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Sample records for continuum electrostatic calculations

  1. Histidine in Continuum Electrostatics Protonation State Calculations

    PubMed Central

    Couch, Vernon; Stuchebruckhov, Alexei

    2014-01-01

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

  2. 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

  3. 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.

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

    PubMed

    Gunner, M R; Baker, N A

    2016-01-01

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

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

    PubMed

    Ritchie, Andrew W; Webb, Lauren J

    2015-11-05

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

  6. Dynamics of water molecules buried in cavities of apolipoprotein E studied by molecular dynamics simulations and continuum electrostatic calculations.

    PubMed

    Prévost, Martine

    2004-10-05

    Molecular dynamics (MD) simulations of several nanoseconds each were used to monitor the dynamic behavior of the five crystal water molecules buried in the interior of the N-terminal domain of apolipoprotein E. These crystal water molecules are fairly well conserved in several apolipoprotein E structures, suggesting that they are not an artifact of the crystal and that they may have a structural and/or functional role for the protein. All five buried crystal water molecules leave the protein interior in the course of the longest simulations and exchange with water molecules from the bulk. The free energies of binding evaluated from the electrostatic binding free energy computed using a continuum model and estimates of the binding entropy changes represent shallow minima. The corresponding calculated residence times of the buried water molecules range from tens of picoseconds to hundreds of nanoseconds, which denote rather short times as for buried water molecules. Several water exchanges monitored in the simulations show that water molecules along the exit/entrance pathway use a relay of H bonds primarily formed with charged residues which helps either the exit or the entrance from or into the buried site. The exit/entrance of water molecules from/into the sites is permitted essentially by local motions of, at most, two side chains, indicating that, in these cases, complex correlated atomic motions are not needed to open the buried site toward the surface of the protein. This provides a possible explanation for the short residence times.

  7. PCE: web tools to compute protein continuum electrostatics

    PubMed Central

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

    2005-01-01

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

  8. PCE: web tools to compute protein continuum electrostatics.

    PubMed

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

    2005-07-01

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

  9. Effect of charge interactions on the carboxylate vibrational stretching frequency in c-type cytochromes investigated by continuum electrostatic calculations and FTIR spectroscopy.

    PubMed

    Laberge, M; Sharp, K A; Vanderkooi, J M

    1998-03-30

    The FTIR spectra of the asymmetric carboxylate absorption region of three c-type cytochromes--namely horse heart, yeast and bonito cytochromes c--as well as continuum electrostatic calculations performed on their respective protein matrices, show that these combined methods can target specific protein regions and yield pertinent protein charge information that correlates with the observed spectral data. Deconvolution of the IR carboxylate stretch frequency region (1525-1675 cm-1) in the three cytochromes yield different v(oco)a distributions. In the case of the bonito cytochrome c carboxylates, two v(oco)a populations are clearly distinguishable in the deconvoluted spectra--which is not the case for the more complex v(oco)a deconvolutions of the other two cytochromes. The frequency distributions of the calculated potentials are consistent with the experimental observations and we conclude that the IR carboxylate absorption in proteins can be modified by the electrostatic environment.

  10. 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.

  11. 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.

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

    SciTech Connect

    Bardhan, J. P.; Knepley, M. G.; Anitescu, M.

    2009-03-01

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

  13. 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)

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

    PubMed

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

    2017-08-16

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

  15. The dependence of electrostatic solvation energy on dielectric constants in Poisson-Boltzmann calculations.

    PubMed

    Tjong, Harianto; Zhou, Huang-Xiang

    2006-11-28

    The Poisson-Boltzmann equation gives the electrostatic free energy of a solute molecule (with dielectric constant epsilon(l)) solvated in a continuum solvent (with dielectric constant epsilon(s)). Here a simple formula is presented that accurately predicts the electrostatic free energy for all combinations of epsilon(l) and epsilon(s) from the calculation on a single set of epsilon(l) and epsilon(s) values.

  16. 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.

  17. 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.)

  18. 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.)

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

    PubMed

    Bonthuis, Douwe Jan; Netz, Roland R

    2013-10-03

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

  20. 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.

  1. General method for calculating derivatives of the lattice electrostatic energy.

    NASA Technical Reports Server (NTRS)

    Macdonald, D. E.; Eftis, J.; Arkilic, G. M.

    1972-01-01

    A method for calculating the derivatives of lattice electrostatic strain energy is proposed. It offers a computation procedure that is more general, concise, and systematic than any of the procedures previously used by Fuchs (1936), Cousins (1967), and Suzuki et al. (1968). The method can also easily be extended to fourth- and higher-order derivatives without undue difficulty.

  2. 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

  3. 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

  4. 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

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

    PubMed

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

    2015-08-04

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

  6. 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

  7. 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

  8. Calculations of electrostatic properties in proteins. Analysis of contributions from induced protein dipoles.

    PubMed

    Van Belle, D; Couplet, I; Prevost, M; Wodak, S J

    1987-12-20

    The calculation of induced dipole moments and of their contribution to electrostatic effects in proteins is implemented following the approach of Warshel. Isotropic polarizabilities are assigned to individual atoms, and the resulting deviation from pairwise interactions is treated by a self-consistent iterative procedure. We give a detailed description of how the formalism is implemented in molecular mechanics and molecular dynamics simulation procedures, and report results based on calculations performed on crystal structures of crambin, liver alcohol dehydrogenase and ribonuclease T1. We focus our analysis on evaluating the contribution of polarizability of the protein matrix to electrostatic energies, local fields, to dipole moments of peptide groups and of secondary structure elements in the polypeptide chain. Our calculations confirm that induced dipole moments in proteins provide important stabilizing contributions to electrostatic energies, and that these contributions cannot be mimicked by the usual approximations where either a continuum dielectric constant, or a distance-dependent dielectric function is used. We find that induced protein dipoles appreciably affect the magnitude and direction of local electrostatic fields in a manner that is strongly influenced by the microscopic environment in the protein. Most strongly affected are fields in charged groups that are involved in close interactions with other charged groups, while the influence on local fields of aliphatic groups is marginal. We find, moreover, that induction effects from surrounding protein atoms tend on average to increase peptide dipoles and helix macro-dipoles by about 16%, again reflecting electrostatic stabilization by the protein matrix, and show that (at least in the alpha/beta domain of alcohol dehydrogenase) the contribution of side-chains to this stabilization is significant.

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations

    PubMed Central

    Vergara-Perez, Sandra; Marucho, Marcelo

    2015-01-01

    One of the most used and efficient approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation. There are several software packages available that solve the PB equation for molecules in aqueous electrolyte solutions. Most of these software packages are useful for scientists with specialized training and expertise in computational biophysics. However, the user is usually required to manually take several important choices, 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. PMID:26924848

  14. Why continuum electrostatics theories cannot explain biological structure, polyelectrolytes or ionic strength effects in ion-protein interactions.

    PubMed

    Collins, Kim D

    2012-06-01

    Continuum electrostatics models for ions in water provide apparent long range electrostatic explanations for the forces on ions. However the electro-chemical free energy of solvation of ions resides largely in the first two water layers, which control the interfacial behavior of the ions and require explicit modeling to capture their distinctive behaviors. The resulting short range forces produce such surprising charge density-dependent behaviors as ion adsorption onto nonpolar surfaces, like charge aggregation of ions, and substantial ion pairing preferences, which arise largely from the affinity of specific ions for individual water molecules. Specific ion effects controlled by the local water affinity of the ion show a diagnostic change of sign between strongly hydrated Na(+) and weakly hydrated K(+) and between strongly hydrated F(-) and weakly hydrated Cl(-), in both cases marking the strength of water-water interactions in bulk solution, a critical benchmark missing from continuum electrostatics models. Copyright © 2012 Elsevier B.V. All rights reserved.

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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

  20. Using multiconformation continuum electrostatics to compare chloride binding motifs in alpha-amylase, human serum albumin, and Omp32.

    PubMed

    Song, Yifan; Gunner, M R

    2009-04-10

    Ions are a ubiquitous component of the cellular environment, transferring into cells through membrane-embedded proteins. Ions bind to proteins to regulate their charge and function. Here, using multiconformation continuum electrostatics (MCCE), we show that the changes of chloride binding to alpha-amylase, human serum albumin (HSA) and Omp32 with pH, and of alpha-amylase with mutation agree well with experimental data. The three proteins represent three different types of binding. In alpha-amylase, chloride is bound in a specific buried site. Chloride binding is strongly coupled to the protonation state of a nearby lysine. MCCE calculates an 11-fold change in chloride affinity between the wild-type alpha-amylase and the K300R mutant, in good agreement with the measured 10-fold change.Without considering the coupled protonation reaction, the calculated affinity change would be more than 10(6)-fold. In HSA, chlorides are distributed on the protein surface. Although HSA has a negative net charge, it binds more anions than cations. There are no highly occupied binding sites in HSA. Rather, there are many partially occupied sites near clusters of basic residues. The relative affinity of bound ions of different charges is shown to depend on the distribution of charged residues on the surface rather than the overall net charge of the protein. The calculated strong pH dependence of the number of chlorides bound and the anion selectivity agree with those of previous experiments. In Omp32, chlorides are stabilized in an anion-selective transmembrane channel in a pH-independent manner. The positive electrostatic potential in Omp32 results in about two chlorides and no cations bound in the transmembrane region of this anion-selective channel. The studies here show that with the ability to sample multiple binding sites and coupled protein protonation states, MCCE provides a powerful tool to analyze and predict ion binding. The calculations overestimate the affinity of surface

  1. 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.

  2. Accurate solution of multi-region continuum biomolecule electrostatic problems using the linearized Poisson-Boltzmann equation with curved boundary elements.

    PubMed

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

    2009-01-15

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

  3. Investigation of Multipole Electrostatics in Hydration Free Energy Calculations

    PubMed Central

    Shi, Yue; Wu, Chuanjie; Ponder, Jay W.; Ren, Pengyu

    2010-01-01

    Hydration free energy (HFE) is generally used for evaluating molecular solubility, which is an important property for pharmaceutical and chemical engineering processes. Accurately predicting HFE is also recognized as one fundamental capability of molecular mechanics force field. Here we present a systematic investigation on HFE calculations with AMOEBA polarizable force field at various parameterization and simulation conditions. The HFEs of seven small organic molecules have been obtained alchemically using the Bennett Acceptance Ratio (BAR) method. We have compared two approaches to derive the atomic multipoles from quantum mechanical (QM) calculations: one directly from the new distributed multipole analysis (DMA) and the other involving fitting to the electrostatic potential around the molecules. Wave functions solved at the MP2 level with four basis sets (6-311G*, 6-311++G(2d,2p), cc-pVTZ, and aug-cc-pVTZ) are used to derive the atomic multipoles. HFEs from all four basis sets show a reasonable agreement with experimental data (root mean square error 0.63 kcal/mol for aug-ccpVTZ). We conclude that aug-cc-pVTZ gives the best performance when used with AMOEBA, and 6-311++G(2d,2p) is comparable but more efficient for larger systems. The results suggest that the inclusion of diffuse basis functions is important for capturing intermolecular interactions. The effect of long-range correction to van der Waals interaction on the hydration free energies is about 0.1 kcal/mol when the cutoff is 12Å, and increases linearly with the number of atoms in the solute/ligand. In addition, we also discussed the results from a hybrid approach that combines polarizable solute with fixed-charge water in the hydration free energy calculation. PMID:20925089

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. From quantum chemistry and the classical theory of polar liquids to continuum approximations in molecular mechanics calculations

    NASA Astrophysics Data System (ADS)

    Hassan, Sergio A.; Mehler, Ernest L.

    Biological macromolecules and other polymers belong to the class of mesoscopic systems, with characteristic length scale of the order of a nanometer. Although microscopic models would be the preferred choice in theoretical calculations, their use in computer simulations becomes prohibitive for large systems or long simulation times. On the other hand, the use of purely macroscopic models in the mesoscopic domain may introduce artifacts, with effects that are difficult to assess and that may compromise the reliability of the calculations. Here is proposed an approach with the aim of minimizing the empirical nature of continuum approximations of solvent effects within the scope of molecular mechanics (MM) approximations in mesoscopic systems. Using quantum chemical methods, the potential generated by the molecular electron density is first decomposed in a multicenter-multipole expansion around predetermined centers. The monopole and dipole terms of the expansion at each site create electric fields that polarize the surrounding aqueous medium whose dielectric properties can be described by the classical theory of polar liquids. Debye's theory allows a derivation of the dielectric profiles created around isolated point charges and dipoles that can incorporate Onsager reaction field corrections. A superposition of screened Coulomb potentials obtained from this theory makes possible a simple derivation of a formal expression for the total electrostatic energy and the polar component of the solvation energy of the system. A discussion is presented on the physical meaning of the model parameters, their transferability, and their convergence to calculable quantities in the limit of simple systems. The performance of this continuum approximation in computer calculations of amino acids in the context of an atomistic force field is discussed. Applications of a continuum model based on screened Coulomb potentials in multinanosecond simulations of peptides and proteins are

  12. 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.

  13. 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.

  14. 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.

  15. 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.

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

    PubMed

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

    2015-12-01

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

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

    PubMed

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

    2017-02-27

    Cytochrome c oxidase (CcO) couples the reduction of dioxygen to water with transmembrane proton pumping, which leads to the generation of an electrochemical gradient. In this study we analyze how one of the components of the electrochemical gradient, the difference in pH across the membrane, or ΔpH, influences the protonation states of residues in CcO. We modified our continuum electrostatics/Monte Carlo (CE/MC) method in order to include the ΔpH and applied it to the study of CcO, in what is, to our best knowledge, the first CE/MC study of CcO in the presence of a pH gradient. The inclusion of a transmembrane pH gradient allows for the identification of residues whose titration behavior depends on the pH on both sides of the membrane. Among the several residues with unusual titration profiles, three are well-known key residues in the proton transfer process of CcO: E286I, Y288I, and K362I. All three residues have been previously identified as being critical for the catalytic or proton pumping functions of CcO. Our results suggest that when the pH gradient increases, these residues may be part of a regulatory mechanism to stem the proton flow.

  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. Cluster-Continuum Calculations of Hydration Free Energies of Anions and Group 12 Divalent Cations.

    PubMed

    Riccardi, Demian; Guo, Hao-Bo; Parks, Jerry M; Gu, Baohua; Liang, Liyuan; Smith, Jeremy C

    2013-01-08

    yields reasonable agreement with experimental values, due in part to fortuitous error cancellation associated with the metal cations. Overall, the results indicate that the careful application of quantum chemical cluster-continuum methods provides valuable insight into aqueous ionic processes that depend on both local and long-range electrostatic interactions with the solvent.

  1. 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

  2. Electrostatic calculations for an ion channel. I. Energy and potential profiles and interactions between ions.

    PubMed Central

    Levitt, D G

    1978-01-01

    The electrostatic energy profile of one, two, or three ions in an aqueous channel through a lipid membrane is calculated. It is shown that the previous solution to this problem (based on the assumption that the channel is infinitely long) significantly overestimates the electrostatic energy barrier. For example, for a 3-A radius pore, the energy is 16 kT for the infinite channel and 6.7 kT for an ion in the center of a channel 25 A long. The energy as a function of the position of the ion is also determined. With this energy profile, the rate of crossing the membrane (using the Nernst-Planck equation) was estimated and found to be compatible with the maximum conductance observed for the gramicidin A channel. The total electrostatic energy (as a function of position) required to place two or three ions in the channel is also calculated. The electrostatic interaction is small for two ions at opposite ends of the channel and large for any positioning of the three ions. Finally, the gradient through the channel of an applied potential is calculated. The solution to these problems is based on solving an equivalent problem in which an appropriate surface charge is placed on the boundary between the lipid and aqueous regions. The magnitude of the surface charge is obtained from the numerical solution for a system of coupled integral equations. PMID:656542

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. New approach to 3D electrostatic calculations for micro-pattern detectors

    NASA Astrophysics Data System (ADS)

    Lazić, P.; Dujmić, D.; Formaggio, J. A.; Abraham, H.; Štefancić, H.

    2011-12-01

    We demonstrate nearly approximation-free electrostatic calculations of micromesh detectors that can be extended to any other type of micropattern detectors. Using a newly developed Boundary Element Method called Robin Hood Method, we can easily handle objects with huge number of boundary elements (hundreds of thousands) without any compromise in numerical accuracy. In this paper we show how such calculations can be applied to Micromegas detectors by comparing electron transparencies and gains for four different types of meshes. We also demonstrate the inclusion of dielectric material by calculating the electric field around different types of dielectric spacers.

  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. 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.

  10. 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/.

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

    PubMed Central

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

    2011-01-01

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

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

    PubMed

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

    2011-05-01

    APBS and PDB2PQR are widely utilized free software packages for biomolecular electrostatics calculations. Using the Opal toolkit, we have developed a Web services framework for these software packages that enables the use of APBS and PDB2PQR by users who do not have local access to the necessary amount of computational capabilities. This not only increases accessibility of the software to a wider range of scientists, educators, and students but 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 of electrostatic 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/. Copyright © 2011 Wiley Periodicals, Inc.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. Calculation and observation of thermal electrostatic noise in solar wind plasma

    NASA Technical Reports Server (NTRS)

    Kellogg, P. J.

    1981-01-01

    Calculations, both approximate algebraic and numerical, have been carried out for the noise due to electrostatic waves incident on a dipole antenna. The noise is calculated both for a thermal equilibrium plasma, and one having several components at different temperatures. The results are compared with measurements from the IMP-6 satellite. In various frequency ranges, the noise power is dominated by Langmuir oscillations, by electron acoustic waves and by ion acoustic waves. The measurements are consistent with all of these, although the ion waves are not definitely observed, due to interference from shot noise.

  18. 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.

  19. 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.

  20. Protein molecular dynamics with electrostatic force entirely determined by a single Poisson-Boltzmann calculation.

    PubMed

    Lu, Ben Zhuo; Chen, Wei Zu; Wang, Cun Xin; Xu, Xiao-jie

    2002-08-15

    The electrostatic force including the intramolecular Coulombic interactions and the electrostatic contribution of solvation effect were entirely calculated by using the finite difference Poisson-Boltzmann method (FDPB), which was incorporated into the GROMOS96 force field to complete a new finite difference stochastic dynamics procedure (FDSD). Simulations were performed on an insulin dimer. Different relative dielectric constants were successively assigned to the protein interior; a value of 17 was selected as optimal for our system. The simulation data were analyzed and compared with those obtained from 500-ps molecular dynamics (MD) simulation with explicit water and a 500-ps conventional stochastic dynamics (SD) simulation without the mean solvent force. The results indicate that the FDSD method with GROMOS96 force field is suitable to study the dynamics and structure of proteins in solution if used with the optimal protein dielectric constant. Copyright 2002 Wiley-Liss, Inc.

  1. 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.

  2. Improved Boundary Element Methods for Poisson-Boltzmann Electrostatic Potential and Force Calculations.

    PubMed

    Lu, Benzhuo; McCammon, J Andrew

    2007-05-01

    A patch representation differing from the traditional treatments in the boundary element method (BEM) is presented, which we call the constant "node patch" method. Its application to solving the Poisson-Boltzmann equation (PBE) demonstrates considerable improvement in speed compared with the constant element and linear element methods. In addition, for the node-based BEMs, we propose an efficient interpolation method for the calculation of the electrostatic stress tensor and PB force on the solvated molecular surface. This force calculation is simply an O(N) algorithm (N is the number of elements). Moreover, our calculations also show that the geometric factor correction in the boundary integral equations significantly increases the accuracy of the potential solution on the boundary, and thereby the PB force calculation.

  3. 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.

  4. 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.

  5. Simple, accurate electrostatics-based formulas for calculating ionization potentials, electron affinities, and capacitances of fullerenes

    NASA Astrophysics Data System (ADS)

    Atanasov, Alexander B.; Ellenbogen, James C.

    2017-03-01

    A set of simple analytic formulas is derived via electrostatics-based methods to accurately calculate the values of electron affinities An and ionization potentials In for n -carbon icosahedral fullerene molecules as a function of their average radii Rn. These formulas reproduce with accuracy the values of An, In, and their scalings with 1 /Rn that were determined previously in detailed, computationally intensive density functional theory calculations. The formula for An is derived from an enhanced image-charge model that treats the valence region of the icosahedral system as a quasispherical conductor of radius (Rn+δ ) , where δ =1 /4 W∞ is a small constant distance determined from the work function W∞ of graphene. Using this model, though, a formula for In that includes only electrostatics-like terms does not exhibit accuracy similar to the analogous formula for An. To make it accurate, a term must be added to account for the large symmetry-induced quantum energy gap in the valence energy levels (i.e., the HOMO-LUMO gap). An elementary two-state model based upon a quantum rotor succeeds in producing a simple expression that evaluates the energy gap as an explicit function of An. Adding this to the electrostatics-like formula for In gives a simple quantum equation that yields accurate values for In and expresses them as a function of An. Further, the simple equations for An and In yield significant insight into both the physics of electron detachment in the fullerenes and the scaling with Rn of their quantum capacitances Cn=1 /(In-An) .

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. Electrostatics-based finite-size corrections for first-principles point defect calculations

    NASA Astrophysics Data System (ADS)

    Kumagai, Yu; Oba, Fumiyasu

    2014-05-01

    Finite-size corrections for charged defect supercell calculations typically consist of image-charge and potential alignment corrections. Regarding the image-charge correction, Freysoldt, Neugebauer, and Van de Walle (FNV) recently proposed a scheme that constructs the correction energy a posteriori through alignment of the defect-induced potential to a model charge potential [C. Freysoldt et al., Phys. Rev. Lett. 102, 016402 (2009), 10.1103/PhysRevLett.102.016402]. This, however, still has two shortcomings in practice. First, it uses a planar-averaged electrostatic potential for determining the potential offset, which can not be readily applied to defects with large atomic relaxation. Second, Coulomb interaction is screened by a macroscopic scalar dielectric constant, which can bring forth large errors for defects in layered and low-dimensional structures. In this study, we use the atomic site potential as a potential marker, and extend the FNV scheme by estimating long-range Coulomb interactions with a point charge model in an anisotropic medium. We also revisit the conventional potential alignment and show that it is unnecessary for correcting defect formation energies after the image-charge correction is properly applied. A systematic assessment of the accuracy of the extended FNV scheme is performed for defects and impurities in diverse materials: β-Li2TiO3, ZnO, MgO, Al2O3,HfO2, cubic and hexagonal BN, Si, GaAs, and diamond. Defect formation energies with -6 to +3 charges calculated using supercells containing around 100 atoms are successfully corrected even after atomic relaxation within 0.2 eV compared to those in the dilute limit.

  15. 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

  16. Darcy-Weisbach friction factor at the nanoscale: From atomistic calculations to continuum models

    NASA Astrophysics Data System (ADS)

    Liakopoulos, A.; Sofos, F.; Karakasidis, T. E.

    2017-05-01

    A modification of the Darcy-Weisbach friction factor applicable to nanoscale liquid transport processes is proposed. Non-equilibrium molecular dynamics simulations allow us to access the atomic behaviour of liquids moving in nanochannels, and by comparing atomistic simulation results with continuum Navier-Stokes solutions, we extend the applicability of continuum theory to nanoscale liquid flows. We find that classical continuum theory predictions of power dissipation do not apply in the case of nanochannels and have to be modified accordingly with input from atomistic simulations such as slip velocity and profiles of variable viscosity. The mathematical form of the friction factor expression persists for quite small nanochannel widths, i.e., the form of the relation for the friction factor f Re = const. is practically maintained even at the nanoscale, but the value of the constant significantly increases with increasing hydrophilicity.

  17. Three oxime ether derivatives: Synthesis, crystallographic study, electronic structure and molecular electrostatic potential calculation

    NASA Astrophysics Data System (ADS)

    Dey, Tanusri; Praveena, Koduru Sri Shanthi; Pal, Sarbani; Mukherjee, Alok Kumar

    2017-06-01

    Three oxime ether derivatives, (E)-3-methoxy-4-(prop-2-ynyloxy)-benzaldehyde-O-prop-2-ynyl-oxime (C14H13NO3) (2), benzophenone-O-prop-2-ynyl-oxime (C16H13NO) (3) and (E)-2-chloro-6-methylquinoline-3-carbaldehyde-O-prop-2-ynyl-oxime (C14H11ClN2O) (4), have been synthesized and their crystal structures have been determined. The DFT optimized molecular geometries in 2-4 agree closely with those obtained from the crystallographic study. An interplay of intermolecular Csbnd H⋯O, Csbnd H⋯N, Csbnd H⋯Cl and Csbnd H···π(arene) hydrogen bonds and π···π interactions assembles molecules into a 2D columnar architecture in 2, a 1D molecular ribbon in 3 and a 3D framework in 4. Hirshfeld surface analysis showed that the structures of 2 and 3 are mainly characterized by H⋯H, H⋯C and H⋯O contacts but some contribution of H⋯N and H⋯Cl contacts is also observed in 4. Hydrogen-bond based interactions in 2-4 have been complemented by calculating molecular electrostatic potential (MEP) surfaces. The electronic structures of molecules reveal that the estimated band gap in 3, in which both aldehyde hydrogen atoms of formaldehyde-O-prop-2-ynyl-oxime (1) have been substituted by two benzene rings, is higher than that of 2 and 4 with only one aldehyde hydrogen atom replaced.

  18. 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

  19. 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.

  20. Electrostatic complementarity in an aldose reductase complex from ultra-high-resolution crystallography and first-principles calculations.

    PubMed

    Muzet, Nicolas; Guillot, Benoît; Jelsch, Christian; Howard, Eduardo; Lecomte, Claude

    2003-07-22

    The electron density and electrostatic potential in an aldose reductase holoenzyme complex have been studied by density functional theory (DFT) and diffraction methods. Aldose reductase is involved in the reduction of glucose in the polyol pathway by using NADPH as a cofactor. The ultra-high resolution of the diffraction data and the low thermal-displacement parameters of the structure allow accurate atomic positions and an experimental charge density analysis. Based on the x-ray structural data, order-N DFT calculations have been performed on subsets of up to 711 atoms in the active site of the molecule. The charge density refinement of the protein was performed with the program MOPRO by using the transferability principle and our database of charge density parameters built from crystallographic analyses of peptides and amino acids. Electrostatic potentials calculated from the charge density database, the preliminary experimental electron density analysis, DFT computations, and atomic charges taken from the amber software dictionary are compared. The electrostatic complementarity between the cofactor NADP+ and the active site shows up clearly. The anchoring of the inhibitor is due mainly to hydrophobic forces and to only two polar interaction sites within the enzyme cavity. The potentials calculated by x-ray and DFT techniques agree reasonably well. At the present stage of the refinement, the potentials obtained directly from the database are in excellent agreement with the experimental ones. In addition, these results demonstrate the significant contribution of electron lone pairs and of atomic polarization effects to the host and guest mechanism.

  1. 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

  2. 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…

  3. 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.

  4. 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…

  5. Influence of accounting for water-vapor continuum absorption on the calculation of radiative processes in the atmosphere

    NASA Astrophysics Data System (ADS)

    Chesnokova, T. Y.

    1999-01-01

    At present, the tendency of global warming of the earth climate is observed. The climate depends on even small changes of radiative processes in the atmosphere. According to recent conceptions, the 'green house' effect can be connected with the increasing concentration of minor gaseous components, such as CO2, CO, CH4, and freons, therewith the contribution of the letter is comparable to that of CO2. A radiance transfer through the atmosphere is performed through spectral transmission windows, in which one of the basic roles belongs to water vapor continuum absorption. Different recent models of continuum absorption, based on the experimental data, are considered here. The long-wave radiance flux calculation is made on the basis of these models. It is shown that the error of the radiative fluxes calculation in the transmission windows is of the same order as the contribution of some atmospheric minor gaseous constituents and often exceeds it. Therefore, the accurate analytical expressions, describing the water continuum absorption and accounting for the nonlinear dependence of the absorption on humidity, temperature, wavelength and other factors, are needed.

  6. 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.

  7. 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.

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

    PubMed Central

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

    2011-01-01

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

  9. 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.

  10. 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

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

    SciTech Connect

    Lu, Benzhuo; Cheng, Xiaolin; Huang, Jingfang; McCammon, Jonathan

    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://mccammon.ucsd.edu/. This paper is a brief summary of the program: the algorithms, the implementation and the usage.

  12. 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.

  13. 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.

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

    PubMed

    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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  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

    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

  20. 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.

  1. 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.

  2. 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/

  3. Interplay among Electrostatic, Dispersion, and Steric Interactions: Spectroscopy and Quantum Chemical Calculations of π-Hydrogen Bonded Complexes.

    PubMed

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

    2017-04-05

    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 experiments 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 and IR-UV double-resonance spectroscopy techniques are used to probe jet-cooled ind⋅⋅⋅n-mb (n=2, 3, 6) complexes, with redshifting 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 to be due to multiple tilted conformations of each dimer possessing similar stabilization energies. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    DTIC Science & Technology

    2016-09-06

    002) rocking curves is shown in Fig. 2(b). Energy-dispersive spectroscopy (EDS) is used as a pre- liminary, qualitative means to check for gross...ing calculated to be 4.31 Å. (b) Omega rocking curves of the (002) peak of the J30 film compared to the MgO sub- strate. The rocking curves were col...consistent cycles was less than 104 eV. For small binary and mixed oxide systems (8 atoms/cell, NaCl structure), the Brillouin-zone was sampled by a C

  5. 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

  6. 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.

  7. Comparison of the charge moment change calculated from electrostatic analysis and from ELF radio observations

    NASA Astrophysics Data System (ADS)

    Nieckarz, Zenon; Baranski, Piotr; Mlynarczyk, Janusz; Kulak, Andrzej; Wiszniowski, Jan

    2015-01-01

    We compare the results of two methods of calculation of the charge moment change (CMC, also called the dipole moment change) of the cloud-to-ground lightning discharges. The first method uses multistation ground-based measurements of the E field change for the purpose of the lightning flash location and charge analysis. Our six stations, called the Local Lightning Detection Network (LLDN), were set up in the Warsaw region. The second method is based on measurements of the horizontal magnetic field component of electromagnetic waves generated by atmospheric discharges in the ELF (extremely low frequency) range. Our ELF station is equipped with two magnetic antennas, east-west and north-south and is located in a sparsely populated area of the Bieszczady Mountains in Poland (49.19°N, 22.55°E). We present and discuss the results obtained by both methods, focusing on the negative return stroke (RS) and the return stroke with continuing current (RS and CC) lightning discharges. Results show a good correlation between the CMC obtained by the two methods. For the negative RS and CC and RS the correlation coefficient is equal to +0.50 and +0.80, respectively.

  8. 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.

  9. Continuum treatment of electronic polarization effect

    NASA Astrophysics Data System (ADS)

    Tan, Yu-Hong; Luo, Ray

    2007-03-01

    A continuum treatment of electronic polarization has been explored for in molecular mechanics simulations in implicit solvents. The dielectric constant for molecule interior is the only parameter in the continuum polarizable model. A value of 4 is found to yield optimal agreement with high-level ab initio quantum mechanical calculations for the tested molecular systems. Interestingly, its performance is not sensitive to the definition of molecular volume, in which the continuum electronic polarization is defined. In this model, quantum mechanical electrostatic field in different dielectric environments from vacuum, low-dielectric organic solvent, and water can be used simultaneously in atomic charge fitting to achieve consistent treatment of electrostatic interactions. The tests show that a single set of atomic charges can be used consistently in different dielectric environments and different molecular conformations, and the atomic charges transfer well from training monomers to tested dimers. The preliminary study gives us the hope of developing a continuum polarizable force field for more consistent simulations of proteins and nucleic acids in implicit solvents.

  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. Molecular modeling and electrostatic potential calculations on chemically modified Cu,Zn superoxide dismutases from Bos taurus and shark Prionace glauca: role of Lys134 in electrostatically steering the substrate to the active site.

    PubMed

    Polticelli, F; Falconi, M; O'Neill, P; Petruzelli, R; Galtieri, A; Lania, A; Calabrese, L; Rotilio, G; Desideri, A

    1994-07-01

    The three-dimensional structure of Cu,Zn superoxide dismutase (SOD) from the shark Prionace glauca was homology modeled on the structure of the bovine enzyme used as a template. Shark SOD displays the conservative substitution of one of the residues involved in the electrostatic guidance of superoxide toward the active site of the enzyme, i.e., Lys134, which is replaced by arginine. The association rate, calculated by brownian dynamics simulations incorporating electrostatic terms, and the enzyme reaction rate, measured by the pulse radiolysis method, were found to be identical for both bovine and shark SODs. In order to quantify the role of Lys134 in electrostatically steering the superoxide to the active site, chemical modification of the lysine residues by carbamoylation was carried out on both bovine and shark SODs. Experimental determination of the enzymatic reaction rate indicated that the charge located on the residue 134 gives 19% contribution to the guidance of superoxide anion at low ionic strength. This value matches the association rates predicted by brownian dynamics.

  14. Molecular surface-free continuum model for electrodiffusion processes

    PubMed Central

    Lu, Benzhuo; McCammon, J. Andrew

    2008-01-01

    Incorporation of van der Waals interactions enables the continuum model of electrodiffusion in biomolecular system to avoid the artifacts of introducing a molecular surface and the painful task of the surface mesh generation. Calculation examples show that the electrostatics, diffusion-reaction kinetics, and molecular surface defined as an isosurface of a certain density distribution can be extracted from the solution of the Poisson-Nernst-Planck equations using this model. The molecular surface-free model enables a wider usage of some modern numerical methodologies such as finite element methods for biomolecular modeling, and sheds light on a new paradigm of continuum modeling for biomolecular systems. PMID:19461944

  15. Linear interaction energy models for beta-secretase (BACE) inhibitors: Role of van der Waals, electrostatic, and continuum-solvation terms.

    PubMed

    Tounge, Brett A; Rajamani, Ramkumar; Baxter, Ellen W; Reitz, Allen B; Reynolds, Charles H

    2006-05-01

    Computing the binding affinity of a protein-ligand complex is one of the most fundamental and difficult tasks in computer-aided drug design. Many approaches for computing binding affinities can be classified as linear interaction energy (LIE) models as they rely on some type of linear fit of computed interaction energies between ligand and protein. We have examined the computed interaction energies of a series of beta-secretase (BACE) inhibitors in terms of van der Waals, coulombic, and continuum-solvation contributions to ligand binding. We have also systematically examined the effect of different protonation states of the protein and ligands. We find that the binding affinities are relatively insensitive to the protonation state of the protein when neutral ligands are considered. Inclusion of charged ligands leads to large deviations in the coulomb, solvation, and even van der Waals terms. The latter is due to increased repulsive van der Waals interactions in the complex due to the strong coulomb attraction found between oppositely charged functional groups in the protein and ligand. In general, we find that the best models are obtained when the protein is judiciously charged (e.g. Asp32-, Arg235+) and the potentially charged ligands are treated as neutral.

  16. 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

  17. 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

  18. 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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

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

  19. 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

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

    2013-11-14

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

  20. 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

  1. 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.

  2. An accurate and efficient empirical approach for calculating the dielectric self-energy and ion-ion pair potential in continuum models of biological ion channels.

    PubMed

    Cheng, Mary Hongying; Coalson, Rob D

    2005-01-13

    This paper presents empirical formulas for calculating the dielectric self-energy and ion-ion pair interactions in cylindrical ion channels. The proposed approach can be extended to more complex channel structures, for example, (i) a "straight" channel with variable radius and (ii) a "curved" channel with constant radius. For calibration purposes, we compare results obtained based on the approximate effective potentials developed herein to exact electrostatic calculations obtained via the algorithm of Graf et al.: the agreement is satisfactory. A dynamic lattice Monte Carlo (DLMC) technique is used to further assess the accuracy and efficiency of the proposed empirical potentials. The concentration profiles and current-voltage curves produced with our simple empirical energy formulas are in excellent agreement with numerical results obtained using the algorithm of Graf et al., which calculates all relevant electrostatic forces exactly. The use of effective ion-ion potentials greatly reduces the computer memory required to perform DLMC ion permeation simulations in dielectrically inhomogeneous environments, thus enabling treatment of larger systems than can be handled by numerically exact techniques.

  3. 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.

  4. 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.

  5. Electrostatic Precipitator

    NASA Image and Video Library

    2017-06-09

    New Electrostatic Precipitator in a flow-through system. The precipitator system is being developed to remove dust from the atmospheric intakes of the MARS ISRU chambers. It uses electrostatic forces for the dust removal.

  6. 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.

  7. 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.

  8. 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.

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

    PubMed

    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.

  10. 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.

  11. Electrostatics 1979,

    DTIC Science & Technology

    1979-11-28

    UK also perform consulting work on elec- trostatic problems. Two of these are the Wolfson Electrostatics Unit of the Department of Electrical...Cross (Wolfson Electrostatics Advisory Unit , Univ. of Southampton, UK ) reported that the application of high electro- static fields does indeed aid heat...062 917 OFFICE OF NAVAL RESEARCH LONDON ( ENGLAND ) F/0 20/3 ELECTROSTATICS 1979. (U) NOV 79 1 KAUFMAN UNCLASSIFIE’ ONLC-1 7 N JJ32 L136 I L. - ’III

  12. Electrostatic precipitation

    SciTech Connect

    Albanese, V.

    1980-07-22

    A method is described of improving the conductivity of particles entrained in a stream of particle-laden gas formed by the burning of coal. The particles are collected by an electrostatic precipitator which comprises treating said gas containing particles prior to contact with the electrostatic precipitator at a temperature not greater than about 800/sup 0/F with a resistivitydecreasing amount of hexamethylene tetramine or its water-soluble salts and thereafter passing the gas to the electrostatic precipitator.

  13. 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.

  14. 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.

  15. Fast finite element calculation of effective conductivity of random continuum microstructures: The recursive Poincaré-Steklov operator method

    NASA Astrophysics Data System (ADS)

    Hardin, Thomas J.; Schuh, Christopher A.

    2017-08-01

    The effective conductivity of a block of composite can be extracted from the Dirichlet-to-Neumann Poincaré-Steklov operator (PSO) for that block. In this paper, a domain decomposition method for computing the PSO over a finite element mesh is discussed. A new numerical strategy is introduced to accelerate the computation of this operator, using the Schur complement to calculate the PSO for the smallest subdomains, then recursively merging subdomain PSOs up to the full domain. At each step of the algorithm, information extraneous to the PSO is discarded. The effective conductivity values computed by this method are identical to those obtained from a basic Finite Element Method, an order of magnitude faster and with much less computer memory consumed. As proof of concept, effective conductivity measurements are presented for a percolating random fractal-like microstructure across a range of phase fractions.

  16. Calculating Standard Reduction Potentials of [4Fe–4S] Proteins

    SciTech Connect

    Perrin, Bradley S.; Niu, Shuqiang; Ichiye, Toshiko

    2013-03-15

    The oxidation–reduction potentials of electron transfer proteins determine the driving forces for their electron transfer reactions. Although the type of redox site determines the intrinsic energy required to add or remove an electron, the electrostatic interaction energy between the redox site and its surrounding environment can greatly shift the redox potentials. Here, a method for calculating the reduction potential versus the standard hydrogen electrode, E°, of a metalloprotein using a combinatio of density functional theory and continuum electrostatics is presented. This work focuses on the methodology for the continuum electrostatics calculations, including various factors that may affect the accuracy. The calculations are demonstrated using crystal structures of six homologous HiPIPs, which give E° that are in excellent agreement with experimental results.

  17. 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.

  18. 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.

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

    NASA Astrophysics Data System (ADS)

    Cai, Kaicong; Zheng, Xuan; Du, Fenfen

    2017-08-01

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

  20. 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.

  1. Charge compensation and electrostatic transferability in three entropy-stabilized oxides: Results from density functional theory calculations

    SciTech Connect

    Rak, Zs.; Rost, C. M.; Lim, M.; Maria, J.-P.; Brenner, D. W.; Sarker, P.; Toher, C.; Curtarolo, S.

    2016-09-07

    Density functional theory calculations were carried out for three entropic rocksalt oxides, (Mg{sub 0.1}Co{sub 0.1}Ni{sub 0.1}Cu{sub 0.1}Zn{sub 0.1})O{sub 0.5}, termed J14, and J14 + Li and J14 + Sc, to understand the role of charge neutrality and electronic states on their properties, and to probe whether simple expressions may exist that predict stability. The calculations predict that the average lattice constants of the ternary structures provide good approximations to that of the random structures. For J14, Bader charges are transferable between the binary, ternary, and random structures. For J14 + Sc and J14 + Li, average Bader charges in the entropic structures can be estimated from the ternary compositions. Addition of Sc to J14 reduces the majority of Cu, which show large displacements from ideal lattice sites, along with reduction of a few Co and Ni cations. Addition of Li to J14 reduces the lattice constant, consistent with experiment, and oxidizes some of Co as well as some of Ni and Cu. The Bader charges and spin-resolved density of states (DOS) for Co{sup +3} in J14 + Li are very different from Co{sup +2}, while for Cu and Ni the Bader charges form continuous distributions and the two DOS are similar for the two oxidation states. Experimental detection of different oxidation states may therefore be challenging for Cu and Ni compared to Co. Based on these results, empirical stability parameters for these entropic oxides may be more complicated than those for non-oxide entropic solids.

  2. 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.

  3. 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.

  4. 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.

  5. Electrostatic Interactions in Proteins: Application to the Photosynthetic Reaction Center.

    NASA Astrophysics Data System (ADS)

    Beroza, Paul

    This is a computational study of electrostatic interactions in the reaction center from the photosynthetic bacterium Rhodobacter sphaeroides. The reaction center is a protein/pigment complex that initiates the conversion of light energy into chemical energy. One of the important reactions in this process is the transfer of an electron from the primary electron acceptor (Q_ A , a ubiquinone-10 molecule) to the secondary electron acceptor (Q_ B, also a ubiquinone -10). In this work, I apply a continuum electrostatic model to calculate the energetics of the electron transfer between the quinones. The protein is treated as a continuum of low dielectric embedded in a high-dielectric continuum (the solvent). The atomic coordinates of the protein, determined by X-ray crystallography, provide the atomic detail necessary to define the dielectric interface and the location of charges in the protein. The electrostatic energy for a charge distribution in the protein is determined from a finite -difference solution to the linearized Poisson-Boltzmann equation. The free energy of electron transfer is coupled to the solution pH by electrostatic interactions with titrating amino acids in the reaction center. The effect of these interactions is approximated by a Monte Carlo sampling of the protonation states of the protein. The calculations show that the major difference between the electrostatic environments of the quinones is the large number of titrating residues near Q _{rm B}. Although there are large desolvation energies for charges near Q _{rm B}, compensating interactions, particularly from the dipoles in the polypeptide backbone of the protein, favor the ionization of acidic residues nearby. The calculated pH dependence of the free energy of electron transfer agrees well with experiment, but there is a systematic error in the absolute free energy. Glu L212, an acidic residue near Q_{rm B}, is calculated to dominate the proton uptake resulting from electron transfer, in

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

    SciTech Connect

    Bardhan, J.; Mathematics and Computer Science; Rush Univ.

    2009-03-07

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

  7. Resonance Raman, electron paramagnetic resonance, and density functional theory calculations of a phenolate-bound iron porphyrin complex: electrostatic versus covalent contribution to bonding.

    PubMed

    Das, Pradip Kumar; Dey, Abhishek

    2014-07-21

    Resonance Raman (rR), electron paramagnetic resonance (EPR), and density functional theory (DFT) calculations of a phenolate-bound iron porphyrin complex are reported. The complex is found to exist in a five-coordinate high-spin state in a noncoordinating solvent and in a six-coordinate low-spin state in a coordinating solvent. The vibrations originating from the iron phenolate-bound chromophores reproduced those reported for heme tyrosine active sites in nature. The EPR parameters and iron-pyrrole (Fe-Npyr) vibrations of phenolate, thiolate, and imidazole ligated iron porphyrin complexes indicate that the phenolate axial ligand acts as a π anisotropic ligand, which is more covalent than a neutral imidazole ligand but less covalent than a thiolate axial ligand. While the Fe(III/II) potential of the phenolate compound in a noncoordinating solvent is 500 mV more negative than that of the imidazole-bound complex, it is also 110 mV more negative than that of the thiolate-bound complex. DFT calculations reproduce the geometry and vibrational frequencies and show that while both phenolate and thiolate axial ligands bear π and σ interaction with the ferric center, the former is significantly less covalent than the thiolate. The higher covalency of the thiolate ligand is responsible for the lower Fe-Npyr vibration and higher V/λ (from EPR) of the thiolate-bound complexes relative to those of the phenolate-bound complex, whereas the greater electrostatic stabilization of the Fe(III)-OPh bond is responsible for lowering the Fe(III/II) E° of the phenolate-bound complex relative to that of the thiolate-bound complex in a medium having a reasonable dielectric constant.

  8. Electrostatic Precipitator

    NASA Image and Video Library

    2017-06-09

    Dr. Carlos Calle, lead scientist in the Kennedy Space Center's Electrostatics and Surface Physics Laboratory, left, and Jay Phillips, a research physicist, are modifying an electrostatic precipitator to help remove dust from simulated Martian atmosphere. NASA's Journey to Mars requires cutting-edge technologies to solve the problems explorers will face on the Red Planet. Scientists are developing some of the needed solutions by adapting a device to remove the ever-present dust from valuable elements in the Martian atmosphere. Those commodities include oxygen, water and methane.

  9. Electrostatic Precipitator

    NASA Image and Video Library

    2017-06-09

    Dr. Carlos Calle, lead scientist in the Kennedy Space Center's Electrostatics and Surface Physics Laboratory, left, and Jay Phillips, a research physicist, are modifying an electrostatic precipitator to help remove dust from a simulated Martian atmosphere. NASA's Journey to Mars requires cutting-edge technologies to solve the problems explorers will face on the Red Planet. Scientists are developing some of the needed solutions by adapting a device to remove the ever-present dust from valuable elements in the Martian atmosphere. Those commodities include oxygen, water and methane.

  10. Electrostatic Precipitator

    NASA Image and Video Library

    2017-06-09

    In their Swamp Works laboratory at NASA's Kennedy Space Center, Dr. Carlos Calle and Jay Phillips are testing an electrostatic precipitator using dust that closely approximates the make-up of that on Mars. They upgraded their electrostatic precipitator to fully simulate Martian atmosphere by designing and constructing a dust aerosolization pre-chamber. The agency's Journey to Mars requires cutting-edge technologies to solve the problems explorers will face on the Red Planet. Scientists are developing some of the needed solutions by adapting a device to remove the ever-present dust from valuable elements in the Martian atmosphere. Those commodities include oxygen, water and methane.

  11. Electrostatic Precipitator

    NASA Image and Video Library

    2017-06-09

    Jay Phillips, a research physicist in the Kennedy Space Center's Electrostatics and Surface Physics Laboratory, left, and Dr. Carlos Calle, lead scientist in the lab, are modifying an electrostatic precipitator to help remove dust from simulated Martian atmosphere. NASA's Journey to Mars requires cutting-edge technologies to solve the problems explorers will face on the Red Planet. Scientists are developing some of the needed solutions by adapting a device to remove the ever-present dust from valuable elements in the Martian atmosphere. Those commodities include oxygen, water and methane.

  12. 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)

  13. Multipolar electrostatics.

    PubMed

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

    2014-06-14

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

  14. 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.

  15. 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.

  16. Electrostatic Steering at Acetylcholine Binding Sites

    PubMed Central

    Meltzer, Robert H.; Thompson, Errol; Soman, Kizhake V.; Song, Xing-Zhi; Ebalunode, Jerry O.; Wensel, Theodore G.; Briggs, James M.; Pedersen, Steen E.

    2006-01-01

    The electrostatic environments near the acetylcholine binding sites on the nicotinic acetylcholine receptor (nAChR) and acetylcholinesterase were measured by diffusion-enhanced fluorescence energy transfer (DEFET) to determine the influence of long-range electrostatic interactions on ligand binding kinetics and net binding energy. Changes in DEFET from variously charged Tb3+-chelates revealed net potentials of −20 mV at the nAChR agonist sites and −14 mV at the entrance to the AChE active site, in physiological ionic strength conditions. The potential at the αδ-binding site of the nAChR was determined independently in the presence of d-tubocurarine to be −14 mV; the calculated potential at the αγ-site was approximately threefold stronger than at the αδ-site. By determining the local potential in increasing ionic strength, Debye-Hückel theory predicted that the potentials near the nAChR agonist binding sites are constituted by one to three charges in close proximity to the binding site. Examination of the binding kinetics of the fluorescent acetylcholine analog dansyl-C6-choline at ionic strengths from 12.5 to 400 mM revealed a twofold decrease in association rate. Debye-Hückel analysis of the kinetics revealed a similar charge distribution as seen by changes in the potentials. To determine whether the experimentally determined potentials are reflected by continuum electrostatics calculations, solutions to the nonlinear Poisson-Boltzmann equation were used to compute the potentials expected from DEFET measurements from high-resolution models of the nAChR and AChE. These calculations are in good agreement with the DEFET measurements for AChE and for the αγ-site of the nAChR. We conclude that long-range electrostatic interactions contribute −0.3 and −1 kcal/mol to the binding energy at the nAChR αδ- and αγ-sites due to an increase in association rates. PMID:16751247

  17. Electrostatic steering at acetylcholine binding sites.

    PubMed

    Meltzer, Robert H; Thompson, Errol; Soman, Kizhake V; Song, Xing-Zhi; Ebalunode, Jerry O; Wensel, Theodore G; Briggs, James M; Pedersen, Steen E

    2006-08-15

    The electrostatic environments near the acetylcholine binding sites on the nicotinic acetylcholine receptor (nAChR) and acetylcholinesterase were measured by diffusion-enhanced fluorescence energy transfer (DEFET) to determine the influence of long-range electrostatic interactions on ligand binding kinetics and net binding energy. Changes in DEFET from variously charged Tb3+ -chelates revealed net potentials of -20 mV at the nAChR agonist sites and -14 mV at the entrance to the AChE active site, in physiological ionic strength conditions. The potential at the alphadelta-binding site of the nAChR was determined independently in the presence of d-tubocurarine to be -14 mV; the calculated potential at the alphagamma-site was approximately threefold stronger than at the alphadelta-site. By determining the local potential in increasing ionic strength, Debye-Hückel theory predicted that the potentials near the nAChR agonist binding sites are constituted by one to three charges in close proximity to the binding site. Examination of the binding kinetics of the fluorescent acetylcholine analog dansyl-C6-choline at ionic strengths from 12.5 to 400 mM revealed a twofold decrease in association rate. Debye-Hückel analysis of the kinetics revealed a similar charge distribution as seen by changes in the potentials. To determine whether the experimentally determined potentials are reflected by continuum electrostatics calculations, solutions to the nonlinear Poisson-Boltzmann equation were used to compute the potentials expected from DEFET measurements from high-resolution models of the nAChR and AChE. These calculations are in good agreement with the DEFET measurements for AChE and for the alphagamma-site of the nAChR. We conclude that long-range electrostatic interactions contribute -0.3 and -1 kcal/mol to the binding energy at the nAChR alphadelta- and alphagamma-sites due to an increase in association rates.

  18. 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.

  19. Continuum radiation in planetary magnetospheres

    SciTech Connect

    Kurth, W.S.

    1991-12-01

    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.

  20. 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.

  1. 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. Copyright © 2013 Wiley Periodicals, Inc.

  2. Continuum Level Density in Complex Scaling Method

    SciTech Connect

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

    2005-11-21

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

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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}.

  9. 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.

  10. 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.

  11. 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.

  12. 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).

  13. 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.

  14. Synthesis of electrostatic multielectrode deflectors

    SciTech Connect

    Cho, H.; Szilagyi, M.

    1995-09-01

    Synthesis of electrostatic deflectors with given source parameters, first-order properties, and minimum aberrations can be realized by using the cubic spline method or the {ital a} {ital priori} given multielectrode approach. Synthesis of electrostatic deflectors was successfully achieved previously by using the cubic spline method. In this paper we present synthesis of electrostatic deflectors based on the {ital a} {ital priori} given multielectrode approach for the purpose of obtaining the minimum beam spot size through a sequential optimization technique. Our calculations show that the third-order geometrical deflection aberrations can be reduced by about two to three orders of magnitude using a multielectrode deflector with three units or five units, each having short cylindrical segments with geometrically octupole symmetry. {copyright} {ital 1995} {ital American} {ital Vacuum} {ital Society}

  15. 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.

  16. 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.

  17. 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.

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

    PubMed Central

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

    2010-01-01

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

  19. Spectroscopic (FTIR, FT-Raman), molecular electrostatic potential, NBO and HOMO-LUMO analysis of P-bromobenzene sulfonyl chloride based on DFT calculations

    NASA Astrophysics Data System (ADS)

    Jeyavijayan, S.

    2015-02-01

    The FTIR and FT-Raman spectra of P-bromobenzene sulfonyl chloride (P-BBSC) have been recorded in the regions 4000-400 cm-1 and 3500-50 cm-1, respectively. Utilizing the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of the fundamental modes of the compound were carried out. The optimum molecular geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities, were calculated by density functional theory (DFT/B3LYP) method. A good agreement between experimental and calculated normal modes of vibrations has been observed. A detailed interpretation of the infrared and Raman spectra of P-BBSC is also reported based on total energy distribution (TED). Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The MEP map shows the negative potential sites are on oxygen atoms as well as the positive potential sites are around the hydrogen atoms. The UV-vis spectral analysis of P-BBSC has also been done which confirms the charge transfer of the molecule.

  20. 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).

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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.…

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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

  15. 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…

  16. 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.

  17. 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…

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. Design of improved protein inhibitors of HIV-1 cell entry: Optimization of electrostatic interactions at the binding interface.

    PubMed

    Green, David F; Tidor, Bruce

    2005-09-01

    Continuum electrostatic methods are a powerful tool for the analysis and design of biomolecular complexes, with methodologies that allow for the detailed analysis of the electrostatic contributions to binding affinities and procedures for computing the properties of electrostatically optimal ligands. We have applied these methods to the design of improved inhibitors of HIV-1 cell entry. HIV infection of a cell requires viral-cell membrane fusion, an event partially driven by a large-scale conformational change in the viral membrane glycoprotein gp41. This transformation involves the docking of a helix from the C-terminal region of three gp41 chains against a pre-formed trimeric-coiled coil; several protein constructs that inhibit membrane fusion act by binding to an isolated C-terminal helix and blocking the formation of the fusogenic structure. A detailed analysis of the electrostatic contributions to the binding of one such inhibitor (5-Helix) to a C-terminal helix was performed using the X-ray crystal structure of the core of the HIV-1 gp41 ectodomain as a structural model, and several residues on 5-Helix that make substantial contributions to binding, both favorable and unfavorable, were identified. An electrostatic affinity optimization methodology was applied to the side chains of 5-Helix, with the results showing that significant improvements in binding affinity are possible if the electrostatic contributions to the binding free energy are optimized. Several mutations accessible by experimental methods are suggested, with calculated improvements in binding affinity of as much as 500-fold and greater. Copyright 2005 Wiley-Liss, Inc.

  4. 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

  5. Polarizable Atomic Multipole Solutes in a Poisson-Boltzmann Continuum

    PubMed Central

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

    2008-01-01

    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 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 (PBE). Only recently have the classical force fields used for studying biomolecules begun to include explicit polarization in their functional forms. Here we 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 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 150 mM salt lowered the electrostatic solvation energy between 2–13 kcal/mole, depending on the formal charge of the protein, but had only a

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

    PubMed

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

    2017-06-13

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

  7. 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

  8. Electrostatic Field Invisibility Cloak.

    PubMed

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

    2015-11-10

    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.

  9. 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.

  10. Voltage limitations of electrostatic accelerators

    SciTech Connect

    Hyder, H.R. )

    1999-04-01

    The history of electrostatic accelerators has been punctuated by a series of projects in which innovative designs have failed to meet the expectations of their designers. From the early, air-insulated Van de Graaffs at Round Hill to certain of the large pressurized heavy ion accelerators of the 1970s and 1980s, increases in size or changes in design and materials have not always led to the maximum voltages expected or extrapolated. Since these failures have continued beyond childhood into a mature technology, it is reasonable to assume that the causes of voltage limitation are varied and complex. They have remained poorly understood for a number of reasons: resources for an extended program of research into breakdown and failure of electrostatic generators have always been meager, especially for large machines devoted to nuclear research; the inaccessibility of pressurized generators makes instrumentation difficult and testing slow; the calculation of transient and dynamic effects is laborious and the results difficult to verify; voltage test experiments on operating accelerators are inhibited by the significant risk of damage due to energy release on breakdown: and the total voltages (though not the local fields) achieved in many electrostatic accelerators exceed those produced in any other man-made environment. In this review, the behavior of several generators of different designs is examined in order to assess the importance of the various design features and operating conditions that control the maximum voltage achievable in a working machine. [copyright] [ital 1999 American Institute of Physics.

  11. Electrostatic effects in DNA stretching

    NASA Astrophysics Data System (ADS)

    Tkachenko, Alexei V.

    2006-10-01

    The response of a semiflexible polyelectrolyte chain to stretching in the regimes of moderate and weak screening is studied theoretically, with a special focus on DNA experiments. By using the nonlinear Poisson-Boltzmann description of electrostatic self-interactions of the chain, we explicitly demonstrate the applicability of the concept of effective charge to certain aspects of the problem. This charge can be extracted from the far-field asymptotic behavior of the electrostatic potential of the fully aligned chain. Surprisingly, in terms of the effective charge, the electrostatically renormalized persistence length can be formally described by the classical Odijk-Skolnick-Fixman formula, whose domain of applicability is normally limited to the linearized Debye-Hückel (DH) approximation. However, the short-scale behavior of the chain in the nonlinear regime deviates from the of DH-based result, even upon charge renormalization. This difference is revealed in the calculated stretching curves for strongly charged DNA. These results are in good agreement with recent experiments. In the limit of weak screening we predict the elastic response to have a distinctive two-stage character, with a peculiar intermediate “unstretchable” regime.

  12. 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.

  13. Micromachined electrostatic vertical actuator

    SciTech Connect

    Lee, A.P.; Sommargren, G.E.; McConaghy, C.F.; Krulevitch, P.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.

  14. 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)

  15. 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)

  16. 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.

  17. Electrostatic discharge test apparatus

    NASA Technical Reports Server (NTRS)

    Smith, William C. (Inventor)

    1989-01-01

    Electrostatic discharge properties of materials are quantitatively measured and ranked. Samples (20) are rotated on a turntable (15) beneath selectable, co-available electrostatic chargers (30/40), one being a corona charging element (30) and the other a sample-engaging triboelectric charging element (40). They then pass under a voltage meter (25) to measure the amount of residual charge on the samples (20). After charging is discontinued, measurements are continued to record the charge decay history over time.

  18. 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.

  19. 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.

  20. Electrostatic Linear Actuator

    NASA Technical Reports Server (NTRS)

    Collins, Earl R., Jr.; Curry, Kenneth C.

    1990-01-01

    Electrically charged helices attract or repel each other. Proposed electrostatic linear actuator made with intertwined dual helices, which holds charge-bearing surfaces. Dual-helix configuration provides relatively large unbroken facing charged surfaces (relatively large electrostatic force) within small volume. Inner helix slides axially in outer helix in response to voltages applied to conductors. Spiral form also makes components more rigid. Actuator conceived to have few moving parts and to be operable after long intervals of inactivity.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Solar radio continuum storms

    NASA Technical Reports Server (NTRS)

    1974-01-01

    Radio noise continuum emission observed in metric and decametric wave frequencies is discussed. The radio noise is associated with actively varying sunspot groups accompanied by the S-component of microwave radio emissions. It is shown that the S-component emission in microwave frequencies generally occurs several days before the emission of the noise continuum storms of lower frequencies. It is likely that energetic electrons, 10 to 100 Kev, accelerated in association with the variation of sunspot magnetic fields, are the sources of the radio emissions. A model is considered to explain the relation of burst storms on radio noise. An analysis of the role of energetic electrons on the emissions of both noise continuum and type III burst storms is presented. It is shown that instabilities associated with the electrons and their relation to their own stabilizing effects are important in interpreting both of these storms.

  6. Local Electrostatic Moments and Periodic Boundary Conditition

    SciTech Connect

    Schultz, P.A.

    1998-12-04

    Electronic structure calculations frequently invoke periodic boundary conditions to solve for electrostatic potentials. For systems that are electronically charged, or contain dipole (or higher) moments, this artifice introduces spurious potentials due to the interactions between the system and multipole moments of its periodic images in aperiodic directions. I describe a method to properly handle the multipole moments of the electron density in electronic structure calculations using periodic boundary conditions. The density for which an electrostatic potential is to be evaluated is divided into two pieces. A local density is constructed that matches the desired moments of the full density, and its potential computed treating this density as isolated. With the density of this local moment countercharge removed from the full density, the remainder density lacks the troublesome moments and its electrostatic potential can be evaluated accurately using periodic boundary conditions.

  7. 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

  8. Electrostatics of DNA complexes with cationic lipids

    NASA Astrophysics Data System (ADS)

    Cherstvy, Andrey

    2007-03-01

    We present the exact solutions of the linear Poisson-Boltzmann theory for several problems relevant to electrostatics of DNA complexes with cationic lipids. We calculate the electrostatic potential and energy for lamellar and inverted hexagonal phases, concentrating on the effects of water-membrane dielectric boundaries. Our results for the complex energy agree qualitatively well with the known numerical solutions of the nonlinear Poisson-Boltzmann equation. Using the solution for the lamellar phase, we calculate its compressibility modulus and compare our findings with experimental data available suggesting a new scaling dependence on DNA-DNA separations in the complex. Also, we treat analytically charge-charge electrostatic interactions across, along, and in between two low-dielectric membranes. We obtain an estimate for the strength of electrostatic interactions of 1D DNA smectic layers across a lipid membrane. We discuss also some aspects of 2D DNA condensation and DNA-DNA attraction in DNA-lipid lamellar phase in the presence of di- and tri-valent cations and analyze the equilibrium intermolecular separations using the recently developed theory of electrostatic interactions of DNA helical charge motifs.

  9. 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.

  10. Electrostatics at the nanoscale

    SciTech Connect

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

    2011-01-01

    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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.…

  15. 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…

  16. 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…

  17. 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.

  18. Electrostatic beneficiation of coal

    SciTech Connect

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

    1994-10-01

    Dry physical beneficiation of coal has many advantages over wet cleaning methods and post combustion flue gas cleanup processes. The dry beneficiation process is economically competitive and environmentally safe and has the potential of making vast amounts of US coal reserves available for energy generation. While the potential of the electrostatic beneficiation has been studied for many years in laboratories and in pilot plants, a successful full scale electrostatic coal cleaning plant has not been commercially realized yet. In this paper the authors review some of the technical problems that are encountered in this method and suggest possible solutions that may lead toward its full utilization in cleaning coal.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. Electrostatic space radiation shielding

    NASA Astrophysics Data System (ADS)

    Tripathi, R.; Wilson, J. W.; Youngquist, R. C.

    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 will be drawn should the electrostatic shielding be successful for the future directions of space radiation protection

  9. 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.

  10. 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.

  11. Electrostatically Enhanced Vortex Separator

    NASA Technical Reports Server (NTRS)

    Collins, Earl R.

    1993-01-01

    Proposed device removes fine particles from high-pressure exhaust gas of chemical reactor. Negatively charged sectors on rotating disks in vortex generator attracts positively charged particles from main stream of exhaust gas. Electrostatic charge enhances particle-separating action of vortex. Gas without particles released to atmosphere.

  12. An asymmetry in electrostatics

    NASA Astrophysics Data System (ADS)

    Ganci, Salvatore

    2013-11-01

    This paper outlines a misuse of the electrostatic induction concept. A non-symmetrical behaviour was observed in a charge by the induction of an insulated hollow metallic conductor (the Faraday ice pail experiment). The major consequence of this experiment is a quick demonstration that the Earth must have a net negative charge.

  13. 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.

  14. 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.

  15. 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

  16. Solar radio continuum storms

    NASA Technical Reports Server (NTRS)

    Sakurai, K.

    1976-01-01

    The paper reviews the current status of research on solar radio continuum emissions from metric to hectometric wave frequencies, emphasizing the role of energetic electrons in the 10-100 keV range in these emissions. It is seen that keV-energy electrons generated in active sunspot groups must be the sources of radio continuum storm emissions for wide frequency bands. These electrons excite plasma oscillations in the medium, which in turn are converted to electromagnetic radiation. The radio noise continuum sources are usually associated with type III burst activity observed above these sources. Although the mechanism for the release of the energetic electrons is not known, it seems they are ejected from storm source regions in association with rapid variation of associated sunspot magnetic fields due to their growth into complex types. To explain some of the observed characteristics, the importance of two-stream instability and the scattering of ambient plasma ions on energetic electron streams is pointed out.

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

    PubMed Central

    Zhang, Zhe; Witham, Shawn; Alexov, Emil

    2011-01-01

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

  18. 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.

  19. 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(+).

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. Electrostatic Levitator Vacuum Chambers

    NASA Technical Reports Server (NTRS)

    1998-01-01

    Optical prots ring the Electrostatic Levitator (ESL) vacuum chamber to admit light from the heating laser (the beam passes through the window at left), poisitioning lasers (one port is at center), and lamps (such as the deuterium arc lamp at right), and 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.

  5. 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

  6. 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.

  7. Electrostatic curtain studies

    SciTech Connect

    Meyer, L C

    1992-05-01

    This report presents the results of experiments using electrostatic curtains (ESCS) as a transuranic (TRU) contamination control technique. The TRU contaminants included small (micrometer to sub micrometer) particles of plutonium and americium compounds associated with defense-related waste. Three series of experiments were conducted. The first was with uncontaminated Idaho National Engineering Laboratory (INEL) soil, the second used contaminated soil containing plutonium-239 (from a mixture of Rocky Flats Plant contaminated soil and INEL uncontaminated soil), and the third was uncontaminated INEL soil spiked with plutonium-239. All experiments with contaminated soil were conducted inside a glove box containing a dust generator, low volume cascade impactor (LVCI), electrostatic separator, and electrostatic materials. The data for these experiments consisted of the mass of dust collected on the various material coupons, plates, and filters; radiochemical analysis of selected samples; and photographs, as well as computer printouts giving particle size distributions and dimensions from the scanning electron microscope (SEM). The following results were found: (a) plutonium content (pCi/g) was found to increase with smaller soil particle sizes and (b) the electrostatic field had a stronger influence on smaller particle sizes compared to larger particle sizes. The SEM analysis indicated that the particle size of the tracer Pu239 used in the spiked soil experiments was below the detectable size limit (0.5 {mu}m) of the SEM and, thus, may not be representative of plutonium particles found in defense-related waste. The use of radiochemical analysis indicated that plutonium could be found on separator plates of both polarities, as well as passing through the electric field and collecting on LVCI filters.

  8. Electrostatic Levitator 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. Electrostatic and induction effects in the solubility of water in alkanes

    NASA Astrophysics Data System (ADS)

    Asthagiri, D.; Valiya Parambathu, Arjun; Ballal, Deepti; Chapman, Walter G.

    2017-08-01

    Experiments show that at 298 K and 1 atm pressure, the transfer free energy, μex, of water from its vapor to liquid normal alkanes CnH2n+2 (n =5 …12 ) is negative. Earlier it was found that with the united-atom TraPPE model for alkanes and the SPC/E model for water, one had to artificially enhance the attractive alkane-water cross interaction to capture this behavior. Here we revisit the calculation of μex using the polarizable AMOEBA and the non-polarizable Charmm General (CGenFF) forcefields. We test both the AMOEBA03 and AMOEBA14 water models; the former has been validated with the AMOEBA alkane model while the latter is a revision of AMOEBA03 to better describe liquid water. We calculate μex using the test particle method. With CGenFF, μex is positive and the error relative to experiments is about 1.5 kBT. With AMOEBA, μex is negative and deviations relative to experiments are between 0.25 kBT (AMOEBA14) and 0.5 kBT (AMOEBA03). Quantum chemical calculations in a continuum solvent suggest that zero point effects may account for some of the deviation. Forcefield limitations notwithstanding, electrostatic and induction effects, commonly ignored in consideration of water-alkane interactions, appear to be decisive in the solubility of water in alkanes.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Hot Magnetic Fibrils: The Slow Continuum Revisited

    NASA Astrophysics Data System (ADS)

    Keppens, R.

    1996-09-01

    We investigate the importance of the slow continuum (from linear, ideal magnetohydrodynamics [MHD]) for hot, evacuated, and strongly magnetic fibrils with nonnegligible radial structure. The radial structure allows for both slow and Alfvén resonant absorption of acoustic power (in linear, visco-resistive MHD). When calculating how efficiently the acoustic power is absorbed by such "hot magnetic fibrils," embedded in a uniform compressible medium, as a function of the real driving frequency, it is found that the axisymmetric component of the acoustic excitation is absorbed quite strongly for frequencies within the range of the slow continuum. Additionally, for these one-dimensional hot magnetic fibrils, a sequence of absorption maxima accumulates in real driving frequency above the range of the slow continuum, still within the Alfvén continuum. The maximal absorption coefficients reach 80% and more. We identify the complex optimal driving frequencies and the associated complex leaky eigenmodes responsible for these absorption maxima. The leaky eigenmodes relate to the well-known tube speed modes of a uniform, hot, and evacuated flux tube. The complex eigenfrequencies of the leaky eigenmodes of the radially structured fibrils are calculated from the impedance criterion that these eigenfrequencies satisfy. We define the generally complex optimal driving frequencies to be those driving frequencies at which total (100%) absorption of the incoming wave field takes place. They also obey an impedance criterion, similar to the one that defines the eigenfrequencies. Both impedance criteria demonstrate clearly the connection between optimal driving frequencies and leaky eigenmodes. This also calls for a reevaluation of the results of Goossens & Hollweg, in which optimal and total resonant absorption for real driving frequencies and the complex leaky eigenmodes was discussed. For network and plage magnetic elements in the solar atmosphere, our results may be relevant for

  2. 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

  3. 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

  4. 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)

  5. 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)

  6. 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

  7. Singular electrostatic energy of nanoparticle clusters

    NASA Astrophysics Data System (ADS)

    Qin, Jian; Krapf, Nathan W.; Witten, Thomas A.

    2016-02-01

    The binding of clusters of metal nanoparticles is partly electrostatic. We address difficulties in calculating the electrostatic energy when high charging energies limit the total charge to a single quantum, entailing unequal potentials on the particles. We show that the energy at small separation h has a singular logarithmic dependence on h . We derive a general form for this energy in terms of the singular capacitance of two spheres in near contact c (h ) , together with nonsingular geometric features of the cluster. Using this form, we determine the energies of various clusters, finding that more compact clusters are more stable. These energies are proposed to be significant for metal-semiconductor binary nanoparticle lattices found experimentally. We sketch how these effects should dictate the relative abundances of metal nanoparticle clusters in nonpolar solvents.

  8. Novel electrostatic trap for cold polar molecules

    NASA Astrophysics Data System (ADS)

    Xu, Xue-Yan; Ma, Hui; Yin, Jian-Ping

    2007-12-01

    We propose a novel scheme in which cold polar molecules are trapped by an electrostatic field generated by the combination of a pair of parallel transparent electrodes (i.e., two infinite transparent plates) and a ring electrode (i.e., a ring wire). The spatial distributions of the electrostatic fields from the above charged wire and the charged plates and the corresponding Stark potentials for cold CO molecules are calculated; the dependences of the trap centre position on the geometric parameters of the electrode are analysed. We also discuss the loading process of cold molecules from a cold molecular beam into our trap. This study shows that the proposed scheme is not only simple and convenient to trap, manipulate and control cold polar molecules in weak-field-seeking states, but also provides an opportunity to study cold collisions and collective quantum effects in a variety of cold molecular systems, etc.

  9. Proton emission with a screened electrostatic barrier

    NASA Astrophysics Data System (ADS)

    Budaca, R.; Budaca, A. I.

    2017-08-01

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

  10. Electrostatic forces in the Poisson-Boltzmann systems.

    PubMed

    Xiao, Li; Cai, Qin; Ye, Xiang; Wang, Jun; Luo, Ray

    2013-09-07

    Continuum modeling of electrostatic interactions based upon numerical solutions of the Poisson-Boltzmann equation has been widely used in structural and functional analyses of biomolecules. A limitation of the numerical strategies is that it is conceptually difficult to incorporate these types of models into molecular mechanics simulations, mainly because of the issue in assigning atomic forces. In this theoretical study, we first derived the Maxwell stress tensor for molecular systems obeying the full nonlinear Poisson-Boltzmann equation. We further derived formulations of analytical electrostatic forces given the Maxwell stress tensor and discussed the relations of the formulations with those published in the literature. We showed that the formulations derived from the Maxwell stress tensor require a weaker condition for its validity, applicable to nonlinear Poisson-Boltzmann systems with a finite number of singularities such as atomic point charges and the existence of discontinuous dielectric as in the widely used classical piece-wise constant dielectric models.

  11. Approaching continuum monopoles

    SciTech Connect

    Kovner, Alex; Khvedelidze, Arsen; McMullan, David

    2006-07-11

    We set up the calculation of the expectation value of the monopole creation operator in the confining phase of the 4d Georgi-Glashow model. We find that in the leading order of the perturbation theory the VEV vanishes as a power of the volume of the system. This is in accordance with our naive expectation. We expect that nonperturbative effects will introduce an effective infrared cutoff on the calculation making the VEV finite.

  12. 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.

  13. 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.

  14. 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)

  15. 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)

  16. The thermal infrared continuum in solar flares

    NASA Astrophysics Data System (ADS)

    Fletcher, Lyndsay; Simoes, Paulo; Kerr, Graham Stewart; Hudson, Hugh S.; Gimenez de Castro, C. Guillermo; Penn, Matthew J.

    2017-08-01

    Observations of the Sun with the Atacama Large Millimeter Array have now started, and the thermal infrared will regularly be accessible from the NSF’s Daniel K. Inouye Solar Telescope. Motivated by the prospect of these new observations, and by recent flare detections in the mid infrared, we set out here to model and understand the source of the infrared continuum in flares, and to explore its diagnostic capability for the physical conditions in the flare atmosphere. We use the 1D radiation hydrodynamics code RADYN to calculate mid-infrared continuum emission from model atmospheres undergoing sudden deposition of energy by non-thermal electrons. We identify and characterise the main continuum thermal emission processes relevant to flare intensity enhancement in the mid- to far-infrared (2-200 micron) spectral range as free-free emission on neutrals and ions. We find that the infrared intensity evolution tracks the energy input to within a second, albeit with a lingering intensity enhancement, and provides a very direct indication of the evolution of the atmospheric ionization. The prediction of highly impulsive emission means that, on these timescales, the atmospheric hydrodynamics need not be considered in analysing the mid-IR signatures.

  17. 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

  18. 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

  19. 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%.

  20. 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.

  1. 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.

  2. 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.

  3. A spherical electrostatic orrery

    NASA Astrophysics Data System (ADS)

    Smetana, Carole; Alexander, David; Robertson, Scott; Vilkaitis, Kim; Walch, Bob

    1996-11-01

    An electrostatic orrery for studying Keplerian orbits has been constructed in which one or more negatively charged hollow glass microparticles orbit a 9.5-mm-diam metal sphere at +8-kV potential in a vacuum. The device is similar to an earlier cylindrical orrery in which particles orbit a rod [Biewer et al., Am. J. Phys. 62(9), 821-827 (1994)]. Electrically biased cylinders covering the rod supporting the sphere give nearly spherical potential surfaces inside the trap. Additional electrodes at the boundary are used to reduce the perturbation of gravity and to prevent motion resulting in collisions with the supporting rod. Orbits last approximately 10 min or about 104 revolutions. The orbiters are illuminated with a slide projector and can be seen with the naked eye as well as videotaped. The trap has been used to observe orbital precession, interparticle collisions, and the effects of time-independent perturbations. This apparatus provides an opportunity for the study and demonstration of orbital motion in a laboratory.

  4. 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.

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

    PubMed Central

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

    2015-01-01

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

  6. A detailed representation of electrostatic energy in prediction of sequence and pH dependence of protein stability.

    PubMed

    Dudek, Michael J

    2014-10-01

    A molecular mechanics model, previously validated in applications to structure prediction, is shown to reproduce experiment in predictions of protein ionization state, and in predictions of sequence and pH dependence of protein stability. Over a large dataset, 1876 values of ΔΔG of folding, the RMSD is 1.34 kcal/mol. Using an alternative measure of accuracy, either the sign of the calculated ΔΔG agrees with experiment or the absolute value of the deviation is less than 1.0 kcal/mol, 1660 of 1876 data points (88.5%) pass the condition. Relative to models used previously in computer-aided protein design, the concept, we propose, most responsible for the performance of our model, and for the extensibility to non-neutral values of pH, is the treatment of electrostatic energy. The electronic structure of the protein is modeled using distributed atomic multipoles. The structured liquid state of the solvent is modeled using a dielectric continuum. A modification to the energetics of the reaction field, induced by the protein in the dielectric continuum, attempts to account for preformed multipoles of solvent water molecules and ions. An adjustable weight (with optimal value.141) applied to the total vacuum energy accounts implicitly for electronic polarization. A threshold distance, beyond which pairwise atomic interactions are neglected, is not used. In searches through subspaces of sequences and conformations, efficiency remains acceptable for useful applications. © 2014 Wiley Periodicals, Inc.

  7. 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.

  8. 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.

  9. 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

  10. 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

  11. 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.

  12. 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

  13. Calculations of the Electric Fields in Liquid Solutions

    PubMed Central

    Fried, Stephen D.; Wang, Lee-Ping; Boxer, Steven G.; Ren, Pengyu; Pande, Vijay S.

    2014-01-01

    The electric field created by a condensed phase environment is a powerful and convenient descriptor for intermolecular interactions. Not only does it provide a unifying language to compare many different types of interactions, but it also possesses clear connections to experimental observables, such as vibrational Stark effects. We calculate here the electric fields experienced by a vibrational chromophore (the carbonyl group of acetophenone) in an array of solvents of diverse polarities using molecular dynamics simulations with the AMOEBA polarizable force field. The mean and variance of the calculated electric fields correlate well with solvent-induced frequency shifts and band broadening, suggesting Stark effects as the underlying mechanism of these key solution phase spectral effects. Compared to fixed-charge and continuum models, AMOEBA was the only model examined that could describe non-polar, polar, and hydrogen bonding environments in a consistent fashion. Nevertheless, we found that fixed-charge force fields and continuum models were able to replicate some results of the polarizable simulations accurately, allowing us to clearly identify which properties and situations require explicit polarization and/or atomistic representations to be modeled properly, and for which properties and situations simpler models are sufficient. We also discuss the ramifications of these results for modeling electrostatics in complex environments, such as proteins. PMID:24304155

  14. The geometric factor of a cylindrical plate electrostatic analyzer

    NASA Technical Reports Server (NTRS)

    Johnstone, A. D.

    1971-01-01

    A method for calculating the geometric factor of cylindrical plate electrostatic energy analyzers with various detector geometries is described. The effects of the fringe-field are estimated. For a special simple case an exact geometric factor is calculated enabling an estimate of the inaccuracies of the approximations used in other cases. The results of some calculations are presented and a simple approximate expression for the geometric factor is deduced.

  15. The geometric factor of a cylindrical plate electrostatic analyzer.

    NASA Technical Reports Server (NTRS)

    Johnstone, A. D.

    1972-01-01

    A method for calculating the geometric factor of cylindrical plate electrostatic energy analyzers with various detector geometries is described. The effects of the fringe field are estimated. For a special simple case an exact geometric factor is calculated, enabling an estimate to be made of the inaccuracies of the approximations used in other cases. The results of some calculations are presented, and a simple approximate expression for the geometric factor is deduced.

  16. Resonance and continuum Gamow shell model with realistic nuclear forces

    NASA Astrophysics Data System (ADS)

    Sun, Z. H.; Wu, Q.; Zhao, Z. H.; Hu, B. S.; Dai, S. J.; Xu, F. R.

    2017-06-01

    Starting from realistic nuclear forces, we have developed a core Gamow shell model which can describe resonance and continuum properties of loosely-bound or unbound nuclear systems. To describe properly resonance and continuum, the Berggren representation has been employed, which treats bound, resonant and continuum states on equal footing in a complex-momentum (complex-k) plane. To derive the model-space effective interaction based on realistic forces, the full Q ˆ -box folded-diagram renormalization has been, for the first time, extended to the nondegenerate complex-k space. The CD-Bonn potential is softened by using the Vlow-k method. Choosing 16O as the inert core, we have calculated sd-shell neutron-rich oxygen isotopes, giving good descriptions of both bound and resonant states. The isotopes 25,26O are calculated to be resonant even in their ground states.

  17. Optimization of electrostatics as a strategy for cold-adaptation: a case study of cold- and warm-active elastases.

    PubMed

    Papaleo, Elena; Olufsen, Magne; De Gioia, Luca; Brandsdal, Bjørn O

    2007-07-01

    Adaptation to both high and low temperatures requires proteins with special properties. While organisms living at or close to the boiling point of water need to have proteins with increased stability, other properties are required at temperatures close to the freezing point of water. Indeed, it has been shown that enzymes adapted to cold environments are less resistant to heat with a concomitant increased activity as compared to their warm-active counter-parts. Several recent studies have pointed in the direction that electrostatic interactions play a central role in temperature adaptation, and in this study we investigate the role such interactions have in adaptation of elastase from Atlantic salmon and pig. Molecular dynamics (MD) simulations have been used to generate structural ensembles at 283 and 310 K of the psychrophilic and mesophilic elastase, and a total of eight 12 ns simulations have been carried out. Even though the two homologues have a highly similar three-dimensional structure, the location and number of charged amino acids are very different. Based on the simulated structures we find that very few salt-bridges are stable throughout the simulations, and provide little stabilization/destabilization of the proteins as judged by continuum electrostatic calculations. However, the mesophilic elastase is characterized by a greater number of salt-bridges as well as a putative salt-bridge network close to the catalytic site, indicating a higher rigidity of the components involved in the catalytic cycle. In addition, subtle differences are also found in the electrostatic potentials in the vicinity of the catalytic residues, which may explain the increased catalytic efficiency of the cold-adapted elastase.

  18. Protonmotive force: development of electrostatic drivers for synthetic molecular motors.

    PubMed

    Crowley, James D; Steele, Ian M; Bosnich, Brice

    2006-12-04

    Ferrocene has been investigated as a platform for developing protonmotive electrostatic drivers for molecular motors. When two 3-pyridine groups are substituted to the (rapidly rotating) cyclopentadienyl (Cp) rings of ferrocene, one on each Cp, it is shown that the (Cp) eclipsed, pi-stacked rotameric conformation is preferred both in solution and in the solid state. Upon quaternization of both of the pyridines substituents, either by protonation or by alkylation, it is shown that the preferred rotameric conformation is one where the pyridinium groups are rotated away from the fully pi-stacked conformation. Electrostatic calculations indicate that the rotation is caused by the electrostatic repulsion between the charges. Consistently, when the pi-stacking energy is increased pi-stacked population increases, and conversely when the electrostatic repulsion is increased pi-stacked population is decreased. This work serves to provide an approximate estimate of the amount of torque that the electrostatically driven ferrocene platform can generate when incorporated into a molecular motor. The overall conclusion is that the electrostatic interaction energy between dicationic ferrocene dipyridyl systems is similar to the pi-stacking interaction energy and, consequently, at least tricationic systems are required to fully uncouple the pi-stacked pyridine substituents.

  19. 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

  20. 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

  1. Halorhodopsin pumps Cl- and bacteriorhodopsin pumps protons by a common mechanism that uses conserved electrostatic interactions.

    PubMed

    Song, Yifan; Gunner, M R

    2014-11-18

    Key mutations differentiate the functions of homologous proteins. One example compares the inward ion pump halorhodopsin (HR) and the outward proton pump bacteriorhodopsin (BR). Of the nine essential buried ionizable residues in BR, six are conserved in HR. However, HR changes three BR acids, D85 in a central cluster of ionizable residues, D96, nearer the intracellular, and E204, nearer the extracellular side of the membrane to the small, neutral amino acids T111, V122, and T230, respectively. In BR, acidic amino acids are stationary anions whose proton affinity is modulated by conformational changes, establishing a sequence of directed binding and release of protons. Multiconformation continuum electrostatics calculations of chloride affinity and residue protonation show that, in reaction intermediates where an acid is ionized in BR, a Cl(-) is bound to HR in a position near the deleted acid. In the HR ground state, Cl(-) binds tightly to the central cluster T111 site and weakly to the extracellular T230 site, recovering the charges on ionized BR-D85 and neutral E204 in BR. Imposing key conformational changes from the BR M intermediate into the HR structure results in the loss of Cl(-) from the central T111 site and the tight binding of Cl(-) to the extracellular T230 site, mirroring the changes that protonate BR-D85 and ionize E204 in BR. The use of a mobile chloride in place of D85 and E204 makes HR more susceptible to the environmental pH and salt concentrations than BR. These studies shed light on how ion transfer mechanisms are controlled through the interplay of protein and ion electrostatics.

  2. Halorhodopsin pumps Cl– and bacteriorhodopsin pumps protons by a common mechanism that uses conserved electrostatic interactions

    PubMed Central

    Gunner, M. R.

    2014-01-01

    Key mutations differentiate the functions of homologous proteins. One example compares the inward ion pump halorhodopsin (HR) and the outward proton pump bacteriorhodopsin (BR). Of the nine essential buried ionizable residues in BR, six are conserved in HR. However, HR changes three BR acids, D85 in a central cluster of ionizable residues, D96, nearer the intracellular, and E204, nearer the extracellular side of the membrane to the small, neutral amino acids T111, V122, and T230, respectively. In BR, acidic amino acids are stationary anions whose proton affinity is modulated by conformational changes, establishing a sequence of directed binding and release of protons. Multiconformation continuum electrostatics calculations of chloride affinity and residue protonation show that, in reaction intermediates where an acid is ionized in BR, a Cl– is bound to HR in a position near the deleted acid. In the HR ground state, Cl– binds tightly to the central cluster T111 site and weakly to the extracellular T230 site, recovering the charges on ionized BR-D85 and neutral E204 in BR. Imposing key conformational changes from the BR M intermediate into the HR structure results in the loss of Cl– from the central T111 site and the tight binding of Cl– to the extracellular T230 site, mirroring the changes that protonate BR-D85 and ionize E204 in BR. The use of a mobile chloride in place of D85 and E204 makes HR more susceptible to the environmental pH and salt concentrations than BR. These studies shed light on how ion transfer mechanisms are controlled through the interplay of protein and ion electrostatics. PMID:25362051

  3. Electrostatically driven complexation

    NASA Astrophysics Data System (ADS)

    Netz, Roland

    2004-03-01

    Many biological and synthetic systems are electrically charged, which makes them soluble in aqueous environments. Often, electrostatic interactions are dominant, and lead to complexation (i.e. tight aggregation) of oppositely charged objects. As an example, charged polymers such as DNA exhibit a number of different complexation modes when mixed with other charged objects such as spheres or cylinders. A simple model for the complexation of semiflexible polyelectrolytes with oppositely charged spheres is considered, which can exhibit tightly wrapped polymer structures. Using the appropriate parameters for DNA-histone complexes, one finds complete wrapping for intermediate salt concentrations only, in agreement with experiments. The forces needed to pull the DNA off from histones show a plateau at 10-40 pN (depending on salt concentration). We also consider the interaction between such complexes, which have been measured using osmometry, and found to be attractive for intermediate salt concentration (suggesting precipitation) and repulsive elsewhere. Chain fluctuations can be treated within a normal-mode analysis and distinguish associated-unwrapped from dissociated structures. Since some time it is known that also similarly charged objects attract each other for sufficiently large surface-charge densities and/or in the presence of multivalent ions, a phenomenon not explicable within standard (Poisson-Boltzmann) approaches. The so-called strong-coupling theory, valid in the limit of large surface charge densities and for multi-valent ions, yields attraction between similarly charged walls, cylinders, and spheres in quantitative agreement with Monte-Carlo simulations. Charged complexes can be destroyed by applying an electric field, which is an important factor in understanding their electrophoresis. By performing dynamic simulations, the relation between the electrophoretic mobility and the non-equilibrium perturbation of the complex structure is investigated. 1

  4. 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. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. FT-IR spectroscopy and DFT calculation study on the solvent effects of benzaldehyde in organic solvents.

    PubMed

    Li, Yi; Zhang, Hui; Liu, Qing

    2012-02-01

    FT-IR spectra of benzaldehyde in 11 different organic solvents were recorded and analyzed. The density functional theory (DFT) B3LYP/6-31G* method was chosen to calculate the infrared spectrum of benzaldehyde in gaseous state. The electrostatic effects of different solvents in benzaldehyde solutions were calculated using DFT with the self-consistent isodensity polarizable continuum model (SCI-PCM). Two remarkable carbonyl (C=O) peaks of benzaldehyde were observed by FT-IR in alcohol solvents, which were caused by different hydrogen bond species and explained by ab initio calculation. The results showed that the combination of SCI-PCM model and ab initio calculation could give excellent agreements with FT-IR spectra of title compound in solutions. Copyright © 2011 Elsevier B.V. All rights reserved.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. Reply to Comment on ``Computing molecular electrostatic potentials with the PRISM algorithm''

    NASA Astrophysics Data System (ADS)

    Johnson, Benny G.; Pople, John A.; Gill, Peter M. W.; Fox, Douglas J.

    1994-02-01

    This Reply clarifies the similarities and differences between our work and that of Gadre et al. in computing ab initio molecular electrostatic potentials. The principal advance described by us was to cast the PRISM algorithm for two-electron repulsion integrals in a form suitable for the calculation of molecular electrostatic potentials.

  12. 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.

  13. 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.

  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. 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.

  16. Surface electrostatics: theory and computations

    PubMed Central

    Chatzigeorgiou, G.; Javili, A.; Steinmann, P.

    2014-01-01

    The objective of this work is to study the electrostatic response of materials accounting for boundary surfaces with their own (electrostatic) constitutive behaviour. The electric response of materials with (electrostatic) energetic boundary surfaces (surfaces that possess material properties and constitutive structures different from those of the bulk) is formulated in a consistent manner using a variational framework. The forces and moments that appear due to bulk and surface electric fields are also expressed in a consistent manner. The theory is accompanied by numerical examples on porous materials using the finite-element method, where the influence of the surface electric permittivity on the electric displacement, the polarization stress and the Maxwell stress is examined. PMID:24711720

  17. 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

  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. Determination of the Bending Rigidity of Graphene via Electrostatic Actuation of Buckled Membranes

    NASA Astrophysics Data System (ADS)

    Lindahl, Niklas; Midtvedt, Daniel; Svensson, Johannes; Nerushev, Oleg A.; Lindvall, Niclas; Isacsson, Andreas; Campbell, Eleanor E. B.

    2012-07-01

    The small mass and atomic-scale thickness of graphene membranes make them highly suitable for nanoelectromechanical devices such as e.g. mass sensors, high frequency resonators or memory elements. Although only atomically thick, many of the mechanical properties of graphene membranes can be described by classical continuum mechanics. An important parameter for predicting the performance and linearity of graphene nanoelectromechanical devices as well as for describing ripple formation and other properties such as electron scattering mechanisms, is the bending rigidity, {\\kappa}. In spite of the importance of this parameter it has so far only been estimated indirectly for monolayer graphene from the phonon spectrum of graphite, estimated from AFM measurements or predicted from ab initio calculations or bond-order potential models. Here, we employ a new approach to the experimental determination of {\\kappa} by exploiting the snap-through instability in pre-buckled graphene membranes. We demonstrate the reproducible fabrication of convex buckled graphene membranes by controlling the thermal stress during the fabrication procedure and show the abrupt switching from convex to concave geometry that occurs when electrostatic pressure is applied via an underlying gate electrode. The bending rigidity of bilayer graphene membranes under ambient conditions was determined to be $35.5^{+20}_{-15}$ eV. Monolayers have significantly lower {\\kappa} than bilayers.

  20. 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.

  1. Simulation of concrete perforation based on a continuum damage model

    SciTech Connect

    Chen, E.P.

    1994-10-01

    Numerical simulation of dynamic fracture of concrete slabs, impacted by steel projectiles, was carried out in this study. The concrete response was described by a continuum damage model. This continuum damage model was originally developed to study rock fragmentation and was modified in the present study with an emphasis on the post-limit structural response. The model was implemented into a transient dynamic explicit finite element code LS-DYNA2D and the code was then used for the numerical simulations. The specific impact configuration of this study follows the experiment series conducted by Hanchak et al. Comparisons between calculated results and measured data were made. Good agreements were found.

  2. 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.

  3. 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.

  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. Electrostatic Unbalances of Transmission Lines.

    DTIC Science & Technology

    1985-08-01

    RD-A±68 742 ELECTROSTATIC UMBALANCES OF TEMNISSION LINES(U) AIR 1V2 FORCE INST OF TECH WRIGHNT-PATTERSON AFD OH J NOUIKOWSKI AUG 85 AFIT/CI/ NR -BS...CONTROLLING OFFICE NAME AND ADORESS 12. REPORT DATE AFIT/ NR 1985 WPAFB OH 45433 - 6583 1i. NUMBER OF PAGES ___102 14. MONITORING AGENCY NAME & ADDRESS...return it to: AF IT/ NR Wright-Patterson AFB OH 45433 RESEARCH TITLE: Electrostatic Unbalances oJCTransmission Lines *AUTHOR: Jioseph Nowikowski

  6. 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.

  7. Electrostatic disturbances aboard LISA Pathfinder

    NASA Astrophysics Data System (ADS)

    Ferroni, Valerio

    Test mass charging and stray electrostatic fields are a potentially important source of force noise for the LISA Pathfinder mission. During the flight we plan to measure the relevant stray electrostatic fields on the surfaces of both the test mass and the electrode housing and compensate them with DC electrode bias voltages. In addition we monitor the charge and reduce it to near zero by UV illumination. We describe the analysis techniques used during the mission and explain the importance of periodic charging/discharging and of long-term charge measurements to limit the force noise at low frequency, which is particularly relevant for the eLISA mission.

  8. 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.

  9. 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.

  10. 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.

  11. Radiation response of a MEMS accelerometer: An electrostatic force

    SciTech Connect

    Edmonds, L.D.; Swift, G.M.; Lee, C.I.

    1998-12-01

    Particle irradiation on the mechanical sensor of the ADXL50 microelectromechanical accelerometer shifts the output voltage. An earlier conclusion, that a dielectric below the sensor becomes charged, is extended by quantifying the effect of this charge on device output. It is shown that an electrostatic force is consistent with the observation that the output voltage shift is independent of acceleration. Possible charging mechanisms are suggested. An appendix derives a convenient algorithm for calculating electrostatic forces, which may also be used for other MEMS devices.

  12. 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.

  13. 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.

  14. 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.

  15. 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)

  16. 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...

  17. 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.

  18. 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...

  19. A sensitive continuum analysis method for gamma ray spectra

    NASA Technical Reports Server (NTRS)

    Thakur, Alakh N.; Arnold, James R.

    1993-01-01

    In this work we examine ways to improve the sensitivity of the analysis procedure for gamma ray spectra with respect to small differences in the continuum (Compton) spectra. The method developed is applied to analyze gamma ray spectra obtained from planetary mapping by the Mars Observer spacecraft launched in September 1992. Calculated Mars simulation spectra and actual thick target bombardment spectra have been taken as test cases. The principle of the method rests on the extraction of continuum information from Fourier transforms of the spectra. We study how a better estimate of the spectrum from larger regions of the Mars surface will improve the analysis for smaller regions with poorer statistics. Estimation of signal within the continuum is done in the frequency domain which enables efficient and sensitive discrimination of subtle differences between two spectra. The process is compared to other methods for the extraction of information from the continuum. Finally we explore briefly the possible uses of this technique in other applications of continuum spectra.

  20. 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.)

  1. Image method for electrostatic energy of polarizable dipolar spheres

    NASA Astrophysics Data System (ADS)

    Gustafson, Kyle S.; Xu, Guoxi; Freed, Karl F.; Qin, Jian

    2017-08-01

    The multiple-scattering theory for the electrostatics of many-body systems of monopolar spherical particles, embedded in a dielectric medium, is generalized to describe the electrostatics of these particles with embedded dipoles and multipoles. The Neumann image line construction for the electrostatic polarization produced by one particle is generalized to compute the energy, forces, and torques for the many-body system as functions of the positions of the particles. The approach is validated by comparison with direct numerical calculation, and the convergence rate is analyzed and expressed in terms of the discontinuity in dielectric contrast and particle density. As an illustration of this formalism, the stability of small particle clusters is analyzed. The theory is developed in a form that can readily be adapted to Monte Carlo and molecular dynamics simulations for polarizable particles and, more generally, to study the interactions among polarizable molecules.

  2. 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.

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

    PubMed

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

    2017-05-09

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

  4. Electron transfer to continuum states

    SciTech Connect

    Macek, J.H. |

    1994-12-31

    Gene Rudd`s analysis of doubly differential cross sections for the ionization of He atoms by proton impact suggested that electrons were being carried along by the proton for a short period of time after being ejected from the target region. Normally, this would represent an electron capture event in which an excited state of atomic hydrogen is formed. Because the electron ends up ionized it was recognized that these states of the proton must be continuum states. This insight was confirmed by observations of the continuum electron capture (CEC) cusp when the electron velocity equals the proton velocity in the final state. The impact of this idea upon the theory of ionization at high energies is reviewed.

  5. Intense electrostatic waves near the upper hybrid resonance frequency. [beyond plasmapause

    NASA Technical Reports Server (NTRS)

    Kurth, W. S.; Craven, J. D.; Frank, L. A.; Gurnett, D. A.

    1979-01-01

    Plasma wave measurements using instruments on the Imp 6 and Hawkeye satellites are utilized in a study of very intense electrostatic waves near the upper hybrid resonance frequency in the region just outside the plasmapause. Studies of these electrostatic disturbances show that the events occur at local times and at magnetic latitudes varying from the equator to 50 deg, and the polarization of these waves is such that the wave electric field vector is oriented perpendicular to the geomagnetic field. In most cases the center frequency of the intense waves corresponds to an (n + 1/2) fg(-) harmonic near the upper hybrid resonance frequency. The hot distribution on function is described for a few events showing temperature anisotropy and a loss cone distribution. A possible mechanism for producing intense waves near the upper hybrid resonance frequency is suggested, and evidence which indicates that the intense electrostatic waves may be a source of nonthermal continuum radiation is given.

  6. Finsler-Geometric Continuum Mechanics

    DTIC Science & Technology

    2016-05-01

    continuum mechanics/ physics of deformable bodies) is emphasized in the present report. In this context, fields describing the motion of material particles ...to physical problems of tensile fracture, shear localization, and cavitation in solid bodies. The pseudo-Finsler approach is demonstrated to be more...Weyl-type transformation of the fundamental tensor, analytical and numerical solutions of representative example problems offer new physical insight

  7. 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.

  8. A Simple Apparatus for Electrostatic Force Measurement.

    ERIC Educational Resources Information Center

    Hale, D. P.

    1981-01-01

    Describes the construction of an apparatus that demonstrates that electrostatic forces can be large and also gives some idea of dependence of electrostatic forces between charged parallel discs on potential differences and separation. (CS)

  9. 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.

  10. 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.

  11. 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.

  12. Relativistic continuum quasiparticle random-phase approximation in spherical nuclei

    SciTech Connect

    Daoutidis, I.; Ring, P.

    2011-04-15

    We have calculated the strength distributions of the dipole response in spherical nuclei, ranging all over the periodic table. The calculations were performed within two microscopic models: the discretized quasiparticle random-phase approximation and the continuum quasiparticle random-phase approximation, which takes into account the coupling of the single-particle continuum in an exact way. Pairing correlations are treated with the BCS model. In the calculations, two density functionals were used, namely, the PC-F1 and the DD-PC1. Both are based on relativistic point-coupling Lagrangians. It is explicitly shown that this model is capable of reproducing the giant- as well as the pygmy-dipole resonance for open-shell nuclei in a high level of quantitative agreement with the available experimental observations.

  13. 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.

  14. 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.

  15. The effect of an electrostatic field on film flow down an inclined plane

    SciTech Connect

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

    1992-10-01

    A study of the interaction of an electrostatic field with a thin liquid film flowing under gravity down an inclined plane is presented. First, the effect of the electric field on the stability of the film flow is examined. Next, several limits of the equations of motion are investigated analytically, and then compared with an explicit numerical calculation of the equations of motion. Also, applications of these calculations to a proposed electrostatic liquid film space radiator are discussed.

  16. 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.

  17. 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.

  18. 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

  19. 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.

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

    PubMed

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

    2015-10-15

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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. Electrostatic Manipulation of Graphene On Graphite

    NASA Astrophysics Data System (ADS)

    Untiedt, Carlos; Rubio-Verdu, Carmen; Saenz-Arce, Giovanni; Martinez-Asencio, Jesús; Milan, David C.; Moaied, Mohamed; Palacios, Juan J.; Caturla, Maria Jose

    2015-03-01

    Here we report the use of a Scanning Tunneling Microscope (STM) under ambient and vacuum conditions to study the controlled exfoliation of the last layer of a graphite surface when an electrostatic force is applied from a STM tip. In this work we have focused on the study of two parameters: the applied voltage needed to compensate the graphite interlayer attractive force and the one needed to break atomic bonds to produce folded structures. Additionally, we have studied the influence of edge structure in the breaking geometry. Independently of the edge orientation the graphite layer is found to tear through the zig-zag direction and the lifled layer shows a zig-zag folding direction. Molecular Dinamics simulations and DFT calculations have been performed to understand our results, showing a strong correlation with the experiments. Comunidad Valenciana through Prometeo project.

  9. 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.

  10. Defining Protein Electrostatic Recognition Processes

    DTIC Science & Technology

    1989-11-30

    making and aligning expanded molecular dot surfaces for each molecule and checking these surfaces for interpenetration. The program TURNIP used these...year of this contract, we have developed and optimized the TURNIP program, which consists of two parts. First, the electrostatic pctcntia! due to mo...supercomputer where the rotation and translation of molecule 2 occurs. The program TURNIP is written in the programming language C, and has been optimized

  11. Defining Protein Electrostatic Recognition Processes

    DTIC Science & Technology

    1992-01-01

    approach. We developed the TURNIP program 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...region of cytochrome c with the negative patch of plastocyanin, consistent with experimental data. Application of TURNIP to the formation of the stable

  12. 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.

  13. Hybrid discrete-continuum modeling for transport, biofilm development and solid restructuring including electrostatic effects

    NASA Astrophysics Data System (ADS)

    Prechtel, Alexander; Ray, Nadja; Rupp, Andreas

    2017-04-01

    We want to present an approach for the mathematical, mechanistic modeling and numerical treatment of processes leading to the formation, stability, and turnover of soil micro-aggregates. This aims at deterministic aggregation models including detailed mechanistic pore-scale descriptions to account for the interplay of geochemistry and microbiology, and the link to soil functions as, e.g., the porosity. We therefore consider processes at the pore scale and the mesoscale (laboratory scale). At the pore scale transport by diffusion, advection, and drift emerging from electric forces can be taken into account, in addition to homogeneous and heterogeneous reactions of species. In the context of soil micro-aggregates the growth of biofilms or other glueing substances as EPS (extracellular polymeric substances) is important and affects the structure of the pore space in space and time. This model is upscaled mathematically in the framework of (periodic) homogenization to transfer it to the mesoscale resulting in effective coefficients/parameters there. This micro-macro model thus couples macroscopic equations that describe the transport and fluid flow at the scale of the porous medium (mesoscale) with averaged time- and space-dependent coefficient functions. These functions may be explicitly computed by means of auxiliary cell problems (microscale). Finally, the pore space in which the cell problems are defined is time and space dependent and its geometry inherits information from the transport equation's solutions. The microscale problems rely on versatile combinations of cellular automata and discontiuous Galerkin methods while on the mesoscale mixed finite elements are used. The numerical simulations allow to study the interplay between these processes.

  14. 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.

  15. 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.

  16. Quantitative nanoscale electrostatics of viruses.

    PubMed

    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

    2015-11-07

    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.

  17. 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.

  18. A Self-Consistent Space-Domain Decomposition Method for QM/MM Computations of Protein Electrostatic Potentials.

    PubMed

    Gascon, Jose A; Leung, Siegfried S F; Batista, Enrique R; Batista, Victor S

    2006-01-01

    This paper introduces a self-consistent computational protocol for modeling protein electrostatic potentials according to static point-charge model distributions. The protocol involves a simple space-domain decomposition scheme where individual molecular domains are modeled as Quantum-Mechanical (QM) layers embedded in the otherwise classical Molecular-Mechanics (MM) protein environment. ElectroStatic-Potential (ESP) atomic charges of the constituent molecular domains are computed, to account for mutual polarization effects, and iterated until obtaining a self-consistent point-charge model of the protein electrostatic potential. The novel protocol achieves quantitative agreement with full QM calculations in the description of electrostatic potentials of small polypeptides where polarization effects are significant, showing a remarkable improvement relative to the corresponding electrostatic potentials obtained with popular MM force fields. The capabilities of the method are demonstrated in several applications, including calculations of the electrostatic potential in the potassium channel protein and the description of protein-protein electrostatic interactions.

  19. 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.

  20. 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.

  1. 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.

  2. Continuum Theory of Retroviral Capsids

    NASA Astrophysics Data System (ADS)

    Nguyen, T. T.; Bruinsma, R. F.; Gelbart, W. M.

    2006-02-01

    We present a self-assembly phase diagram for the shape of retroviral capsids, based on continuum elasticity theory. The spontaneous curvature of the capsid proteins drives a weakly first-order transition from spherical to spherocylindrical shapes. The conical capsid shape which characterizes the HIV-1 retrovirus is never stable under unconstrained energy minimization. Only under conditions of fixed volume and/or fixed spanning length can the conical shape be a minimum energy structure. Our results indicate that, unlike the capsids of small viruses, retrovirus capsids are not uniquely determined by the molecular structure of the constituent proteins but depend in an essential way on physical constraints present during assembly.

  3. Continuum modeling of myxobacteria clustering

    NASA Astrophysics Data System (ADS)

    Harvey, Cameron W.; Alber, Mark; Tsimring, Lev S.; Aranson, Igor S.

    2013-03-01

    In this paper we develop a continuum theory of clustering in ensembles of self-propelled inelastically colliding rods with applications to collective dynamics of common gliding bacteria Myxococcus xanthus. A multi-phase hydrodynamic model that couples densities of oriented and isotropic phases is described. This model is used for the analysis of an instability that leads to spontaneous formation of directionally moving dense clusters within initially dilute isotropic ‘gas’ of myxobacteria. Numerical simulations of this model confirm the existence of stationary dense moving clusters and also elucidate the properties of their collisions. The results are shown to be in a qualitative agreement with experiments.

  4. 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.

  5. Collective excitations in the continuum

    SciTech Connect

    Dussel, G. G.; Betan, R. Id; Liotta, R. J.; Vertse, T.

    2009-12-15

    Pairing (particle-particle) giant resonances are analyzed within a shell-model formalism in the complex energy plane with the aim of understanding why they have not been observed so far. A comparison is made with the equivalent particle-hole mode by applying the formalism to the analysis of the well-understood particle-hole giant resonance. It is found that because of the proper treatment of the continuum intrinsic to the formalism, giant pairing resonances lie much higher than previously predicted and that some of them may be too wide to be observed, whereas others are meaningful excitations. For these, new experimental searches are proposed.

  6. 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.

  7. Electrostatic field around cytochrome c: theory and energy transfer experiment.

    PubMed

    Northrup, S H; Wensel, T G; Meares, C F; Wendoloski, J J; Matthew, J B

    1990-12-01

    Energy transfer in the "rapid diffusion" limit from electronically excited terbium(III) chelates in three different charge states to horse heart ferricytochrome c was measured as a function of ionic strength. Theoretical rate constants calculated by numerical integration of the Forster integral (containing the Poisson-Boltzmann-generated protein electrostatic potential) were compared with the experimental data to evaluate the accuracy of protein electrostatic field calculations at the protein/solvent interface. Two dielectric formalisms were used: a simple coulombic/Debye-Hückel procedure and a finite difference method [Warwicker, J. & Watson, H. C. (1982) J. Mol. Biol. 157, 671-679] that accounts for the low-dielectric protein interior and the irregular protein/solvent boundary. Good agreement with experiment was obtained and the ionic-strength dependence of the reaction was successfully reproduced. The sensitivity of theoretical rate constants to the choices of effective donor sphere size and the energy transfer distance criterion was analyzed. Electrostatic potential and rate-constant calculations were carried out on sets of structures collected along two molecular dynamics trajectories of cytochrome c. Protein conformational fluctuations were shown to produce large variations in the calculated energy transfer rate constant. We conclude that protein fluctuations and the resulting transient structures can play significant roles in biological or catalytic activities that are not apparent from examination of a static structure. For calculating protein electrostatics, large-scale low-frequency conformational fluctuations, such as charged side-chain reorientation, are established to be as important as the computational method for incorporating dielectric boundary effects.

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. Nuclear rotation in the continuum

    NASA Astrophysics Data System (ADS)

    Fossez, K.; Nazarewicz, W.; Jaganathen, Y.; Michel, N.; Płoszajczak, M.

    2016-01-01

    Background: Atomic nuclei often exhibit collective rotational-like behavior in highly excited states, well above the particle emission threshold. What determines the existence of collective motion in the continuum region is not fully understood. Purpose: In this work, by studying the collective rotation of the positive-parity deformed configurations of the one-neutron halo nucleus 11Be, we assess different mechanisms that stabilize collective behavior beyond the limits of particle stability. Method: To solve a particle-plus-core problem, we employ a nonadiabatic coupled-channel formalism and the Berggren single-particle ensemble, which explicitly contains bound states, narrow resonances, and the scattering continuum. We study the valence-neutron density in the intrinsic rotor frame to assess the validity of the adiabatic approach as the excitation energy increases. Results: We demonstrate that collective rotation of the ground band of 11Be is stabilized by (i) the fact that the ℓ =0 one-neutron decay channel is closed, and (ii) the angular momentum alignment, which increases the parentage of high-ℓ components at high spins; both effects act in concert to decrease decay widths of ground-state band members. This is not the case for higher-lying states of 11Be, where the ℓ =0 neutron-decay channel is open and often dominates. Conclusion: We demonstrate that long-lived collective states can exist at high excitation energy in weakly bound neutron drip-line nuclei such as 11Be.

  13. 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.

  14. 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.

  15. 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.

  16. 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.}

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. Electrostatic Plugging of Multidipole Cusps.

    DTIC Science & Technology

    1982-05-01

    IN, rtid’( rio~ s I REORTNUMER 2 GOVT ACCESSION No 3 RECIPtE%T’. CATALOG, # MtSF.P 4. TTLE wd Sbt,( ) TYPE OF REPDRT & PER,00 COvERED jElectrostatic...corresponding loss widths are W = 9 mm and W = 3 mm. This L ~ L2 analysis was performed for many ’PE, and a linear relationship was found between n and...VE)/Te (18)e t o reP Now V/rp = A the surface area of the plasma: A = SL , (19)c with S the distance between cusps ( 8 cm) and L the magnetic cuspc

  3. 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.

  4. 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.

  5. 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... and renewal funding. State and local governments, public housing authorities and nonprofit...: Colette Pollard., Reports Management Officer, QDAM, Department of Housing and Urban Development,...

  6. Electrostatic focusing system with high value of demagnification

    NASA Astrophysics Data System (ADS)

    Abgaryan, Artush A.; Levi, Eli

    2012-10-01

    For E-beam transmission and transforming we developed an electrostatic focusing device with extraordinary demagnification and abilities for 100% transmission of an electron beam with uniform distribution of current density. This experimental electrostatic focusing system consists of two sections; the first is field formation and second is field free - for measurement space1. The purpose of this article is to present the experimental results from our electro-optical system. The measurement instrument used in the laboratory set up is an adjustable scanning system, which includes a faraday cup with a 14um diameter tungsten wire, for measuring different cross sections. The measurement of the crossover point is based on a combination of theoretical and experimental processes. The theoretical uses calculations from the "CPO"2 program and the experimental measures different cross sections which are much larger than the diameter of the tungsten wire. Theoretically, from trajectory calculations, the crossover point is approximately 0.446μm. This estimation is obtained by drawing an isosceles triangle from the experimental results and comparing it to another isosceles triangle created from the theoretically calculated trajectories. Both triangles together have a geometrically proportional ratio and differ by about one percent or less. The design of the electrostatic focusing system is achieved utilizing the CGMR (Cone and Golden Mean Ratio) approach 1, 3 and 4. This system is suitable for use in X-ray tubes5, e-beam lithography, SEM, high speed photonic technology, and also for any EOS.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. Computational Methods in Continuum Mechanics

    DTIC Science & Technology

    1993-11-30

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  14. 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.

  15. Electrostatics in pharmaceutical aerosols for inhalation.

    PubMed

    Wong, Jennifer; Chan, Hak-Kim; Kwok, Philip Chi Lip

    2013-08-01

    Electrostatics continues to play an important role in pharmaceutical aerosols for inhalation. Despite its ubiquitous nature, the charging process is complex and not well understood. Nonetheless, significant advances in the past few years continue to improve understanding and lead to better control of electrostatics. The purpose of this critical review is to present an overview of the literature, with an emphasis on how electrostatic charge can be useful in improving pulmonary drug delivery.

  16. 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.

  17. 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.

  18. 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).

  19. 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

  20. Electrostatic discharge concepts and definitions

    SciTech Connect

    Borovina, Dan L

    2008-01-01

    Many objects -like a human body, plastic wrap, or a rolling cart -that are electrically neutral, overall, can gain a net electrostatic charge by means of one of three methods: induction, physical transfer, or triboelectric charging (separation of conductive surfaces). The result is a voltage difference between the charged object and other objects, creating a situation where current flow is likely if two objects come into contact or close proximity. This current flow is known as electrostatic discharge, or ESD. The energy and voltage of the discharge can be influenced by factors such as the temperature and humidity in the room, the types of materials or flooring involved, or the clothing and footwear a person uses. Given the possible ranges of the current and voltage characteristic of an ESD pulse, it is important to consider the safety risks associated with detonator handling, assembly and disassembly, transportation and maintenance. For main charge detonators, these safety risks include high explosive violent reactions (HEVR) as well as inadvertent nuclear detonations (lND).

  1. Electrostatics of Deformable Lipid Membranes

    PubMed Central

    Vorobyov, Igor; Bekker, Borislava; Allen, Toby W.

    2010-01-01

    Abstract It was recently demonstrated that significant local deformations of biological membranes take place due to the fields of charged peptides and ions, challenging the standard model of membrane electrostatics. The ability of ions to retain their immediate hydration environment, combined with the lack of sensitivity of permeability to ion type or even ion pairs, led us to question the extent to which hydration energetics and electrostatics control membrane ion permeation. Using the arginine analog methyl-guanidinium as a test case, we find that although hydrocarbon electronic polarizability causes dramatic changes in ion solvation free energy, as well as a significant change (∼0.4 V) in the membrane dipole potential, little change in membrane permeation energetics occurs. We attribute this to compensation of solvation terms from polar and polarizable nonpolar components within the membrane, and explain why the dipole potential is not fully sensed in terms of the locally deformed bilayer interface. Our descriptions provide a deeper understanding of the translocation process and allow predictions for poly-ions, ion pairs, charged lipids, and lipid flip-flop. We also report simulations of large hydrophobic-ion-like membrane defects and the ionophore valinomycin, which exhibit little membrane deformation, as well as hydrophilic defects and the ion channel gramicidin A, to provide parallels to membranes deformed by unassisted ion permeation. PMID:20550903

  2. Extended Debye-Hückel theory for studying the electrostatic solvation energy.

    PubMed

    Xiao, Tiejun

    2015-03-16

    The electrostatic part of the solvation energy has been studied by using extended Debye-Hückel (DH) theories. Specifically, our molecular Debye-Hückel theory [J. Chem. Phys. 2011, 135, 104104] and its simplified version, an energy-scaled Debye-Hückel theory, were applied to electrolytes with strong electrostatic coupling. Our theories provide a practical methodology for calculating the electrostatic solvation free energies, and the accuracy was verified for atomic and diatomic charged solutes. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. 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.

  4. 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.

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

    PubMed Central

    Mahvash, Mohsen; Dupont, Pierre E.

    2010-01-01

    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. PMID:21399719

  6. 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

  7. Preconceptual design for the electrostatic enclosure

    SciTech Connect

    Meyer, L.C.

    1992-09-01

    This report presents a preconceptual design (design criteria and assumptions) for electrostatic enclosures to be used during buried transuranic waste recovery operations. These electrostatic enclosures (along with the application of dust control products) will provide an in-depth contamination control strategy. As part of this preconceptual design, options for electrostatic curtain design are given including both hardwall and fabric enclosures. Ventilation systems, doors, air locks, electrostatic curtains, and supporting systems also are discussed. In addition to the conceptual design, engineering scale tests are proposed to be run at the Test Reactor Area. The planned engineering scale tests will give final material specifications for full-scale retrieval demonstrations.

  8. Limiting assumptions in molecular modeling: electrostatics.

    PubMed

    Marshall, Garland R

    2013-02-01

    Molecular mechanics attempts to represent intermolecular interactions in terms of classical physics. Initial efforts assumed a point charge located at the atom center and coulombic interactions. It is been recognized over multiple decades that simply representing electrostatics with a charge on each atom failed to reproduce the electrostatic potential surrounding a molecule as estimated by quantum mechanics. Molecular orbitals are not spherically symmetrical, an implicit assumption of monopole electrostatics. This perspective reviews recent evidence that requires use of multipole electrostatics and polarizability in molecular modeling.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. A continuum model for interconnected lattice trusses

    NASA Technical Reports Server (NTRS)

    Balakrishnan, A. V.

    1992-01-01

    A continuum model for interconnected lattice trusses based on the 1D Timoshenko beam approximation is developed using the NASA-LRC Phase Zero Evolutionary Model. The continuum model dynamics is presented in the canonical wave-equation form in a Hilbert space.

  15. 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).

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Continuum Mapping of Low Mass Star Forming Cores using SCUBA

    NASA Astrophysics Data System (ADS)

    Shirley, Y. L.; Evans, N. J.; Rawlings, J. M. C.; Gregersen, E. M.

    1998-12-01

    Recent studies in star formation have been guided by a putative evolutionary sequence based on the spectral energy distribution (SED) of young stellar objects. We are testing this idea by tracing the changes in the distribution of matter across this sequence. We have obtained 850 and 450 micron continuum maps of 21 low mass cores with SED's ranging from Pre-protostellar to Class I (20K < Tbol < 140K) using the SCUBA bolometer array at the JCMT. By combining our maps with continuum emission at other wavelengths and using a radiative transport code, we can compare model predictions of the spatial extent of emission and the SED with observations. This method allows for a self-consistent calculation of the temperature distribution and for smoothing effects caused by a finite beam. We present observations and models of the dust density and temperature distributions as well as SEDs for our sources.