostatic potential.

  1. An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions

    NASA Astrophysics Data System (ADS)

    Lin, Yuchun; Baumketner, Andrij; Deng, Shaozhong; Xu, Zhenli; Jacobs, Donald; Cai, Wei

    2009-10-01

    In this paper, a new solvation model is proposed for simulations of biomolecules in aqueous solutions that combines the strengths of explicit and implicit solvent representations. Solute molecules are placed in a spherical cavity filled with explicit water, thus providing microscopic detail where it is most needed. Solvent outside of the cavity is modeled as a dielectric continuum whose effect on the solute is treated through the reaction field corrections. With this explicit/implicit model, the electrostatic potential represents a solute molecule in an infinite bath of solvent, thus avoiding unphysical interactions between periodic images of the solute commonly used in the lattice-sum explicit solvent simulations. For improved computational efficiency, our model employs an accurate and efficient multiple-image charge method to compute reaction fields together with the fast multipole method for the direct Coulomb interactions. To minimize the surface effects, periodic boundary conditions are employed for nonelectrostatic interactions. The proposed model is applied to study liquid water. The effect of model parameters, which include the size of the cavity, the number of image charges used to compute reaction field, and the thickness of the buffer layer, is investigated in comparison with the particle-mesh Ewald simulations as a reference. An optimal set of parameters is obtained that allows for a faithful representation of many structural, dielectric, and dynamic properties of the simulated water, while maintaining manageable computational cost. With controlled and adjustable accuracy of the multiple-image charge representation of the reaction field, it is concluded that the employed model achieves convergence with only one image charge in the case of pure water. Future applications to pKa calculations, conformational sampling of solvated biomolecules and electrolyte solutions are briefly discussed.

  2. Some improvements in DNA interaction calculations

    NASA Technical Reports Server (NTRS)

    Egan, J. T.; Swissler, T. J.; Rein, R.

    1974-01-01

    Calculations are made on specific DNA-type complexes using refined expressions for electrostatic and polarization energies. Dispersion and repulsive terms are included in the evaluation of the total interaction energy. It is shown that the expansion of the electrostatic potential to include multipole moments up to octopole is necessary to achieve convergence of first-order energies. Polarization energies are not as sensitive to this expansion. The calculations also support the usefulness of the hard sphere model for DNA hydrogen bonds and indicate how stacking interactions are influenced by second-order energies.

  3. Multiscale gas-kinetic simulation for continuum and near-continuum flows.

    PubMed

    Xu, Kun; Liu, Hongwei

    2007-01-01

    It is well known that for increasingly rarefied flow fields, predictions from continuum formulations, such as the Navier-Stokes equations, lose accuracy. The inclusion of higher-order terms, such as Burnett or high-order moment equations, could improve the predictive capabilities of such continuum formulations, but there has been only limited success. Here, we present a multiscale model. On the macroscopic level, the flow variables are updated based on the mass, momentum, and energy conservation through the fluxes. On the other hand, the fluxes are constructed on the microscopic level based on the gas-kinetic equation, which is valid in both continuum and near-continuum flow regimes. Based on this model, the nonequilibrium shock structure, Poiseuille flow, nonlinear heat conduction problems, and unsteady Rayleigh problem will be studied. In the near-continuum flow regime, the current gas-kinetic simulation is more efficient than microscopic methods, such as the direction Boltzmann solver and direct-simulation Monte Carlo method. In the continuum flow limit, the current formulation will go back to the gas-kinetic Navier-Stokes flow solver automatically.

  4. Stratospheric infrared continuum absorptions observed by the ATMOS instrument

    NASA Technical Reports Server (NTRS)

    Rinsland, C. P.; Zander, R.; Namkung, J. S.; Farmer, C. B.; Norton, R. H.

    1989-01-01

    A quantitative analysis of infrared continuum absorption features observed in ATMOS/Spacelab 3 (1985) spectra of the lower stratosphere is reported. Continuous absorption produced primarily by the collision-induced fundamental vibration-rotation band of O2 and to a lesser extent by the superposition of H2O far line wings has been observed in the 1400 to 1800/cm interval below tangent heights of about 25 km. Continuum optical depths measured in microwindows nearly free of atmospheric line absorption are 0.78 + or - 0.06 times those calculated with the O2 absorption coefficients of Timofeyev and Tonkov (1978). Transmittance measurements in microwindows between 2395 and 2535/cm have been used to study continuous absorption from the collision induced fundamental vibration-rotation band of N2 and the far wings of strong CO2 lines. The measured transmittances have been analyzed to derive best fit absorption coefficients for the N2 pressure-induced band at lower stratospheric temperatures (about 210 K).

  5. Progress toward bridging from atomistic to continuum modeling to predict nuclear waste glass dissolution.

    SciTech Connect

    Zapol, Peter; Bourg, Ian; Criscenti, Louise Jacqueline; Steefel, Carl I.; 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.

  6. Investigation of Electrostatic Charge in Hose Lines

    DTIC Science & Technology

    2006-10-01

    storage tanks and, thereby, impose hazardous electrical energy concentrations sufficient to cause incendive arc discharges. This hazard problem... dissipater additives with the objective of quantifying and minimizing electrostatic charging in flexible fuel transport hoses. 0 1 2 3 4 5 6 7 8

  7. Electrostatic 'bounce' instability in a magnetotail configuration

    SciTech Connect

    Fruit, G.; Louarn, P.; Tur, A.

    2013-02-15

    To understand the possible destabilization of two-dimensional current sheets, a kinetic model is proposed to describe the resonant interaction between electrostatic modes and trapped particles that bounce within the sheet. This work follows the initial investigation by Tur et al.[Phys. Plasmas 17, 102905 (2010)] that is revised and extended. Using a quasi-parabolic equilibrium state, the linearized gyro-kinetic Vlasov equation is solved for electrostatic fluctuations with period of the order of the electron bounce period. Using an appropriated Fourier expansion of the particle motion along the magnetic field, the complete time integration of the non-local perturbed distribution functions is performed. The dispersion relation for electrostatic modes is then obtained through the quasineutrality condition. It is found that strongly unstable electrostatic modes may develop provided that the current sheet is moderately stretched and, more important, that the proportion of passing particle remains small (less than typically 10%). This strong but finely tuned instability may offer opportunities to explain features of magnetospheric substorms.

  8. Electrostatics of a Family of Conducting Toroids

    ERIC Educational Resources Information Center

    Lekner, John

    2009-01-01

    An exact solution is found for the electrostatic potential of a family of conducting charged toroids. The toroids are characterized by two lengths "a" and "b", with "a" greater than or equal to "2b". They are closed, with no hole in the "doughnut". The results are obtained by considering the potential of two equal charges, displaced from the…

  9. Electrostatic Enhancement of Coagulation in Protoplanetary Nebulae

    NASA Technical Reports Server (NTRS)

    Marshall, J.; Cuzzi, J.

    2001-01-01

    Microgravity experiments suggest that electrostatic forces (overwhelmed by normal Earth gravity) could greatly enhance cohesive strength of preplanetary aggregates. Cohesive forces may be 103 times larger than those for van der Waals adhesion. Additional information is contained in the original extended abstract.

  10. Electrostatic sampling of trace DNA from clothing.

    PubMed

    Zieger, Martin; Defaux, Priscille Merciani; Utz, Silvia

    2016-05-01

    During acts of physical aggression, offenders frequently come into contact with clothes of the victim, thereby leaving traces of DNA-bearing biological material on the garments. Since tape-lifting and swabbing, the currently established methods for non-destructive trace DNA sampling from clothing, both have their shortcomings in collection efficiency and handling, we thought about a new collection method for these challenging samples. Testing two readily available electrostatic devices for their potential to sample biological material from garments made of different fabrics, we found one of them, the electrostatic dust print lifter (DPL), to perform comparable to well-established sampling with wet cotton swabs. In simulated aggression scenarios, we had the same success rate for the establishment of single aggressor profiles, suitable for database submission, with both the DPL and wet swabbing. However, we lost a substantial amount of information with electrostatic sampling, since almost no mixed aggressor-victim profiles suitable for database entry could be established, compared to conventional swabbing. This study serves as a proof of principle for electrostatic DNA sampling from items of clothing. The technique still requires optimization before it might be used in real casework. But we are confident that in the future it could be an efficient and convenient contribution to the toolbox of forensic practitioners.

  11. The Electrostatic Environments of Mars: Atmospheric Discharges

    NASA Technical Reports Server (NTRS)

    Calle, Carlos I.; Mackey, Paul J.; Johansen, Michael R.; Hogue, Michael D.; Phillips, James, III; Cox, Rachel E.

    2016-01-01

    The electrostatic environment on Mars is controlled by its ever present atmospheric dust. Dust devils and dust storms tribocharge this dust. Theoretical studies predict that lightning and/or glow discharges should be present on Mars, but none have been directly observed. Experiments are planned to shed light on this issue.

  12. Electrostatic transfer of epitaxial graphene to glass.

    SciTech Connect

    Ohta, Taisuke; Pan, Wei; Howell, Stephen Wayne; Biedermann, Laura Butler; Beechem Iii, Thomas Edwin; Ross, Anthony Joseph, III

    2010-12-01

    We report on a scalable electrostatic process to transfer epitaxial graphene to arbitrary glass substrates, including Pyrex and Zerodur. This transfer process could enable wafer-level integration of graphene with structured and electronically-active substrates such as MEMS and CMOS. We will describe the electrostatic transfer method and will compare the properties of the transferred graphene with nominally-equivalent 'as-grown' epitaxial graphene on SiC. The electronic properties of the graphene will be measured using magnetoresistive, four-probe, and graphene field effect transistor geometries [1]. To begin, high-quality epitaxial graphene (mobility 14,000 cm2/Vs and domains >100 {micro}m2) is grown on SiC in an argon-mediated environment [2,3]. The electrostatic transfer then takes place through the application of a large electric field between the donor graphene sample (anode) and the heated acceptor glass substrate (cathode). Using this electrostatic technique, both patterned few-layer graphene from SiC(000-1) and chip-scale monolayer graphene from SiC(0001) are transferred to Pyrex and Zerodur substrates. Subsequent examination of the transferred graphene by Raman spectroscopy confirms that the graphene can be transferred without inducing defects. Furthermore, the strain inherent in epitaxial graphene on SiC(0001) is found to be partially relaxed after the transfer to the glass substrates.

  13. Electrostatic fuel conditioning of internal combustion engines

    NASA Technical Reports Server (NTRS)

    Gold, P. I.

    1982-01-01

    Diesel engines were tested to determine if they are influenced by the presence of electrostatic and magnetic fields. Field forces were applied in a variety of configurations including pretreatment of the fuel and air, however, no affect on engine performance was observed.

  14. Electrostatic sensitivity of secondary high explosives

    SciTech Connect

    Campos, C.A.

    1980-06-01

    An Electrostatic Sensitivity Test System designed at Pantex was used to evaluate the secondary high explosives PETN, HMX, RDX, HNS I, HNS II and TATB. The purpose of this study was to establish test conditions for a standard electrostatic sensitivity test and measure baseline data of a few secondary explosives. Although secondary explosives are often considered quite insensitive to an electrostatic discharge, PETN, HMX, and RDX were initiated. Several external elements to the high explosive were found to have an influence on sensitivity. Initiation appeared to be dependent on the nature of the discharge current curve. Those elements recognized as having a significant effect on the results were held constant in this study. These included: distance between discharge plates; sample moisture content; material density; and system resistance, capacitance and inductance. However, no attempt was made in this study to determine the extent to which the high explosive response to electrostatic discharge is affected by these factors since such correlation is not necessary to determine relative sensitivities.

  15. Electrostatic dust protection for optical elements

    NASA Astrophysics Data System (ADS)

    Hoenig, S. A.

    1982-02-01

    The application of electrostatic technology to the protection of optical components in earth-mounted and satellite orbital systems has been investigated. Theory and experiment indicate it is quite practical to prevent dust deposition in an earth environment. A mathematical analysis indicates even better results should be obtained in an orbital vehicle.

  16. Electrostatic MEMS devices with high reliability

    SciTech Connect

    Goldsmith, Charles L; Auciello, Orlando H; Sumant, Anirudha V; Mancini, Derrick C; Gudeman, Chris; Sampath, Suresh; Carlilse, John A; Carpick, Robert W; Hwang, James

    2015-02-24

    The present invention provides for an electrostatic microelectromechanical (MEMS) device comprising a dielectric layer separating a first conductor and a second conductor. The first conductor is moveable towards the second conductor, when a voltage is applied to the MEMS device. The dielectric layer recovers from dielectric charging failure almost immediately upon removal of the voltage from the MEMS device.

  17. Test progress on the electrostatic membrane reflector

    NASA Technical Reports Server (NTRS)

    Goslee, J. W.; Mihora, D. J.

    1981-01-01

    NASA is currently developing a low mass antenna which derives its reflector surface quality from the application of electrostatic forces to form a thin membrane into the desired concave reflector surface. The shuttle-deployed antenna would have a diameter of 100 m and an RMS surface smoothness of 10 to 1 mm for operation at 1 to 10 GHz. Surface quality measurements have been made on a highly deformable elastic membrane, pressurized by electrostatic forces. Included are the effects of the perimeter boundary, splicing of the membrane, the long-scale smoothness of commercial membranes, and the spatial controllability of the membrane using voltage adjustments to alter the electrostatic forces. The electrostatic membrane was found to operate well in an open-loop sense, showing a high degree of position stability and negligible power consumption in dry air. Visco-electric creep was not evident, but the polymer membrane did expand and contract considerably due to its hygroscopic expansion coefficient. A residual roughness of about 0.75 mm existed with the polymer used in these tests; this error is attributed to seams and membrane anisotropy where the material is stiffer in one direction.

  18. Dynamics of electrostatic microelectromechanical systems actuators

    NASA Astrophysics Data System (ADS)

    Yang, Yisong; Zhang, Ruifeng; Zhao, Le

    2012-02-01

    Electrostatic actuators are simple but important switching devices for microelectromechanical systems applications. Due to the difficulties associated with the electrostatic nonlinearity, precise mathematical description is often hard to obtain for the dynamics of these actuators. Here we present two sharp theorems concerning the dynamics of an undamped electrostatic actuator with one-degree of freedom, subject to linear and nonlinear elastic forces, respectively. We prove that both situations are characterized by the onset of one-stagnation-point periodic response below a well-defined pull-in voltage and a finite-time touch-down or collapse of the actuator above this pull-in voltage. In the linear-force situation, the stagnation level, pull-in voltage, and pull-in coordinate of the movable electrode may all be determined explicitly, following the recent work of Leus and Elata based on numerics. Furthermore, in the nonlinear-force situation, the stagnation level, pull-in voltage, and pull-in coordinate may be described completely in terms of the electrostatic and mechanical parameters of the model so that they approach those in the linear-force situation monotonically in the zero nonlinear-force limit.

  19. OPERATION AND MAINTENANCE MANUAL FOR ELECTROSTATIC PRECIPITATORS

    EPA Science Inventory

    The manual focuses on the operation and maintenance (O/M) of typical electrostatic precipitators (ESPs). It summarizes available information on theory and design in sufficient detail to provide a basic background O/M portions of the manual. Although O/M-related air pollution prob...

  20. Microstructure of sheared monosized colloidal suspensions resulting from hydrodynamic and electrostatic interactions

    SciTech Connect

    Xu, Bu; Gilchrist, James F.

    2014-05-28

    Hydrodynamic and near-particle interactions in sheared suspensions are communicated through suspension microstructure to produce a wide variety of rheological behaviors. To characterize this microstructure, the individual positions of monosized silica particles flowing through a microchannel are obtained with near simulation-level detail. The pair distribution functions of the microstructure at moderate to high Péclet number shear rates are very similar to previous numerical studies. Viscometric functions calculated based on the detailed microstructure obtained through this technique show qualitative agreement with computational results. These results elucidate the origins of shear-thickening of suspensions at high shear rates. While efforts are taken to screen electrostatic interactions to study hydrodynamic and Brownian interactions, the role of electrostatic interaction between particles is also investigated by reducing suspension ionic strength. These non-hydrodynamic electrostatic interactions result in a loss of anisotropy that generally agrees with previous findings of “soft” particle systems.

  1. Measurement of the cross spectrum of HF electrostatic waves in an auroral plasma

    NASA Astrophysics Data System (ADS)

    Pottelette, R.; Illiano, J. M.

    1983-06-01

    A method for the metrology of space plasmas, based on the reception of electrostatic waves by a pair of small dipole antennas was tested in PORCUPINE project rocket experiments. Both dipoles received signals from the natural electrostatic microfield in the plasma; the cross spectrum of these random signals was measured. Data obtained during a weak auroral activity are presented. Natural electrostatic emissions were observed around the upper hybrid frequency and also around the three-halves harmonic of the electron gyrofrequency. A linear calculation shows that the amplitudes of these emissions are above the thermal noise level of the plasma. To explain the observations, it is necessary to take into account the presence of low-energy precipitating electrons (1 to 20 eV), which are highly anisotropic.

  2. Electrostatic interactions at the microscale modulate dynamics and distribution of lipids in bilayers.

    PubMed

    Mangiarotti, Agustín; Wilke, Natalia

    2017-01-18

    For decades, it has been assumed that electrostatic long-range (micron distances) repulsions in lipid bilayers are negligible due to screening from the aqueous milieu. This concept, mostly derived from theoretical calculations, is broadly accepted in the biophysical community. Here we present experimental evidence showing that domain-domain electrostatic repulsions in charged and also in neutral lipid bilayers regulate the diffusion, in-plane structuring and merging of lipid domains in the micron range. All the experiments were performed on both, lipid monolayers and bilayers, and the remarkable similarity in the results found in bilayers compared to monolayers led us to propose that inter-domain repulsions occur mainly within the plane of the membrane. Finally, our results indicate that electrostatic interactions between the species inserted in a cell membrane are not negligible, not only at nanometric but also at larger distances, suggesting another manner for regulating the membrane properties.

  3. Microstructure of sheared monosized colloidal suspensions resulting from hydrodynamic and electrostatic interactions.

    PubMed

    Xu, Bu; Gilchrist, James F

    2014-05-28

    Hydrodynamic and near-particle interactions in sheared suspensions are communicated through suspension microstructure to produce a wide variety of rheological behaviors. To characterize this microstructure, the individual positions of monosized silica particles flowing through a microchannel are obtained with near simulation-level detail. The pair distribution functions of the microstructure at moderate to high Péclet number shear rates are very similar to previous numerical studies. Viscometric functions calculated based on the detailed microstructure obtained through this technique show qualitative agreement with computational results. These results elucidate the origins of shear-thickening of suspensions at high shear rates. While efforts are taken to screen electrostatic interactions to study hydrodynamic and Brownian interactions, the role of electrostatic interaction between particles is also investigated by reducing suspension ionic strength. These non-hydrodynamic electrostatic interactions result in a loss of anisotropy that generally agrees with previous findings of "soft" particle systems.

  4. Modeling the elastic energy of alloys: Potential pitfalls of continuum treatments.

    PubMed

    Baskaran, Arvind; Ratsch, Christian; Smereka, Peter

    2015-12-01

    Some issues that arise when modeling elastic energy for binary alloys are discussed within the context of a Keating model and density-functional calculations. The Keating model is a simplified atomistic formulation based on modeling elastic interactions of a binary alloy with harmonic springs whose equilibrium length is species dependent. It is demonstrated that the continuum limit for the strain field are the usual equations of linear elasticity for alloys and that they correctly capture the coarse-grained behavior of the displacement field. In addition, it is established that Euler-Lagrange equation of the continuum limit of the elastic energy will yield the same strain field equation. This is the same energy functional that is often used to model elastic effects in binary alloys. However, a direct calculation of the elastic energy atomistic model reveals that the continuum expression for the elastic energy is both qualitatively and quantitatively incorrect. This is because it does not take atomistic scale compositional nonuniformity into account. Importantly, this result also shows that finely mixed alloys tend to have more elastic energy than segregated systems, which is the exact opposite of predictions made by some continuum theories. It is also shown that for strained thin films the traditionally used effective misfit for alloys systematically underestimate the strain energy. In some models, this drawback is handled by including an elastic contribution to the enthalpy of mixing, which is characterized in terms of the continuum concentration. The direct calculation of the atomistic model reveals that this approach suffers serious difficulties. It is demonstrated that elastic contribution to the enthalpy of mixing is nonisotropic and scale dependent. It is also shown that such effects are present in density-functional theory calculations for the Si-Ge system. This work demonstrates that it is critical to include the microscopic arrangements in any elastic

  5. Modeling the elastic energy of alloys: Potential pitfalls of continuum treatments

    NASA Astrophysics Data System (ADS)

    Baskaran, Arvind; Ratsch, Christian; Smereka, Peter

    2015-12-01

    Some issues that arise when modeling elastic energy for binary alloys are discussed within the context of a Keating model and density-functional calculations. The Keating model is a simplified atomistic formulation based on modeling elastic interactions of a binary alloy with harmonic springs whose equilibrium length is species dependent. It is demonstrated that the continuum limit for the strain field are the usual equations of linear elasticity for alloys and that they correctly capture the coarse-grained behavior of the displacement field. In addition, it is established that Euler-Lagrange equation of the continuum limit of the elastic energy will yield the same strain field equation. This is the same energy functional that is often used to model elastic effects in binary alloys. However, a direct calculation of the elastic energy atomistic model reveals that the continuum expression for the elastic energy is both qualitatively and quantitatively incorrect. This is because it does not take atomistic scale compositional nonuniformity into account. Importantly, this result also shows that finely mixed alloys tend to have more elastic energy than segregated systems, which is the exact opposite of predictions made by some continuum theories. It is also shown that for strained thin films the traditionally used effective misfit for alloys systematically underestimate the strain energy. In some models, this drawback is handled by including an elastic contribution to the enthalpy of mixing, which is characterized in terms of the continuum concentration. The direct calculation of the atomistic model reveals that this approach suffers serious difficulties. It is demonstrated that elastic contribution to the enthalpy of mixing is nonisotropic and scale dependent. It is also shown that such effects are present in density-functional theory calculations for the Si-Ge system. This work demonstrates that it is critical to include the microscopic arrangements in any elastic

  6. Role of the electrostatic depletion attraction on the structure of charged liposome-polymer mixtures.

    PubMed

    Peláez-Fernández, M; Moncho-Jordá, A; García-Jimeno, S; Estelrich, J; Callejas-Fernández, J

    2012-05-01

    The effect of adding charged nonadsorbing polymers to electrostatically structured suspensions of charged liposomes has been experimentally studied by means of light scattering techniques. The static structure factor of the mixtures is analyzed using two polymers of different sizes. As the polymer concentration increases, the main peak of the structure factor decreases and shows an important shift to larger values of the scattering vector. Such displacement is the consequence of the electrostatic-enhanced depletion attraction induced by the polymers that counteracts the electrostatic repulsion. For the shorter polymer, the system remains stable for all studied polymer concentrations. However, for the long polymer chains, the effective attraction induced at the highest polymer density studied is strong enough to destabilize the mixture. In this case, the aggregation of the liposomes leads to clusters of nearly linear morphology. The PRISM theory is employed to calculate the effective pair potential between liposomes. The theoretical predictions are able to support the experimental observations, and provide an explanation of the interplay between the electrostatic repulsive interaction and the depletion attraction. In particular, they show that the depletion attraction is especially long ranged, and is dominated by electrostatic effects rather than entropic.

  7. Continuum of Collaboration: Little Steps for Little Feet

    ERIC Educational Resources Information Center

    Powell, Gwynn M.

    2013-01-01

    This mini-article outlines a continuum of collaboration for faculty within a department of the same discipline. The goal of illustrating this continuum is showcase different stages of collaboration so that faculty members can assess where they are as a collective and consider steps to collaborate more. The separate points along a continuum of…

  8. Mesoscopic and continuum modelling of angiogenesis

    PubMed Central

    Spill, F.; Guerrero, P.; Alarcon, T.; Maini, P. K.; Byrne, H. M.

    2016-01-01

    Angiogenesis is the formation of new blood vessels from pre-existing ones in response to chemical signals secreted by, for example, a wound or a tumour. In this paper, we propose a mesoscopic lattice-based model of angiogenesis, in which processes that include proliferation and cell movement are considered as stochastic events. By studying the dependence of the model on the lattice spacing and the number of cells involved, we are able to derive the deterministic continuum limit of our equations and compare it to similar existing models of angiogenesis. We further identify conditions under which the use of continuum models is justified, and others for which stochastic or discrete effects dominate. We also compare different stochastic models for the movement of endothelial tip cells which have the same macroscopic, deterministic behaviour, but lead to markedly different behaviour in terms of production of new vessel cells. PMID:24615007

  9. Robot strings: Long, thin continuum robots

    NASA Astrophysics Data System (ADS)

    Walker, I. D.

    We describe and discuss the development of long, thin, continuous “ string-like” robots aimed at Space exploration missions. These continuous backbone “ continuum” robots are inspired by numerous biological structures, particularly vines, worms, and the tongues of animals such as the anteater. The key novelty is the high length-to-diameter ratio of the robots. This morphology offers penetration into, and exploration of, significantly narrower and deeper environments than accessible using current robot technology. In this paper, we introduce new design alternatives for long thin continuum robots, based on an analysis and extension of three core existing continuum robot design types. The designs are evaluated based on their mechanical feasibility, structural properties, kinematic simplicity, and degrees of freedom.

  10. A continuum model of transcriptional bursting

    PubMed Central

    Corrigan, Adam M; Tunnacliffe, Edward; Cannon, Danielle; Chubb, Jonathan R

    2016-01-01

    Transcription occurs in stochastic bursts. Early models based upon RNA hybridisation studies suggest bursting dynamics arise from alternating inactive and permissive states. Here we investigate bursting mechanism in live cells by quantitative imaging of actin gene transcription, combined with molecular genetics, stochastic simulation and probabilistic modelling. In contrast to early models, our data indicate a continuum of transcriptional states, with a slowly fluctuating initiation rate converting the gene between different levels of activity, interspersed with extended periods of inactivity. We place an upper limit of 40 s on the lifetime of fluctuations in elongation rate, with initiation rate variations persisting an order of magnitude longer. TATA mutations reduce the accessibility of high activity states, leaving the lifetime of on- and off-states unchanged. A continuum or spectrum of gene states potentially enables a wide dynamic range for cell responses to stimuli. DOI: http://dx.doi.org/10.7554/eLife.13051.001 PMID:26896676

  11. Models of Uranium continuum radio emission

    NASA Technical Reports Server (NTRS)

    Romig, Joseph H.; Evans, David R.; Sawyer, Constance B.; Schweitzer, Andrea E.; Warwick, James W.

    1987-01-01

    Uranium continuum radio emission detected by the Voyager 2 Planetary Radio Astronomy experiment during the January 1986 encounter is considered. The continuum emissions comprised four components (equatorial emissions, anomaly emissions, strong nightside emissions, and weak nightside emissions) associated with different sources. The equatorial emissions appeared most prominently during the days before closest approach and extended from 40 kHz or below to about 120 kHz. The anomaly emissions were seen about 12 hours before closest approach and extended to about 250 kHz. The agreement found between Miranda's phase and strong radio emission at 20.4 kHz, just after closest approach, suggests intense dynamic activity on the Miranda L shell.

  12. Continuum Statistics of the Airy2 Process

    NASA Astrophysics Data System (ADS)

    Corwin, Ivan; Quastel, Jeremy; Remenik, Daniel

    2013-01-01

    We develop an exact determinantal formula for the probability that the Airy_2 process is bounded by a function g on a finite interval. As an application, we provide a direct proof that {sup({A}2(x)-x^2)} is distributed as a GOE random variable. Both the continuum formula and the GOE result have applications in the study of the end point of an unconstrained directed polymer in a disordered environment. We explain Johansson's (Commun. Math. Phys. 242(1-2):277-329, 2003) observation that the GOE result follows from this polymer interpretation and exact results within that field. In a companion paper (Moreno Flores et al. in Commun. Math. Phys. 2012) these continuum statistics are used to compute the distribution of the endpoint of directed polymers.

  13. Entropic formulation of relativistic continuum mechanics.

    PubMed

    Fukuma, Masafumi; Sakatani, Yuho

    2011-08-01

    An entropic formulation of relativistic continuum mechanics is developed in the Landau-Lifshitz frame. We introduce two spatial scales, one being the small scale representing the linear size of each material particle and the other the large scale representing the linear size of a large system which consists of material particles and is to linearly regress to the equilibrium. We propose a local functional which is expected to represent the total entropy of the larger system and require the entropy functional to be maximized in the process of linear regression. We show that Onsager's original idea on linear regression can then be realized explicitly as current conservations with dissipative currents in the desired form. We demonstrate the effectiveness of this formulation by showing that one can treat a wide class of relativistic continuum materials, including standard relativistic viscous fluids and relativistic viscoelastic materials.

  14. Automatic continuum analysis of reflectance spectra

    NASA Technical Reports Server (NTRS)

    Clark, Roger N.; King, Trude V. V.

    1987-01-01

    A continuum algorithm based on a Segmented Upper Hull method (SUH) is described. An upper hull is performed on segments of a spectrum defined by local minima and maxima. The segments making a complete spectrum are then combined. The definition of the upper hull allows the continuum to be both concave and/or convex, adapting to the shape of the spectrum. The method performs multiple passes on a spectrum by segmenting each local maximum to minimum and performing an upper hull. The algorithm naturally adapts to the widths of absorption features, so that all features are found, including the nature of doublets, triplets, etc. The algorithm is also reasonably fast on common minicomputers so that it might be applied to the large data sets from imaging spectrometers.

  15. Electrostatics in dissipative particle dynamics using Ewald sums with point charges

    NASA Astrophysics Data System (ADS)

    Terrón-Mejía, Ketzasmin A.; López-Rendón, Roberto; Gama Goicochea, Armando

    2016-10-01

    A proper treatment of electrostatic interactions is crucial for the accurate calculation of forces in computer simulations. Electrostatic interactions are typically modeled using Ewald-based methods, which have become some of the cornerstones upon which many other methods for the numerical computation of electrostatic interactions are based. However, their use with charge distributions rather than point charges requires the inclusion of ansatz for the solutions of the Poisson equation, since there is no exact solution known for smeared out charges. The interest in incorporating electrostatic interactions at the scales of length and time that are relevant for the study the physics of soft condensed matter has increased considerably. Using mesoscale simulation techniques, such as dissipative particle dynamics (DPD), allows us to reach longer time scales in numerical simulations, without abandoning the particulate description of the problem. The main problem with incorporating electrostatics into DPD simulations is that DPD particles are soft and those particles with opposite charge can form artificial clusters of ions. Here we show that one can incorporate the electrostatic interactions through Ewald sums with point charges in DPD if larger values of coarse-graining degree are used, where DPD is truly mesoscopic. Using point charges with larger excluded volume interactions, the artificial formation of ionic pairs with point charges can be avoided and one obtains correct predictions. We establish ranges of parameters useful for detecting boundaries where artificial formation of ionic pairs occurs. Lastly, using point charges we predict the scaling properties of polyelectrolytes in solvents of varying quality, and obtain predictions that are in agreement with calculations that use other methods and with recent experimental results.

  16. Electrostatic Switching in Vertically Oriented Nanotubes for Nonvolatile Memory Applications

    NASA Technical Reports Server (NTRS)

    Kaul, Anupama B.; Khan, Paul; Jennings, Andrew T.; Greer, Julia R.; Megerian, Krikor G.; Allmen, Paul von

    2009-01-01

    We have demonstrated electrostatic switching in vertically oriented nanotubes or nanofibers, where a nanoprobe was used as the actuating electrode inside an SEM. When the nanoprobe was manipulated to be in close proximity to a single tube, switching voltages between 10 V - 40 V were observed, depending on the geometrical parameters. The turn-on transitions appeared to be much sharper than the turn-off transitions which were limited by the tube-to-probe contact resistances. In many cases, stiction forces at these dimensions were dominant, since the tube appeared stuck to the probe even after the voltage returned to 0 V, suggesting that such structures are promising for nonvolatile memory applications. The stiction effects, to some extent, can be adjusted by engineering the switch geometry appropriately. Nanoscale mechanical measurements were also conducted on the tubes using a custom-built anoindentor inside an SEM, from which preliminary material parameters, such as the elastic modulus, were extracted. The mechanical measurements also revealed that the tubes appear to be well adhered to the substrate. The material parameters gathered from the mechanical measurements were then used in developing an electrostatic model of the switch using a commercially available finite-element simulator. The calculated pull-in voltages appeared to be in agreement to the experimentally obtained switching voltages to first order.

  17. CRTs: electrostatic focusing systems for performing Laminar electron gun

    NASA Astrophysics Data System (ADS)

    Abgarian, Artoush H.

    2004-09-01

    Current CRT technology suffers from a reduced bright image response, and a reduced image resolution due to the distribution of beam current densities following a Gaussian rather than a uniform distribution. A uniform distribution of beam current necessary achieved by proper manipulation of CRT's electro-static focusing system. Functional connection has been found between three electrodes of CRT's electro-static focusing systems, which provide "Laminar" electron flow in system. This technology provides unique characteristics that is providing uniformly distributed output current density. Theoretical analysis is given for some current Electro-optical systems through the calculation of trajectories of electrons in the system without taking into account the different starting velocities. This analysis proves the importance of producing the Electro-optical systems with uniform distribution of current density. As the result it has been achieved ideal explicitness of the image and picture compression from 1 (transfer 1:1, for night vision devices) to 50 times (transfer 1:0.02, for electron-optics transmission) and more accompanied by uniform distribution of current density. Usage of this technology allows 10 time's reduction of time resolution and 2500 times increasing of light intensity for a compression of 50x. There is no need in corrective electrode in order to achieve high power brightness. With this technology no gain correction is required.

  18. Multilevel Summation of Electrostatic Potentials Using Graphics Processing Units*

    PubMed Central

    Hardy, David J.; Stone, John E.; Schulten, Klaus

    2009-01-01

    Physical and engineering practicalities involved in microprocessor design have resulted in flat performance growth for traditional single-core microprocessors. The urgent need for continuing increases in the performance of scientific applications requires the use of many-core processors and accelerators such as graphics processing units (GPUs). This paper discusses GPU acceleration of the multilevel summation method for computing electrostatic potentials and forces for a system of charged atoms, which is a problem of paramount importance in biomolecular modeling applications. We present and test a new GPU algorithm for the long-range part of the potentials that computes a cutoff pair potential between lattice points, essentially convolving a fixed 3-D lattice of “weights” over all sub-cubes of a much larger lattice. The implementation exploits the different memory subsystems provided on the GPU to stream optimally sized data sets through the multiprocessors. We demonstrate for the full multilevel summation calculation speedups of up to 26 using a single GPU and 46 using multiple GPUs, enabling the computation of a high-resolution map of the electrostatic potential for a system of 1.5 million atoms in under 12 seconds. PMID:20161132

  19. A continuum model of a multilayer nanosheet

    NASA Astrophysics Data System (ADS)

    Morozov, N. F.; Tovstik, P. E.; Tovstik, T. P.

    2016-11-01

    A continuum model for describing the bending and free vibrations of a crystalline graphite sheet consisting of graphene layers is proposed. Graphene is modeled by a two-dimensional layer having a finite rigidity under extension and bending. The interval between graphene layers through which their Van-der-Waals interaction occurs is modeled by a fictitious layer with relatively low rigidity. In the solution, formulas describing the bending of a multilayer sheet with alternating rigid and soft layers are used.

  20. Optimization design combined with coupled structural-electrostatic analysis for the electrostatically controlled deployable membrane reflector

    NASA Astrophysics Data System (ADS)

    Liu, Chao; Yang, Guigeng; Zhang, Yiqun

    2015-01-01

    The electrostatically controlled deployable membrane reflector (ECDMR) is a promising scheme to construct large size and high precision space deployable reflector antennas. This paper presents a novel design method for the large size and small F/D ECDMR considering the coupled structure-electrostatic problem. First, the fully coupled structural-electrostatic system is described by a three field formulation, in which the structure and passive electrical field is modeled by finite element method, and the deformation of the electrostatic domain is predicted by a finite element formulation of a fictitious elastic structure. A residual formulation of the structural-electrostatic field finite element model is established and solved by Newton-Raphson method. The coupled structural-electrostatic analysis procedure is summarized. Then, with the aid of this coupled analysis procedure, an integrated optimization method of membrane shape accuracy and stress uniformity is proposed, which is divided into inner and outer iterative loops. The initial state of relatively high shape accuracy and uniform stress distribution is achieved by applying the uniform prestress on the membrane design shape and optimizing the voltages, in which the optimal voltage is computed by a sensitivity analysis. The shape accuracy is further improved by the iterative prestress modification using the reposition balance method. Finally, the results of the uncoupled and coupled methods are compared and the proposed optimization method is applied to design an ECDMR. The results validate the effectiveness of this proposed methods.