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Sample records for continuum electrostatic calculations

  1. Variable atomic radii for continuum-solvent electrostatics calculation.

    PubMed

    Zhou, Baojing; Agarwal, Manish; Wong, Chung F

    2008-07-01

    We have developed a method to improve the description of solute cavity defined by the interlocking-sphere model for continuum-solvent electrostatics calculations. Many models choose atomic radii from a finite set of atom types or uses an even smaller set developed by Bondi [J. Phys. Chem. 68, 441 (1964)]. The new model presented here allowed each atom to adapt its radius according to its chemical environment. This was achieved by first approximating the electron density of a molecule by a superposition of atom-centered spherical Gaussian functions. The parameters of the Gaussian functions were then determined by optimizing a function that minimized the difference between the properties from the model and those from ab initio quantum calculations. These properties included the electrostatics potential on molecular surface and the electron density within the core of each atom. The size of each atom was then determined by finding the radius at which the electron density associated with the atom fell to a prechosen value. This value was different for different chemical elements and was chosen such that the averaged radius for each chemical element in a training set of molecules matched its Bondi radius. Thus, our model utilized only a few adjustable parameters-the above density cutoff values for different chemical elements-but had the flexibility of allowing every atom to adapt its radius according to its chemical environment. This variable-radii model gave better solvation energy for 31 small neutral molecules than the Bondi radii did, especially for a quantum mechanics/Poisson-Boltzmann approach we developed earlier. The improvement was most significant for molecules with large dipole moment. Future directions for further improvement are also discussed.

  2. Variable atomic radii for continuum-solvent electrostatics calculation

    NASA Astrophysics Data System (ADS)

    Zhou, Baojing; Agarwal, Manish; Wong, Chung F.

    2008-07-01

    We have developed a method to improve the description of solute cavity defined by the interlocking-sphere model for continuum-solvent electrostatics calculations. Many models choose atomic radii from a finite set of atom types or uses an even smaller set developed by Bondi [J. Phys. Chem. 68, 441 (1964)]. The new model presented here allowed each atom to adapt its radius according to its chemical environment. This was achieved by first approximating the electron density of a molecule by a superposition of atom-centered spherical Gaussian functions. The parameters of the Gaussian functions were then determined by optimizing a function that minimized the difference between the properties from the model and those from ab initio quantum calculations. These properties included the electrostatics potential on molecular surface and the electron density within the core of each atom. The size of each atom was then determined by finding the radius at which the electron density associated with the atom fell to a prechosen value. This value was different for different chemical elements and was chosen such that the averaged radius for each chemical element in a training set of molecules matched its Bondi radius. Thus, our model utilized only a few adjustable parameters—the above density cutoff values for different chemical elements—but had the flexibility of allowing every atom to adapt its radius according to its chemical environment. This variable-radii model gave better solvation energy for 31 small neutral molecules than the Bondi radii did, especially for a quantum mechanics/Poisson-Boltzmann approach we developed earlier. The improvement was most significant for molecules with large dipole moment. Future directions for further improvement are also discussed.

  3. 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

  4. Ion transport through membrane-spanning nanopores studied by molecular dynamics simulations and continuum electrostatics calculations.

    PubMed

    Peter, Christine; Hummer, Gerhard

    2005-10-01

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

  5. 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

    2016-08-01

    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. PMID:27471775

  6. Accurate Molecular Polarizabilities Based on Continuum Electrostatics

    PubMed Central

    Truchon, Jean-François; Nicholls, Anthony; Iftimie, Radu I.; Roux, Benoît; Bayly, Christopher I.

    2013-01-01

    A novel approach for representing the intramolecular polarizability as a continuum dielectric is introduced to account for molecular electronic polarization. It is shown, using a finite-difference solution to the Poisson equation, that the Electronic Polarization from Internal Continuum (EPIC) model yields accurate gas-phase molecular polarizability tensors for a test set of 98 challenging molecules composed of heteroaromatics, alkanes and diatomics. The electronic polarization originates from a high intramolecular dielectric that produces polarizabilities consistent with B3LYP/aug-cc-pVTZ and experimental values when surrounded by vacuum dielectric. In contrast to other approaches to model electronic polarization, this simple model avoids the polarizability catastrophe and accurately calculates molecular anisotropy with the use of very few fitted parameters and without resorting to auxiliary sites or anisotropic atomic centers. On average, the unsigned error in the average polarizability and anisotropy compared to B3LYP are 2% and 5%, respectively. The correlation between the polarizability components from B3LYP and this approach lead to a R2 of 0.990 and a slope of 0.999. Even the F2 anisotropy, shown to be a difficult case for existing polarizability models, can be reproduced within 2% error. In addition to providing new parameters for a rapid method directly applicable to the calculation of polarizabilities, this work extends the widely used Poisson equation to areas where accurate molecular polarizabilities matter. PMID:23646034

  7. Electrostatic potentials of proteins in water: a structured continuum approach.

    PubMed

    Hildebrandt, Andreas; Blossey, Ralf; Rjasanow, Sergej; Kohlbacher, Oliver; Lenhof, Hans-Peter

    2007-01-15

    Electrostatic interactions play a crucial role in many biomolecular processes, including molecular recognition and binding. Biomolecular electrostatics is modulated to a large extent by the water surrounding the molecules. Here, we present a novel approach to the computation of electrostatic potentials which allows the inclusion of water structure into the classical theory of continuum electrostatics. Based on our recent purely differential formulation of nonlocal electrostatics [Hildebrandt, et al. (2004) Phys. Rev. Lett., 93, 108104] we have developed a new algorithm for its efficient numerical solution. The key component of this algorithm is a boundary element solver, having the same computational complexity as established boundary element methods for local continuum electrostatics. This allows, for the first time, the computation of electrostatic potentials and interactions of large biomolecular systems immersed in water including effects of the solvent's structure in a continuum description. We illustrate the applicability of our approach with two examples, the enzymes trypsin and acetylcholinesterase. The approach is applicable to all problems requiring precise prediction of electrostatic interactions in water, such as protein-ligand and protein-protein docking, folding and chromatin regulation. Initial results indicate that this approach may shed new light on biomolecular electrostatics and on aspects of molecular recognition that classical local electrostatics cannot reveal. PMID:17237112

  8. Electrostatic ion thruster optics calculations

    NASA Technical Reports Server (NTRS)

    Whealton, John H.; Kirkman, David A.; Raridon, R. J.

    1992-01-01

    Calculations have been performed which encompass both a self-consistent ion source extraction plasma sheath and the primary ion optics including sheath and electrode-induced aberrations. Particular attention is given to the effects of beam space charge, accelerator geometry, and properties of the downstream plasma sheath on the position of the electrostatic potential saddle point near the extractor electrode. The electron blocking potential blocking is described as a function of electrode thickness and secondary plasma processes.

  9. Investigating the mechanisms of photosynthetic proteins using continuum electrostatics.

    PubMed

    Ullmann, G Matthias; Kloppmann, Edda; Essigke, Timm; Krammer, Eva-Maria; Klingen, Astrid R; Becker, Torsten; Bombarda, Elisa

    2008-07-01

    Computational methods based on continuum electrostatics are widely used in theoretical biochemistry to analyze the function of proteins. Continuum electrostatic methods in combination with quantum chemical and molecular mechanical methods can help to analyze even very complex biochemical systems. In this article, applications of these methods to proteins involved in photosynthesis are reviewed. After giving a short introduction to the basic concepts of the continuum electrostatic model based on the Poisson-Boltzmann equation, we describe the application of this approach to the docking of electron transfer proteins, to the comparison of isofunctional proteins, to the tuning of absorption spectra, to the analysis of the coupling of electron and proton transfer, to the analysis of the effect of membrane potentials on the energetics of membrane proteins, and to the kinetics of charge transfer reactions. Simulations as those reviewed in this article help to analyze molecular mechanisms on the basis of the structure of the protein, guide new experiments, and provide a better and deeper understanding of protein functions. PMID:18478354

  10. 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.

  11. Continuum electrostatic approach for evaluating positions and interactions of proteins in a bilayer membrane.

    PubMed

    Supunyabut, Chirayut; Fuklang, Sunit; Sompornpisut, Pornthep

    2015-06-01

    Orientations of proteins in the membranes are crucial to their function and stability. Unfortunately the exact positions of these proteins in the lipid bilayer are mostly undetermined. Here, the spatial orientation of membrane proteins within the lipid membrane was evaluated using a Poisson-Boltzmann solvent continuum approach to calculate the electrostatic free energy of the protein solvation at various orientations in an implicit bilayer. The solvation energy was obtained by computing the difference in electrostatic energies of the protein in water and in lipid/water environments, treating each as an implicit solvent model. The optimal position of transmembrane proteins (TMP) in a lipid bilayer is identified by the minimum in the "downhill" pathway of the solvation energy landscape. The energy landscape pattern was considerably conserved in various TMP classes. Evaluation of the position of 1060 membrane proteins from the orientations of proteins in membranes (OPM) database revealed that most of the polytopic and β-barrel proteins were in good agreement with those of the OPM database. The study provides a useful scheme for estimating the membrane solvation energy made by lipid-exposed amino acids in membrane proteins. In addition, our results tested with the bacterial potassium channel model demonstrated the potential usefulness of the approach in assessing the quality of membrane protein models. The present approach should be applicable for constructing transmembrane proteins-lipid configuration suitable for membrane protein simulations and will have utility for the structural modeling of membrane proteins. PMID:25912455

  12. Dielectric pressure in continuum electrostatic solvation of biomolecules.

    PubMed

    Cai, Qin; Ye, Xiang; Luo, Ray

    2012-12-01

    Continuum solvation representations based on the Poisson-Boltzmann equation have become widely accepted in biomolecular applications after years of basic research and development. Since analytical solution of the differential equation can be achieved only in a few specific cases with simple solute geometry, only numerical solution is possible for biomolecular applications. However, it is conceptually difficult to assign solvation forces in the numerical methods, limiting their applications into direct simulations of energy minimization and molecular dynamics. In this study a dielectric pressure formulation was derived from the general Maxwell stress tensor for continuum solvation of biomolecules modeled with the widely used abrupt-transitioned dielectrics. A charge-central strategy was then proposed to improve the numerical behavior of the computed pressure. An interesting observation is the highly similar charge-central formulations between the smooth-transition dielectric and the abrupt-transition dielectric models utilized in the biomolecular solvation treatments. The connections of the new formulation with both the Davis-McCammon and Gilson et al. approaches were further presented after applying the normal field approximation. The consistency was verified with the numerical tests on a realistic biomolecule. The numerical experiments on the tested biomolecule further indicate that the charge-central strategy combined with the normal field approximation not only improves the accuracy of the dielectric boundary force but also reduces its grid dependence for biomolecular applications. PMID:23093365

  13. Electronic structure calculations in arbitrary electrostatic environments

    NASA Astrophysics Data System (ADS)

    Watson, Mark A.; Rappoport, Dmitrij; Lee, Elizabeth M. Y.; Olivares-Amaya, Roberto; Aspuru-Guzik, Alán

    2012-01-01

    Modeling of electronic structure of molecules in electrostatic environments is of considerable relevance for surface-enhanced spectroscopy and molecular electronics. We have developed and implemented a novel approach to the molecular electronic structure in arbitrary electrostatic environments that is compatible with standard quantum chemical methods and can be applied to medium-sized and large molecules. The scheme denoted CheESE (chemistry in electrostatic environments) is based on the description of molecular electronic structure subject to a boundary condition on the system/environment interface. Thus, it is particularly suited to study molecules on metallic surfaces. The proposed model is capable of describing both electrostatic effects near nanostructured metallic surfaces and image-charge effects. We present an implementation of the CheESE model as a library module and show example applications to neutral and negatively charged molecules.

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

    NASA Astrophysics Data System (ADS)

    Bardhan, Jaydeep P.

    2011-09-01

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

  15. The electrostatic response of water to neutral polar solutes: Implications for continuum solvent modeling

    NASA Astrophysics Data System (ADS)

    Muddana, Hari S.; Sapra, Neil V.; Fenley, Andrew T.; Gilson, Michael K.

    2013-06-01

    Continuum solvation models are widely used to estimate the hydration free energies of small molecules and proteins, in applications ranging from drug design to protein engineering, and most such models are based on the approximation of a linear dielectric response by the solvent. We used explicit-water molecular dynamics simulations with the TIP3P water model to probe this linear response approximation in the case of neutral polar molecules, using miniature cucurbituril and cyclodextrin receptors and protein side-chain analogs as model systems. We observe supralinear electrostatic solvent responses, and this nonlinearity is found to result primarily from waters' being drawn closer and closer to the solutes with increased solute-solvent electrostatic interactions; i.e., from solute electrostriction. Dielectric saturation and changes in the water-water hydrogen bonding network, on the other hand, play little role. Thus, accounting for solute electrostriction may be a productive approach to improving the accuracy of continuum solvation models.

  16. 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.

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

    PubMed

    Bonthuis, Douwe Jan; Netz, Roland R

    2013-10-01

    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. PMID:24063251

  18. Studying proton pumping mechanism of bacteriorhodopsin and cytochrome c oxidase with multi-conformation continuum electrostatics

    NASA Astrophysics Data System (ADS)

    Song, Yifan

    The proton gradient across the biological membrane is important for the biological systems. Bacteriorhodopsin and cytochrome c oxidase convert different energy sources into this gradient. The focus of this thesis is to understand the mechanism of these proteins using computational methods. In bacteriorhodopsin, residue ionization states were calculated in 9 crystal structures trapped in bR, early M and late M states by Multi-Conformation Continuum Electrostatics (MCC). The three groups in the central cluster are ionized in bR structures while a proton has transferred from the SB+ to Asp 85 - in the late M structures matching prior experimental results. The proton release cluster binds one proton in bR structure which is lost to water by pH 8 in late M. Modest changes in intra-protein interactions cause the charge shifts within the clusters. Motions of Arg 82 couple the proton shift in the central cluster to proton release. Changes in the total charge of the two clusters are coupled by direct long-range interactions. Cytochrome c oxidase is a transmembrane proton pump that builds an electrochemical gradient using chemical energy from the reduction of O2. Ionization states of all residues were calculated with MCCE in seven anaerobic oxidase redox states ranging from fully oxidized to fully reduced in Rb. sphaeroides cytochrome c oxidase. At pH 7, only a hydroxide coordinated to CuB shifts its pKa from below 7 to above 7, and so picks up a proton when Heme a3 and CuB are reduced. Glu I-286, Tyr I-288, His I-334 and a second hydroxide on Heme a3 all have pKas above 7. The propionic acids near the BNC are deprotonated with pKas well below 7. This suggests electroneutrality in the BNC is not maintained during the anaerobic reduction. The electrochemical midpoint potential (E m) of Heme a is calculated to shift down when the BNC is reduced, which agrees with prior experiments. If the BNC reduction is electroneutral, then the Heme a Em is independent of the BNC redox state.

  19. APBSmem: A Graphical Interface for Electrostatic Calculations at the Membrane

    PubMed Central

    Callenberg, Keith M.; Choudhary, Om P.; de Forest, Gabriel L.; Gohara, David W.; Baker, Nathan A.; Grabe, Michael

    2010-01-01

    Electrostatic forces are one of the primary determinants of molecular interactions. They help guide the folding of proteins, increase the binding of one protein to another and facilitate protein-DNA and protein-ligand binding. A popular method for computing the electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation, and there are several easy-to-use software packages available that solve the PB equation for soluble proteins. Here we present a freely available program, called APBSmem, for carrying out these calculations in the presence of a membrane. The Adaptive Poisson-Boltzmann Solver (APBS) is used as a back-end for solving the PB equation, and a Java-based graphical user interface (GUI) coordinates a set of routines that introduce the influence of the membrane, determine its placement relative to the protein, and set the membrane potential. The software Jmol is embedded in the GUI to visualize the protein inserted in the membrane before the calculation and the electrostatic potential after completing the computation. We expect that the ease with which the GUI allows one to carry out these calculations will make this software a useful resource for experimenters and computational researchers alike. Three examples of membrane protein electrostatic calculations are carried out to illustrate how to use APBSmem and to highlight the different quantities of interest that can be calculated. PMID:20949122

  20. An improved fragment-based quantum mechanical method for calculation of electrostatic solvation energy of proteins.

    PubMed

    Jia, Xiangyu; Wang, Xianwei; Liu, Jinfeng; Zhang, John Z H; Mei, Ye; He, Xiao

    2013-12-01

    An efficient approach that combines the electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method with conductor-like polarizable continuum model (CPCM), termed EE-GMFCC-CPCM, is developed for ab initio calculation of the electrostatic solvation energy of proteins. Compared with the previous MFCC-CPCM study [Y. Mei, C. G. Ji, and J. Z. H. Zhang, J. Chem. Phys. 125, 094906 (2006)], quantum mechanical (QM) calculation is applied to deal with short-range non-neighboring interactions replacing the classical treatment. Numerical studies are carried out for proteins up to 3837 atoms at the HF/6-31G* level. As compared to standard full system CPCM calculations, EE-GMFCC-CPCM shows clear improvement over the MFCC-CPCM method for both the total electrostatic solvation energy and its components (the polarized solute-solvent reaction field energy and wavefunction distortion energy of the solute). For large proteins with 1000-4000 atoms, where the standard full system ab initio CPCM calculations are not affordable, the EE-GMFCC-CPCM gives larger relative wavefunction distortion energies and weaker relative electrostatic solvation energies for proteins, as compared to the corresponding energies calculated by the Divide-and-Conquer Poisson-Boltzmann (D&C-PB) method. Notwithstanding, a high correlation between EE-GMFCC-CPCM and D&C-PB is observed. This study demonstrates that the linear-scaling EE-GMFCC-CPCM approach is an accurate and also efficient method for the calculation of electrostatic solvation energy of proteins.

  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. 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

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

    PubMed

    Fuller, Jonathan C; Martinez, Michael; Wade, Rebecca C

    2014-01-01

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

  4. 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.

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

    PubMed Central

    You, T J; Bashford, D

    1995-01-01

    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. Images FIGURE 1 PMID:8580316

  6. 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.

  7. Adding explicit solvent molecules to continuum solvent calculations for the calculation of aqueous acid dissociation constants.

    PubMed

    Kelly, Casey P; Cramer, Christopher J; Truhlar, Donald G

    2006-02-23

    Aqueous acid dissociation free energies for a diverse set of 57 monoprotic acids have been calculated using a combination of experimental and calculated gas and liquid-phase free energies. For ionic species, aqueous solvation free energies were calculated using the recently developed SM6 continuum solvation model. This model combines a dielectric continuum with atomic surface tensions to account for bulk solvent effects. For some of the acids studied, a combined approach that involves attaching a single explicit water molecule to the conjugate base (anion), and then surrounding the resulting anion-water cluster by a dielectric continuum, significantly improves the agreement between the calculated pK(a) value and experiment. This suggests that for some anions, particularly those concentrating charge on a single exposed heteroatom, augmenting implicit solvent calculations with a single explicit water molecule is required, and adequate, to account for strong short-range hydrogen bonding interactions between the anion and the solvent. We also demonstrate the effect of adding several explicit waters by calculating the pK(a) of bicarbonate (HCO(3)(-)) using as the conjugate base carbonate (CO(3)(2-)) bound by up to three explicit water molecules.

  8. 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.

  9. Comparison of methods for numerical calculation of continuum damping

    SciTech Connect

    Bowden, G. W.; Hole, M. J.; Dennis, G. R.; Könies, A.; Gorelenkov, N. N.

    2014-05-15

    Continuum resonance damping is an important factor in determining the stability of certain global modes in fusion plasmas. A number of analytic and numerical approaches have been developed to compute this damping, particularly, in the case of the toroidicity-induced shear Alfvén eigenmode. This paper compares results obtained using an analytical perturbative approach with those found using resistive and complex contour numerical approaches. It is found that the perturbative method does not provide accurate agreement with reliable numerical methods for the range of parameters examined. This discrepancy exists even in the limit where damping approaches zero. When the perturbative technique is implemented using a standard finite element method, the damping estimate fails to converge with radial grid resolution. The finite elements used cannot accurately represent the eigenmode in the region of the continuum resonance, regardless of the number of radial grid points used.

  10. 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.

  11. 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.

  12. 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.

  13. Electrostatics

    NASA Astrophysics Data System (ADS)

    Wallace, John P.; Wallace, Michael J.

    2015-12-01

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

  14. 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.

  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. PMID:26210154

  17. 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.

  18. 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

    2013-01-01

    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.

  19. Unified calculation of generalized oscillator strength of argon ranging from bound to continuum states

    NASA Astrophysics Data System (ADS)

    Gao, Xiang; Jin, Rui; Zeng, De-Ling; Han, Xiao-Ying; Yan, Jun; Li, Jia-Ming

    2015-11-01

    The electron and photon scattering data of an atom are crucial for many scientific fields, including plasma physics, astrophysics, and so on. For high enough but nonrelativistic incident energies, the first Born approximation is applicable for calculating these data, in which the key physics quantity is the generalized oscillator strength (GOS). In high-energy electron impact excitation processes, atoms will be excited into various excited states including strongly perturbed Rydberg and adjacent continuum states. How to calculate these quantities of a nontrivial many-electron atom rapidly and accurately is still a great challenge. Based on our eigenchannel R -matrix method R -eigen, we further extend it to calculate the GOS of a whole channel in an atom, which includes all Rydberg and adjacent continuum states. The Jπ=1- states of argon are chosen as an illustrating example. The calculation results are in good agreement with the available benchmark absolute experimental measurements. The calculated eigenchannel GOS matrix elements are smooth functions of the excitation energy and momentum transfer. From such smooth eigenchannel GOS matrix elements, we can obtain the GOS of any specific excited state through multichannel quantum defect theory, e.g., infinite Rydberg (including a strongly perturbed one), autoionization, and continuum states.

  20. 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

    2012-09-01

    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.

  1. Convolution based method for calculating inputs from dendritic fields in a continuum model of the retina.

    PubMed

    Al Abed, Amr; Yin, Shijie; Suaning, Gregg J; Lovell, Nigel H; Dokos, Socrates

    2012-01-01

    Computational models are valuable tools that can be used to aid the design and test the efficacy of electrical stimulation strategies in prosthetic vision devices. In continuum models of retinal electrophysiology, the effective extracellular potential can be considered as an approximate measure of the electrotonic loading a neuron's dendritic tree exerts on the soma. A convolution based method is presented to calculate the local spatial average of the effective extracellular loading in retinal ganglion cells (RGCs) in a continuum model of the retina which includes an active RGC tissue layer. The method can be used to study the effect of the dendritic tree size on the activation of RGCs by electrical stimulation using a hexagonal arrangement of electrodes (hexpolar) placed in the suprachoroidal space.

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

    SciTech Connect

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

    2009-04-24

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

  3. 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.

  4. 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.

  5. 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/.

  6. 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.

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

    PubMed Central

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

    2015-01-01

    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. PMID:26233103

  8. 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.

  9. 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.

  10. Continuum reaction field calculation of dielectric constant and vapor pressures for water and carbon disulfide.

    PubMed

    Nir, S

    1976-01-01

    Continuum reaction field theory is applied to calculations of dielectric constant, contribution of intermolecular interactions to the free energy of a liquid, and heat of vaporization. Introduction of repulsive interactions and the use of one adjustable parameter, the free volume, enables prediction of vapor pressures. The calculations are illustrated for a simple nonpolar liquid, carbon disulfide, and for liquid water. It is shown that when Onsager's equation is rearranged to a quadratic equation, and a recently found value of the polarizability is employed, its solutions for liquid water yield good agreement with experimental values throughout the whole temperature range. The decrease of the dielectric constant with temperature is essentially linear with the inverse of absolute temperature, but there is additional significant decrease due to the decrease of density with temperature. The relatively high value of the heat of vaporization of liquid water is expressed in terms of large dipolar interaction of a water molecule with the environment, which is due to polarization effects.

  11. 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. PMID:22168680

  12. 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.

  13. Computational antigenic epitope prediction by calculating electrostatic desolvation penalties of protein surfaces.

    PubMed

    Fiorucci, Sébastien; Zacharias, Martin

    2014-01-01

    The prediction of antigenic epitopes on the surface of proteins is of great importance for vaccine development and to specifically design recombinant antibodies. Computational methods based on the three-dimensional structure of the protein allow for the detection of noncontinuous epitopes in contrast to methods based on the primary amino-acid sequence only. A method recently developed to predict protein-protein binding sites is presented, and the application to predict putative antigenic epitopes is described in detail. The prediction approach is based on the local perturbation of the electrostatic field at the surface of a protein due to a neutral probe of low dielectric constant that represents an approaching binding partner. The calculated change in electrostatic energy corresponds to an energy penalty of desolvating a protein surface region, and antigenic epitope surface regions tend to be associated with a lower penalty compared to the average protein surface. The protocol to perform the calculations is described and illustrated on an example antigen, the outer surface protein A of Borrelia burgdorferi, a pathogenic organism causing lyme disease.

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

    PubMed

    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.

  15. 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.

  16. Calculation of ionized fields in DC electrostatic precipitators in the presence of dust and electric wind

    SciTech Connect

    Cristina, S.; Feliziani, M.

    1995-11-01

    This paper describes a new procedure for the numerical computation of the electric field and current density distributions in a dc electrostatic precipitator in the presence of dust, taking into account the particle-size distribution. Poisson`s and continuity equations are numerically solved by supposing that the coronating conductors satisfy Kaptzov`s assumption on the emitter surfaces. Two iterative numerical procedures, both based on the finite element method (FEM), are implemented for evaluating, respectively, the unknown ionic charge density and the particle charge density distributions. The V-I characteristic and the precipitation efficiencies for the individual particle-size classes, calculated with reference to the pilot precipitator installed by ENEL (Italian Electricity Board) at its Marghera (Venice) coal-fired power station, are found to be very close to those measured experimentally.

  17. Electrostatic potential and Born energy of charged molecules interacting with phospholipid membranes: calculation via 3-D numerical solution of the full Poisson equation.

    PubMed

    Schnitzer, J E; Lambrakis, K C

    1991-09-21

    Understanding the physicochemical basis of the interaction of molecules with lipid bilayers is fundamental to membrane biology. In this study, a new, three-dimensional numerical solution of the full Poisson equation including local dielectric variation is developed using finite difference techniques in order to model electrostatic interactions of charged molecules with a non-uniform dielectric. This solution is used to describe the electric field and electrostatic potential profile of a charged molecule interacting with a phospholipid bilayer in a manner consistent with the known composition and structure of the membrane. Furthermore, the Born interaction energy is then calculated by appropriate integration of the electric field over whole space. Numerical computations indicate that the electrostatic potential profile surrounding a charge molecule and its resultant Born interaction energy are a function of molecular position within the membrane and change most significantly within the polar region of the bilayer. The maximum interaction energy is observed when the charge is placed at the center of the hydrophobic core of the membrane and is strongly dependent on the size of the charge and on the thickness of the hydrocarbon core of the bilayer. The numerical results of this continuum model are compared with various analytical approximations for the Born energy including models established for discontinuous slab dielectrics. The calculated energies agree with the well-known Born analytical expression only when the charge is located near the center of a hydrocarbon core of greater than 60 A in thickness. The Born-image model shows excellent agreement with the numerical results only when modified to include an appropriate effective thickness of the low dielectric region. In addition, a newly derived approximation which considers the local mean dielectric provides a simple and continuous solution that also agrees well with the numerical results.

  18. An auxilliary grid method for the calculation of electrostatic terms in density functional theory on a real-space grid.

    PubMed

    Zuzovski, Michael; Boag, Amir; Natan, Amir

    2015-12-21

    In this work we show the implementation of a linear scaling algorithm for the calculation of the Poisson integral. We use domain decomposition and non-uniform auxiliary grids (NGs) to calculate the electrostatic interaction. We demonstrate the approach within the PARSEC density functional theory code and perform calculations of long 1D carbon chains and other long molecules. Finally, we discuss possible applications to additional problems and geometries. PMID:26123448

  19. Sampling field heterogeneity at the heme of c-type cytochromes by spectral hole burning spectroscopy and electrostatic calculations.

    PubMed Central

    Laberge, M; Köhler, M; Vanderkooi, J M; Friedrich, J

    1999-01-01

    We report on a comparative investigation of the heme pocket fields of two Zn-substituted c-type cytochromes-namely yeast and horse heart cytochromes c-using a combination of hole burning Stark spectroscopy and electrostatic calculations. The spectral hole burning experiments are consistent with different pocket fields experienced at the hemes of the respective cytochromes. In the case of horse heart Zn-cytochrome c, two distinguishable electronic origins with different electrostatic properties are observed. The yeast species, on the other hand, displays a single electronic origin. Electrostatic calculations and graphics modeling using the linearized finite-difference Poisson-Boltzmann equation performed at selected time intervals on nanosecond-molecular dynamics trajectories show that the hemes of the respective cytochromes sample different potentials as they explore conformational space. The electrostatic potentials generated by the protein matrix at the heme show different patterns in both cytochromes, and we suggest that the cytochromes differ by the number of "electrostatic substates" that they can sample, thus accounting for the different spectral populations observed in the two cytochromes. PMID:10585951

  20. 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

  1. 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…

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. Speeding Up and Quantifying Approximation Error in Continuum Quantum Monte Carlo Solid-State Calculations

    NASA Astrophysics Data System (ADS)

    Parker, William David

    Quantum theory has successfully explained the mechanics of much of the microscopic world. However, Schrodinger's equations are difficult to solve for many-particle systems. Mean-field theories such as Hartree-Fock and density functional theory account for much of the total energy of electronic systems but fail on the crucial correlation energy that predicts solid cohesion and material properties. Monte Carlo methods solve differential and integral equations with error independent of the number of dimensions in the problem. Variational Monte Carlo (VMC) applies the variational principle to optimize the wave function used in the Monte Carlo integration of Schrodinger's time-independent equation. Diffusion Monte Carlo (DMC) represents the wave function by electron configurations diffusing stochastically in imaginary time to the ground state. Approximations in VMC and DMC make the problem tractable but introduce error in parameter-controlled and uncontrolled ways. The many-electron wave function consists of single-particle orbitals. The orbitals are combined in a functional form to account for electron exchange and correlation. Plane waves are a convenient basis for the orbitals. However, plane-wave orbitals grow in evaluation cost with basis-set completeness and system size. To speed up the calculation, polynomials approximate the plane-wave sum. Four polynomial methods tested are: Lagrange interpolation, pp-spline interpolation, B-spline interpolation and B-spline approximation. The polynomials all increase speed by an order of the number of particles. B-spline approximation most consistently maintains accuracy in the seven systems tested. However, polynomials increase the memory needed by a factor of two to eight. B-spline approximation with a separate approximation for the Laplacian of the orbitals increases the memory by a factor of four over plane waves. Polynomial-based orbitals enable larger calculations and careful examination of error introduced by

  9. 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.

  10. 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

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

    PubMed

    Horn, Paul R; Mao, Yuezhi; Head-Gordon, Martin

    2016-03-21

    In energy decomposition analysis of Kohn-Sham density functional theory calculations, the so-called frozen (or pre-polarization) interaction energy contains contributions from permanent electrostatics, dispersion, and Pauli repulsion. The standard classical approach to separate them suffers from several well-known limitations. We introduce an alternative scheme that employs valid antisymmetric electronic wavefunctions throughout and is based on the identification of individual fragment contributions to the initial supersystem wavefunction as determined by an energetic optimality criterion. The density deformations identified with individual fragments upon formation of the initial supersystem wavefunction are analyzed along with the distance dependence of the new and classical terms for test cases that include the neon dimer, ammonia borane, water-Na(+), water-Cl(-), and the naphthalene dimer. PMID:27004862

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

    NASA Astrophysics Data System (ADS)

    Horn, Paul R.; Mao, Yuezhi; Head-Gordon, Martin

    2016-03-01

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

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

    NASA Astrophysics Data System (ADS)

    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.

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

    SciTech Connect

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

    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.

  15. Conversion of electrostatic plasma waves into electromagnetic waves - Numerical calculation of the dispersion relation for all wavelengths.

    NASA Technical Reports Server (NTRS)

    Oya, H.

    1971-01-01

    The dispersion curves have been computed for a wide range of wavelengths from electromagnetic waves to electrostatic waves in a magnetoactive warm plasma with a Maxwellian velocity distribution function. The computation was carried out mainly for the perpendicular propagation mode. The upper hybrid resonance is the connection point of the electrostatic waves and the electromagnetic waves. The electrostatic waves not associated with the upper hybrid resonance are subjected to electron cyclotron damping when the wavelength becomes long. Oblique propagation is allowed for the electrostatic waves in a frequency range from the plasma frequency to the upper hybrid resonance frequency in the long-wavelength region where Landau damping can be neglected and where the electrostatic mode smoothly connects to the electromagnetic X-mode. In a slightly inhomogeneous plasma, the Bernstein-mode electrostatic wave can escape by being converted into the O-mode electromagnetic wave; two reflections take place during this escape process.

  16. Intrinsic electrostatic resonances of heterostructures with negative permittivity from finite-element calculations: Application to core-shell inclusions

    NASA Astrophysics Data System (ADS)

    Mejdoubi, Abdelilah; Brosseau, Christian

    2007-11-01

    Herein, we report finite-element calculations of the effective (relative) permittivity of composite materials consisting of inclusions and inclusion arrays with a core-shell structure embedded in a surrounding host. The material making up the core of the two-dimensional structures, or cross sections of infinite three-dimensional objects (parallel, infinitely long, and identical cylinders) where the properties and characteristics are invariant along the perpendicular cross sectional plane, is assumed to have a negative real part of the permittivity, while the coating material (annular shell) is considered to be lossless. While strictly valid only in a dc situation, our analysis can be extended to treat electric fields that oscillate with time, provided that the wavelengths and attenuation lengths associated with the fields are much larger than the microstructure dimension in order that the homogeneous (effective-medium) representation of the composite structure makes sense. While one may identify features of the electrostatic resonance (ER) which are common to core-shell structures characterized by permittivities with real parts of opposite signs, it appears that the predicted ER positions are sensitive to the shell thickness and can be tuned through varying this geometric parameter. For example, we observe that the ER is broadened and shifted as the loss and the shell thickness are increased, respectively. We also argue that such core shell may also be valuable in controlling ER characteristics via polarization in an external electric field. In addition, by considering calculations of the electric field distribution, we find that the ER results in very strong and local-field enhancements into small parts of the shell perimeter. Our findings open up possibilities for the development of hybrid structures that could exploit the ER features for a particular application.

  17. 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

  18. 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.

  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

    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

  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. A polarizable continuum model for molecules at spherical diffuse interfaces

    NASA Astrophysics Data System (ADS)

    Di Remigio, Roberto; Mozgawa, Krzysztof; Cao, Hui; Weijo, Ville; Frediani, Luca

    2016-03-01

    We present an extension of the Polarizable Continuum Model (PCM) to simulate solvent effects at diffuse interfaces with spherical symmetry, such as nanodroplets and micelles. We derive the form of the Green's function for a spatially varying dielectric permittivity with spherical symmetry and exploit the integral equation formalism of the PCM for general dielectric environments to recast the solvation problem into a continuum solvation framework. This allows the investigation of the solvation of ions and molecules in nonuniform dielectric environments, such as liquid droplets, micelles or membranes, while maintaining the computationally appealing characteristics of continuum solvation models. We describe in detail our implementation, both for the calculation of the Green's function and for its subsequent use in the PCM electrostatic problem. The model is then applied on a few test systems, mainly to analyze the effect of interface curvature on solvation energetics.

  2. A polarizable continuum model for molecules at spherical diffuse interfaces.

    PubMed

    Di Remigio, Roberto; Mozgawa, Krzysztof; Cao, Hui; Weijo, Ville; Frediani, Luca

    2016-03-28

    We present an extension of the Polarizable Continuum Model (PCM) to simulate solvent effects at diffuse interfaces with spherical symmetry, such as nanodroplets and micelles. We derive the form of the Green's function for a spatially varying dielectric permittivity with spherical symmetry and exploit the integral equation formalism of the PCM for general dielectric environments to recast the solvation problem into a continuum solvation framework. This allows the investigation of the solvation of ions and molecules in nonuniform dielectric environments, such as liquid droplets, micelles or membranes, while maintaining the computationally appealing characteristics of continuum solvation models. We describe in detail our implementation, both for the calculation of the Green's function and for its subsequent use in the PCM electrostatic problem. The model is then applied on a few test systems, mainly to analyze the effect of interface curvature on solvation energetics. PMID:27036423

  3. Calculation of the Gibbs free energy of solvation and dissociation of HCl in water via Monte Carlo simulations and continuum solvation models.

    PubMed

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

    2013-08-28

    The Gibbs 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 Gibbs 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 Gibbs 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 Gibbs 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 Gibbs free energies agree very well with available experimental data.

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

    NASA Astrophysics Data System (ADS)

    Lian, Zengju

    2016-07-01

    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/d3 (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.

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

    PubMed

    Lian, Zengju

    2016-07-01

    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. PMID:27394119

  6. Charge-density distribution and electrostatic flexibility of ZIF-8 based on high-resolution X-ray diffraction data and periodic calculations.

    PubMed

    Novaković, Sladjana B; Bogdanović, Goran A; Heering, Christian; Makhloufi, Gamall; Francuski, Djordje; Janiak, Christoph

    2015-03-16

    The electron-density distribution in a prototypical porous coordination polymer ZIF-8 has been obtained in an approach combining high-resolution X-ray diffraction data and Invariom refinement. In addition, the periodic quantum-chemical calculation has been used to describe the theoretical density features of ZIF-8 in the same geometry (m1) and also in a "high-pressure" form of ZIF-8 (m2) characterized by conformational change with respect to the methylimidazolate linker. A thorough comparison of the electronic and electrostatic properties in two limiting structural forms of ZIF-8 proposes additional aspects on diffusion and adsorption processes occurring within the framework. The dimensions of the four-membered (FM) and six-membered (SM) apertures of the β cage are reliably determined from the total electron-density distribution. The analysis shows that FM in m2 becomes competitive in size to the SM aperture and should be considered for the diffusion of small molecules and cations. Bader's topological analysis (quantum theory of atoms in molecules) shows similar properties of both ZIF-8 forms. On the other hand, analysis of their electrostatic properties reveals tremendous differences. The study suggests exceptional electrostatic flexibility of the ZIF-8 framework, where small conformational changes lead to a significantly different electrostatic potential (EP) distribution, a feature that could be important for the function and dynamics of the ZIF-8 framework. The cavity surface in m1 contains 38 distinct regions with moderately positive, negative, or neutral EP and weakly positive EP in the cavity volume. In contrast to m1, the m2 form displays only two regions of different EP, with the positive one taking the whole cavity surface and the strong negative one localized entirely in the FM apertures. The EP in the cavity volume is also more positive than that in m1. A pronounced influence of the linker reorientation on the EP of the ZIF-8 forms is related to the

  7. 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.

  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. 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.

  10. Acidity constants and its dependence on solvent selection from first-principles calculations using cluster-continuum models

    NASA Astrophysics Data System (ADS)

    Pham, Hieu H.; Taylor, Christopher D.; Henson, Neil J.

    2014-08-01

    Dissociation constants of selected carboxylic acids in aqueous and organic solvents were calculated at quantum chemical level. We considered cases in which trace quantities of water may be present, as well as cases in which water was entirely absent. In the latter cases, alternative proton acceptors need to be considered. For aqueous solvent, short-range solvation effects are considered by adding explicit water molecules as the first solvent shell. In the absence of water, corresponding organic solvents are used directly as the proton acceptors and the resulted pKa are quite comparable to those obtained from previous case of aqueous solvent.

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

    PubMed

    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(')-bipyridine)tetracarbonyltungsten [W(CO)4(bpy), bpy = 2,2(')-bipyridine] and bis(pentacarbonyltungsten)pyrazine [(OC)5W(pyz)W(CO)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.

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

    NASA Astrophysics Data System (ADS)

    Fukuda, Ryoichi; Ehara, Masahiro; Cammi, Roberto

    2014-02-01

    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'-bipyridine)tetracarbonyltungsten [W(CO)4(bpy), bpy = 2,2'-bipyridine] and bis(pentacarbonyltungsten)pyrazine [(OC)5W(pyz)W(CO)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.

  13. 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.

  14. 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.

  15. Electrostatic Interaction-Induced Room-Temperature Phosphorescence in Pure Organic Molecules from QM/MM Calculations.

    PubMed

    Ma, Huili; Shi, Wen; Ren, Jiajun; Li, Wenqiang; Peng, Qian; Shuai, Zhigang

    2016-08-01

    Room temperature phosphorescence (RTP) from pure organic material is rare due to the low phosphorescence quantum efficiency. That is why the recent discovery of crystallization induced RTP for several organic molecules aroused strong interests. Through a combined quantum and molecular mechanics CASPT2/AMBER scheme taking terephthalic acid (TPA) as example, we found that electrostatic interaction not only can induce an enhanced radiative decay T1 → S0 through the dipole-allowed S1 intermediate state, but also can hinder the nonradiative decay process upon crystallization. From gas phase to crystal, the nature of S1 state is converted to (1)(π,π*) from (1)(n,π*) character, enhancing transition dipole moment and serving as an efficient intermediate radiative pathway for T1 → S0 transition, and eventually leading to a boosted RTP. The intermolecular packing also blocks the nonradiative decay channel of the high-frequency C═O stretching vibration with large vibronic coupling, rather than the conventional low-frequency aromatic rotation in crystal. This mechanism also holds for other organic compounds that contain both ketones and aromatic rings. PMID:27414718

  16. Electrostatic Interaction-Induced Room-Temperature Phosphorescence in Pure Organic Molecules from QM/MM Calculations.

    PubMed

    Ma, Huili; Shi, Wen; Ren, Jiajun; Li, Wenqiang; Peng, Qian; Shuai, Zhigang

    2016-08-01

    Room temperature phosphorescence (RTP) from pure organic material is rare due to the low phosphorescence quantum efficiency. That is why the recent discovery of crystallization induced RTP for several organic molecules aroused strong interests. Through a combined quantum and molecular mechanics CASPT2/AMBER scheme taking terephthalic acid (TPA) as example, we found that electrostatic interaction not only can induce an enhanced radiative decay T1 → S0 through the dipole-allowed S1 intermediate state, but also can hinder the nonradiative decay process upon crystallization. From gas phase to crystal, the nature of S1 state is converted to (1)(π,π*) from (1)(n,π*) character, enhancing transition dipole moment and serving as an efficient intermediate radiative pathway for T1 → S0 transition, and eventually leading to a boosted RTP. The intermolecular packing also blocks the nonradiative decay channel of the high-frequency C═O stretching vibration with large vibronic coupling, rather than the conventional low-frequency aromatic rotation in crystal. This mechanism also holds for other organic compounds that contain both ketones and aromatic rings.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: calculation of structural and dynamic properties.

    PubMed

    Li, Xianfeng; Hassan, Sergio A; Mehler, Ernest L

    2005-08-15

    Long dynamics simulations were carried out on the B1 immunoglobulin-binding domain of streptococcal protein G (ProtG) and bovine pancreatic trypsin inhibitor (BPTI) using atomistic descriptions of the proteins and a continuum representation of solvent effects. To mimic frictional and random collision effects, Langevin dynamics (LD) were used. The main goal of the calculations was to explore the stability of tens-of-nanosecond trajectories as generated by this molecular mechanics approximation and to analyze in detail structural and dynamical properties. Conformational fluctuations, order parameters, cross correlation matrices, residue solvent accessibilities, pKa values of titratable groups, and hydrogen-bonding (HB) patterns were calculated from all of the trajectories and compared with available experimental data. The simulations comprised over 40 ns per trajectory for ProtG and over 30 ns per trajectory for BPTI. For comparison, explicit water molecular dynamics simulations (EW/MD) of 3 ns and 4 ns, respectively, were also carried out. Two continuum simulations were performed on each protein using the CHARMM program, one with the all-atom PAR22 representation of the protein force field (here referred to as PAR22/LD simulations) and the other with the modifications introduced by the recently developed CMAP potential (CMAP/LD simulations). The explicit solvent simulations were performed with PAR22 only. Solvent effects are described by a continuum model based on screened Coulomb potentials (SCP) reported earlier, i.e., the SCP-based implicit solvent model (SCP-ISM). For ProtG, both the PAR22/LD and the CMAP/LD 40-ns trajectories were stable, yielding C(alpha) root mean square deviations (RMSD) of about 1.0 and 0.8 A respectively along the entire simulation time, compared to 0.8 A for the EW/MD simulation. For BPTI, only the CMAP/LD trajectory was stable for the entire 30-ns simulation, with a C(alpha) RMSD of approximately 1.4 A, while the PAR22/LD trajectory

  2. Continuum mechanics

    NASA Astrophysics Data System (ADS)

    Khristianovich, S. A.

    The volume contains a collection of papers dealing with various problems of continuum mechanics which were written by the author at different times during the period 1936-1974. Topics covered include supersonic gas flow, design of Laval nozzles, physical foundations of transonic aerodynamics, theory of short waves, cohesion modulus in the theory of cracks, and deformation of strain-hardening plastic materials.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

    Density functional theory calculations were carried out for three entropic rocksalt oxides, (Mg0.1Co0.1Ni0.1Cu0.1Zn0.1)O0.5, 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+3 in J14 + Li are very different from Co+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.

  4. Electrostatic Explorations.

    ERIC Educational Resources Information Center

    Gallai, Ditta; Stewart, Gay

    1998-01-01

    Presents a set of hands-on electrostatics experiments in the form of an activity guide and worksheet through which students discover the different types of electric charge, Coulomb's Law, induced charge separation, and grounding. (DDR)

  5. 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.

  6. 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.

  7. 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.

  8. Implicit electrostatic solvent model with continuous dielectric permittivity function.

    PubMed

    Basilevsky, Mikhail V; Grigoriev, Fedor V; Nikitina, Ekaterina A; Leszczynski, Jerzy

    2010-02-25

    The modification of the electrostatic continuum solvent model considered in the present work is based on the exact solution of the Poisson equation, which can be constructed provided that the dielectric permittivity epsilon of the total solute and solvent system is an isotropic and continuous spatial function. This assumption allows one to formulate a numerically efficient and universal computational scheme that covers the important case of a variable epsilon function inherent to the solvent region. The obtained type of solution is unavailable for conventional dielectric continuum models such as the Onsager and Kirkwood models for spherical cavities and the polarizable continuum model (PCM) for solute cavities of general shape, which imply that epsilon is discontinuous on the boundary confining the excluded volume cavity of the solute particle. Test computations based on the present algorithm are performed for water and several nonaqueous solvents. They illustrate specific features of this approach, called the "smooth boundary continuum model" (SBCM), as compared to the PCM procedure, and suggest primary tentative results of its parametrization for different solvents. The calculation for the case of a binary solvent mixture with variable epsilon in the solvent space region demonstrates the applicability of this approach to a novel application field covered by the SBCM.

  9. The Contribution of Electrostatic and van der Waals Interactions to the Stereospecificity of the Reaction Catalyzed by Lactate Dehydrogenase

    PubMed Central

    van Beek, Jeroen; Callender, Robert; Gunner, M. R.

    1997-01-01

    Continuum electrostatic calculations in conjunction with molecular dynamics simulations have been used to investigate the source of the stereospecificity in the hydride transfer reaction catalyzed by lactate dehydrogenase (LDH). These studies show that favorable electrostatic interactions between the carboxamide group of the reduced nicotinamide adenine dinucleotide coenzyme and protein residues of the active site of LDH can account for much if not all of the stereospecificity of the LDH-catalyzed reaction, with A-side hydride transfer more than 107 times greater than B-side transfer. Unfavorable steric interactions within the binding complex for B-side transfer are not found. ImagesFIGURE 2 PMID:9017191

  10. The electrostatic origin of Abraham's solute polarity parameter.

    PubMed

    Arey, J Samuel; Green, William H; Gschwend, Philip M

    2005-04-21

    A computational method was developed which relates the empirical linear solvation energy relationship (LSER) solute polarity parameter, S (formerly denoted ), to two more fundamental quantities: a polarizability term and a computed solvent-accessible-surface electrostatic term. Electrostatics computations were conducted explicitly or with dielectric field polarizable continuum models (PCM, SCIPCM, IPCM), employing a density functional theory (B3LYP/6-311G(2df,2p)) or efficient Hartree-Fock (HF/MIDI!) method for 90 polar and nonpolar organic solutes. Electrostatic parameters calculated at electron isodensity solute surfaces were found to produce significantly better correlations with empirical S values than the same electrostatic parameters deduced from a fixed Bondi atomic radii based surface. The best-fit expression was found employing SCIPCM/IPCM at the 0.0004 e(-)/bohr(3) solvent-accessible-surface: S(fit)() = 0.46E - 0.091SigmaV(s)()(2), with squared correlation coefficient = 0.96 and standard deviation = 0.10, where E is a measured solute excess polarizability scale and SigmaV(s)()(2) is a quantum-calculated solute electrostatic descriptor in kcal A/mol. The resulting model is more accurate than previously developed estimation approaches and relies on only two fitted coefficients; it has the potential advantage of applicability to any solute composed of C, H, N, O, S, F, Cl, and Br. Finally, this investigation offers quantitative insight into the relative contributions of solute polarity and solute polarizability to the empirical LSER polarity parameter, S.

  11. 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.

  12. Electrostatic precipitator

    SciTech Connect

    Hayashi, T.

    1982-08-03

    An electrostatic precipitator comprising a plurality of flat plate dust-collecting electrodes, arranged in substantially equally spaced and parallel relationship with one another and each having a discharge electrode, or electrodes, on and along the edge of one side thereof with the discharge electrodes of the adjacent dust-collecting electrodes alternately facing in opposite directions; the edges having the discharge electrodes are arranged in a setback relation by some distance in relation to the nearby edges of the adjacent dust-collecting plates, where no discharge electrodes are provided, so that uniform and nonuniform electric fields may be produced.

  13. Electrostatic thrusters.

    NASA Technical Reports Server (NTRS)

    Kaufman, H. R.; Reader, P. D.

    1972-01-01

    The current status of research and development programs on electrostatic thrusters is reviewed. Current programs that utilize mercury electron-bombardment thrusters range from 5- to 30-cm in diameter. Recent progress on the 5-cm thruster has emphasized durability, with accelerator time exceeding 6300 hours and total time on the rest of the thruster exceeding 8300 hours. Recent progress on the 30-cm thruster has been outstanding in dished-grid accelerator systems. Ion beams up to 5 amperes have been obtained for short periods with 1000 volts net accelerating potential difference. The cesium electron-bombardment and cesium contact programs are also described.

  14. 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.

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

    PubMed Central

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

    2013-01-01

    Due to the enormous importance of electrostatics in molecular biology, calculating the electrostatic potential and corresponding energies has become a standard computational approach for the study of biomolecules and nano-objects immersed in water and salt phase or other media. However, the electrostatics of large macromolecules and macromolecular complexes, including nano-objects, may not be obtainable via explicit methods and even the standard continuum electrostatics methods may not be applicable due to high computational time and memory requirements. Here, we report further development of the parallelization scheme reported in our previous work (J Comput Chem. 2012 Sep 15; 33(24):1960–6.) to include parallelization of the molecular surface and energy calculations components of the algorithm. The parallelization scheme utilizes different approaches such as space domain parallelization, algorithmic parallelization, multi-threading, and task scheduling, depending on the quantity being calculated. This allows for efficient use of the computing resources of the corresponding computer cluster. The parallelization scheme is implemented in the popular software DelPhi and results in speedup of several folds. As a demonstration of the efficiency and capability of this methodology, the electrostatic potential and electric field distributions are calculated for the bovine mitochondrial supercomplex illustrating their complex topology which cannot be obtained by modeling the supercomplex components alone. PMID:23733490

  16. Perspective: Polarizable continuum models for quantum-mechanical descriptions

    NASA Astrophysics Data System (ADS)

    Lipparini, Filippo; Mennucci, Benedetta

    2016-04-01

    Polarizable continuum solvation models are nowadays the most popular approach to describe solvent effects in the context of quantum mechanical calculations. Unexpectedly, despite their widespread use in all branches of quantum chemistry and beyond, important aspects of both their theoretical formulation and numerical implementation are still not completely understood. In particular, in this perspective we focus on the numerical issues of their implementation when applied to large systems and on the theoretical framework needed to treat time dependent problems and excited states or to deal with electronic correlation. Possible extensions beyond a purely electrostatic model and generalizations to environments beyond common solvents are also critically presented and discussed. Finally, some possible new theoretical approaches and numerical strategies are suggested to overcome the obstacles which still prevent a full exploitation of these models.

  17. Continuum kinetic modeling of the tokamak plasma edge

    DOE PAGES

    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 anomalousmore » radial transport.« less

  18. 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.

  19. Electrostatic Return of Contaminants

    NASA Technical Reports Server (NTRS)

    Rantanen, R.; Gordon, T.

    2003-01-01

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

  20. 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.

  1. Dielectric relaxation of cytochrome c oxidase: Comparison of the microscopic and continuum models.

    PubMed

    Leontyev, I V; Stuchebrukhov, A A

    2009-02-28

    We have studied a charge-insertion process that models the deprotonation of a histidine side chain in the active site of cytochrome c oxidase (CcO) using both the continuum electrostatic calculations and the microscopic simulations. The group of interest is a ligand to Cu(B) center of CcO, which has been previously suggested to play the role of the proton pumping element in the enzyme; the group is located near a large internal water cavity in the protein. Using the nonpolarizable Amber-99 force field in molecular dynamics (MD) simulations, we have calculated the nuclear part of the reaction-field energy of charging of the His group and combined it with the electronic part, which we estimated in terms of the electronic continuum (EC) model, to obtain the total reaction-field energy of charging. The total free energy obtained in this MDEC approach was then compared with that calculated using pure continuum electrostatic model with variable dielectric parameters. The dielectric constant for the "dry" protein and that of the internal water cavity of CcO were determined as those parameters that provide best agreement between the continuum and microscopic MDEC model. The nuclear (MD) polarization alone (without electronic part) of a dry protein was found to correspond to an unphysically low dielectric constant of only about 1.3, whereas the inclusion of electronic polarizability increases the protein dielectric constant to 2.6-2.8. A detailed analysis is presented as to how the protein structure should be selected for the continuum calculations, as well as which probe and atomic radii should be used for cavity definition. The dielectric constant of the internal water cavity was found to be 80 or even higher using "standard" parameters of water probe radius, 1.4 A, and protein atomic radii from the MD force field for cavity description; such high values are ascribed to the fact that the standard procedure produces unphysically small cavities. Using x-ray data for

  2. Effects of electrostatic correlations on electrokinetic phenomena.

    PubMed

    Storey, Brian D; Bazant, Martin Z

    2012-11-01

    The classical theory of electrokinetic phenomena is based on the mean-field approximation that the electric field acting on an individual ion is self-consistently determined by the local mean charge density. This paper considers situations, such as concentrated electrolytes, multivalent electrolytes, or solvent-free ionic liquids, where the mean-field approximation breaks down. A fourth-order modified Poisson equation is developed that captures the essential features in a simple continuum framework. The model is derived as a gradient approximation for nonlocal electrostatics of interacting effective charges, where the permittivity becomes a differential operator, scaled by a correlation length. The theory is able to capture subtle aspects of molecular simulations and allows for simple calculations of electrokinetic flows in correlated ionic fluids. Charge-density oscillations tend to reduce electro-osmotic flow and streaming current, and overscreening of surface charge can lead to flow reversal. These effects also help to explain the suppression of induced-charge electrokinetic phenomena at high salt concentrations. PMID:23214872

  3. Accelerating electrostatic interaction calculations with graphical processing units based on new developments of Ewald method using non-uniform fast Fourier transform.

    PubMed

    Yang, Sheng-Chun; Wang, Yong-Lei; Jiao, Gui-Sheng; Qian, Hu-Jun; Lu, Zhong-Yuan

    2016-01-30

    We present new algorithms to improve the performance of ENUF method (F. Hedman, A. Laaksonen, Chem. Phys. Lett. 425, 2006, 142) which is essentially Ewald summation using Non-Uniform FFT (NFFT) technique. A NearDistance algorithm is developed to extensively reduce the neighbor list size in real-space computation. In reciprocal-space computation, a new algorithm is developed for NFFT for the evaluations of electrostatic interaction energies and forces. Both real-space and reciprocal-space computations are further accelerated by using graphical processing units (GPU) with CUDA technology. Especially, the use of CUNFFT (NFFT based on CUDA) very much reduces the reciprocal-space computation. In order to reach the best performance of this method, we propose a procedure for the selection of optimal parameters with controlled accuracies. With the choice of suitable parameters, we show that our method is a good alternative to the standard Ewald method with the same computational precision but a dramatically higher computational efficiency. PMID:26584145

  4. 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.

  5. Electrostatic precipitator manual

    SciTech Connect

    McDonald, J.R.; Dean, A.H.

    1982-01-01

    Studies performed by various individuals and organizations on the application of electrostatic precipitators to the collection of fly ash produced in the combustion of pulverized fuel are summarized in this manual. The scope of the studies evaluated include full scale precipitators and laboratory investigations. It covers measurement of fly ash resistivity, rapping reentrainment, conditioning agents, fundamental operations of hot-side precipitators. The major chapter headings are: Terminology and General Design Features Associated with Electrostatic Precipitators Used to Collect Fly Ash Particles; Fundamental Principles of Electrostatic Precipitation; Limiting Factors Affecting Precipitator Performance; Use of Electrostatic Precipitators for the Collection of Fly Ash; Analysis of Factors influencing ESP Performance; Emissions from Electrostatic Precipitators; Choosig an Electrostatic Precipitator: Cold-side versus Hot-side; Safety Aspects of Working with Electrostatic Precipitators; Maintenance Procedures; Troubleshooting; An Electrostatic Precipitator Computer Model; Features of a Well-equipped Electrostatic Precipitator.

  6. 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.

  7. A continuum solvent model of the multipolar dispersion solvation energy.

    PubMed

    Duignan, Timothy T; Parsons, Drew F; Ninham, Barry W

    2013-08-15

    The dispersion energy is an important contribution to the total solvation energies of ions and neutral molecules. Here, we present a new continuum model calculation of these energies, based on macroscopic quantum electrodynamics. The model uses the frequency dependent multipole polarizabilities of molecules in order to accurately calculate the dispersion interaction of a solute particle with surrounding water molecules. It includes the dipole, quadrupole, and octupole moment contributions. The water is modeled via a bulk dielectric susceptibility with a spherical cavity occupied by the solute. The model invokes damping functions to account for solute-solvent wave function overlap. The assumptions made are very similar to those used in the Born model. This provides consistency and additivity of electrostatic and dispersion (quantum mechanical) interactions. The energy increases in magnitude with cation size, but decreases slightly with size for the highly polarizable anions. The higher order multipole moments are essential, making up more than 50% of the dispersion solvation energy of the fluoride ion. This method provides an accurate and simple way of calculating the notoriously problematic dispersion contribution to the solvation energy. The result establishes the importance of using accurate calculations of the dispersion energy for the modeling of solvation. PMID:23837890

  8. Observations of Electrostatic and Electromagnetic Waves in the Earth's Magnetosphere.

    NASA Astrophysics Data System (ADS)

    Filbert, Paul Charles

    Using data from the University of Minnesota Plasma Wave Experiment aboard the IMP-6 (Explorer 43) satellite, three topics are addressed. The first concerns the wave lengths of certain electrostatic waves in the earth's magnetosphere. Using the fact that the X and Y dipole antennas on IMP-6 are of unequal length, the antenna response to electrostatic waves is calculated as a function of wavelength. This result is used to experimentally determine the wavelengths of Bernstein mode waves observed just beyond the plasmapause. These wavelengths are then used in conjunction with present theoretical models to determine the energy of the electrons driving these waves and a range of energies between (TURN) several tens to (TURN) several hundreds of electron volts is found. This procedure is also applied to Langmuir waves observed upstream of the earth's bow shock and the results are in good agreement with theoretical predictions. Second it is demonstrated that enhanced levels of the so-called continuum radiation are correlated with AE enhancements. In addition, a source region of continuum radiation is directly observed and movement of the source region is seen which is consistent with a cloud of electrons having been injected into the night side magnetosphere and undergoing gradient drifts in an eastward direction towards local dawn. This drift movement is then used to estimate the energy of the electrons which produce the observed continuum enhancement and a range between 10 kev to 50 kev is found. Spectral properties of the directly observed source are also presented, and indicate a high frequency spectral index of (TURN)f('-5.5). A new type of continuum radiation which correlates with TKR on a time scale of (TURN)1 minute is also observed and is found to have a source region distinct from that mentioned above. Third, a correlation between TKR and VLF auroral hiss has been observed for several high latitude passes of IMP-6 through the midnight auroral zone. This

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

    NASA Astrophysics Data System (ADS)

    Sorimachi, Jun-ya; Okada, Susumu

    2016-08-01

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

  10. Fluctuations between stabilizing and destabilizing electrostatic contributions of ion pairs in conformers of the c-Myc-Max leucine zipper.

    PubMed

    Kumar, S; Nussinov, R

    2000-12-01

    In solution proteins often exhibit backbone and side-chain flexibility. Yet electrostatic interactions in proteins are sensitive to motions. Hence, here we study the contribution of ion pairs toward protein stability in a range of conformers which sample the conformational space in solution. Specifically, we focus on the electrostatic contributions of ion pairs to the stability of each of the conformers in the NMR ensemble of the c-Myc-Max leucine zipper and to their average energy minimized structure. We compute the electrostatic contributions of inter- and intra-helical ion pairs and of an ion pair network. We find that the electrostatic contributions vary considerably among the 40 NMR conformers. Each ion pair, and the network, fluctuates between being stabilizing and being destabilizing. This fluctation reflects the variability in the location of the ion pairing residues and in the geometric orientation of these residues, both with respect to each other and with respect to other charged groups in the rest of the protein. Ion pair interactions in the c-Myc-Max leucine zipper in solution depend on the protein conformer which is analyzed. Hence, the overall stabilizing (or destabilizing) contribution of an ion pair is conformer population-dependent. This study indicates that free energy calculations performed using the continuum electrostatics methodology are sensitive to protein conformational details.

  11. 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.

  12. A Role for Weak Electrostatic Interactions in Peripheral Membrane Protein Binding.

    PubMed

    Khan, Hanif M; He, Tao; Fuglebakk, Edvin; Grauffel, Cédric; Yang, Boqian; Roberts, Mary F; Gershenson, Anne; Reuter, Nathalie

    2016-03-29

    Bacillus thuringiensis phosphatidylinositol-specific phospholipase C (BtPI-PLC) is a secreted virulence factor that binds specifically to phosphatidylcholine (PC) bilayers containing negatively charged phospholipids. BtPI-PLC carries a negative net charge and its interfacial binding site has no obvious cluster of basic residues. Continuum electrostatic calculations show that, as expected, nonspecific electrostatic interactions between BtPI-PLC and membranes vary as a function of the fraction of anionic lipids present in the bilayers. Yet they are strikingly weak, with a calculated ΔGel below 1 kcal/mol, largely due to a single lysine (K44). When K44 is mutated to alanine, the equilibrium dissociation constant for small unilamellar vesicles increases more than 50 times (∼2.4 kcal/mol), suggesting that interactions between K44 and lipids are not merely electrostatic. Comparisons of molecular-dynamics simulations performed using different lipid compositions reveal that the bilayer composition does not affect either hydrogen bonds or hydrophobic contacts between the protein interfacial binding site and bilayers. However, the occupancies of cation-π interactions between PC choline headgroups and protein tyrosines vary as a function of PC content. The overall contribution of basic residues to binding affinity is also context dependent and cannot be approximated by a rule-of-thumb value because these residues can contribute to both nonspecific electrostatic and short-range protein-lipid interactions. Additionally, statistics on the distribution of basic amino acids in a data set of membrane-binding domains reveal that weak electrostatics, as observed for BtPI-PLC, might be a less unusual mechanism for peripheral membrane binding than is generally thought. PMID:27028646

  13. Electrostatic interactions of Hsp-organizing protein tetratricopeptide domains with Hsp70 and Hsp90: computational analysis and protein engineering.

    PubMed

    Kajander, Tommi; Sachs, Jonathan N; Goldman, Adrian; Regan, Lynne

    2009-09-11

    The Hsp-organizing protein (HOP) binds to the C termini of the chaperones Hsp70 and Hsp90, thus bringing them together so that substrate proteins can be passed from Hsp70 to Hsp90. Because Hsp90 is essential for the correct folding and maturation of many oncogenic proteins, it has become a significant target for anti-cancer drug design. HOP binds to Hsp70 and Hsp90 via two independent tetratricopeptide (TPR) domains, TPR1 and TPR2A, respectively. We have analyzed ligand binding using Poisson-Boltzmann continuum electrostatic calculations, free energy perturbation, molecular dynamics simulations, and site-directed mutagenesis to delineate the contribution of different interactions to the affinity and specificity of the TPR-peptide interactions. We found that continuum electrostatic calculations could be used to guide protein design by removing unfavorable interactions to increase binding affinity, with an 80-fold increase in affinity for TPR2A. Contributions at buried charged residues, however, were better predicted by free energy perturbation calculations. We suggest using a combination of the two approaches for increasing the accuracy of results, with free energy perturbation calculations used only at selected buried residues of the ligand binding pocket. Finally we present the crystal structure of TPR2A in complex with its non-cognate Hsp70 ligand, which provides insight on the origins of specificity in TPR domain-peptide recognition. PMID:19586912

  14. Electrostatically Guided Rydberg Positronium.

    PubMed

    Deller, A; Alonso, A M; Cooper, B S; Hogan, S D; Cassidy, D B

    2016-08-12

    We report experiments in which positronium (Ps) atoms were guided using inhomogeneous electric fields. Ps atoms in Rydberg-Stark states with principal quantum number n=10 and electric dipole moments up to 610 D were prepared via two-color two-photon optical excitation in the presence of a 670  V cm^{-1} electric field. The Ps atoms were created at the entrance of a 0.4 m long electrostatic quadrupole guide, and were detected at the end of the guide via annihilation gamma radiation. When the lasers were tuned to excite low-field-seeking Stark states, a fivefold increase in the number of atoms reaching the end of the guide was observed, whereas no signal was detected when high-field-seeking states were produced. The data are consistent with the calculated geometrical guide acceptance. PMID:27563960

  15. Electrostatically Guided Rydberg Positronium

    NASA Astrophysics Data System (ADS)

    Deller, A.; Alonso, A. M.; Cooper, B. S.; Hogan, S. D.; Cassidy, D. B.

    2016-08-01

    We report experiments in which positronium (Ps) atoms were guided using inhomogeneous electric fields. Ps atoms in Rydberg-Stark states with principal quantum number n =10 and electric dipole moments up to 610 D were prepared via two-color two-photon optical excitation in the presence of a 670 V cm-1 electric field. The Ps atoms were created at the entrance of a 0.4 m long electrostatic quadrupole guide, and were detected at the end of the guide via annihilation gamma radiation. When the lasers were tuned to excite low-field-seeking Stark states, a fivefold increase in the number of atoms reaching the end of the guide was observed, whereas no signal was detected when high-field-seeking states were produced. The data are consistent with the calculated geometrical guide acceptance.

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

    PubMed

    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.

  17. 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.

  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. Rationalizing the effects of modified electrostatic interactions in computer simulations: The dielectric self-consistent field method

    NASA Astrophysics Data System (ADS)

    Boresch, Stefan; Steinhauser, Othmar

    1999-11-01

    The dielectric self-consistent field method, a novel tool to study solvated systems based on continuum electrostatics, is introduced. It permits the qualitative and even semiquantitative calculation of orientational correlation functions, i.e., it gives insights into the orientational structure of a solute-solvent system. Further, modified Coulomb potentials and periodic boundary conditions can easily be integrated. One possible application is rapid, yet detailed methodological studies of the effects resulting from the various modified electrostatic interactions that are used regularly in computer simulations with explicit solvent molecules. As an example, we report the distance dependent Kirkwood g-factor and ion-dipole correlation functions of a solvated glycine zwitterion obtained with a simple cutoff, a shifted potential, two reaction field techniques, and Ewald summation. For the reaction fields and Ewald summation, conducting and adjusted dielectric boundary conditions are compared.

  20. 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.

  1. 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.

  2. 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

  3. Electrostatically controlled micromechanical gyroscope

    NASA Technical Reports Server (NTRS)

    Hawkey, Timothy (Inventor); Torti, Richard (Inventor); Johnson, Bruce (Inventor)

    1994-01-01

    An integrated electrostatically-controlled micromechanical gyroscope with a rotor encompassed within a rotor cavity and electrostatically spun within the cavity. The gyroscope includes a plurality of axial electrostatic rotor actuators above and below the rotor for controlling the axial and tilt position of the rotor within the cavity, and a plurality of radial electrostatic actuators spaced circumferentially around the rotor for controlling the radial and tilt position of the rotor within the cavity. The position of the rotor within the cavity is then resolved to determine the external forces acting on the rotor.

  4. The Aquatic Systems Continuum

    NASA Astrophysics Data System (ADS)

    Winter, T. C.

    2004-12-01

    The Aquatic Systems Continuum is a proposed framework for interrelating the physical, chemical, and biological characteristics of aquatic ecosystems. The continuum can be represented by a three-dimensional matrix that relates aquatic ecosystems to their position within hydrologic flow paths (x-axis, a spatial dimension) and their response to climate variability (y-axis). The z-axis describes the structure of biological communities as they relate to the hydrological conditions defined by the x and y axes. The concept is an extension of the Wetland Continuum that was derived from field studies of a prairie pothole wetland complex in North Dakota. At that site, the hydrologic continuum in space is defined by ground-water flow systems. The wetlands are surface-water expressions of larger ground-water watersheds, in which wetlands serve recharge, flow-through, and discharge functions with respect to ground water. The water balance of the wetlands is dominated by precipitation and evaporation. However, the interaction of the wetlands with ground water, although a small part of their water budget, provides the primary control on delivery of major solutes to and from the wetlands. Having monitored these wetlands for more than 25 years, during which time the site had a complete range of climate conditions from drought to deluge, the response of the aquatic communities to a wide variety of climate conditions has been well documented. The Aquatic Systems Continuum extends the model provided by the Wetland Continuum to include rivers and their interaction with ground water. As a result, both ground water and surface water are used to describe terrestrial water flows for all types of aquatic ecosystems. By using the Aquatic Systems Continuum to describe the hydrologic flow paths in all types of terrain, including exchange with atmospheric water, it is possible to design studies, monitoring programs, and management plans for nearly any type of aquatic ecosystem.

  5. 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

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

    PubMed

    Bardhan, Jaydeep P; Knepley, Matthew G

    2011-09-28

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

  7. 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…

  8. Electrostatic precipitator efficiency enhancement

    SciTech Connect

    Polizzotti, D.M.; Steelhammer, J.C.

    1983-05-24

    Method for enhancing the removal of particles from a particleladen gas stream utilizing an electrostatic precipitator, which comprises treating the gas with morpholine or derivatives thereof. Treated particles are found to also have desirable flow characteristics. Particularly effective compositions for the purpose comprise a combination of the morpholine, or derivative thereof, with an electrostatic precipitator efficiency enhancer, and in particular an alkanolamine.

  9. Analysis of an Electrostatic Wobble Motor

    NASA Astrophysics Data System (ADS)

    Sonobe, Tadashi; Fujita, Hiroyuki

    Analysis of an electrostatic wobble motor is first strictly done by conformal mapping, especially by image method. Capacitances and torques calculated theoretically are in very good agreement with those calculated by FEM simulation, ANSYS, whose relative errors are within 1 %. Then, the effectiveness of detection of commutation timing is suggested by some numerical experiment based on this proposed analysis.

  10. Electrostatic Changes Observed with Narrow Bipolar Pulses

    NASA Astrophysics Data System (ADS)

    Karunarathne, S.; Marshall, T. C.; Stolzenburg, M.; Karunarathna, N.

    2015-12-01

    Narrow bipolar pulses (NBPs) or compact intracloud discharges are impulsive discharges that are considered to be the strongest natural emitters in the HF radio band; they usually occur at high altitudes in some thunderstorms. In the summer of 2011, we collected E-change data with wideband flat-plate antennas (0.16 Hz - 2.5 MHz) at ten stations covering an area of nearly 70 km x 100 km in and around Kennedy Space Center, Florida, USA. On one thunderstorm day, 14 August 2011, we detected 226 positive NBPs, and some observations of these pulses were published in Karunarathne et al. [2015, JGR-atmospheres]. Of these 226 NBPs, 50 (22.1 %) occurred within 10 km horizontally of at least one sensor. All of these closer sensors show electrostatic changes associated with corresponding NBPs, with a net electrostatic change in the main bipolar pulse and with a slower electrostatic change after the bipolar pulse that seems similar to short continuing current immediately after some cloud-to-ground return strokes. Although NBPs have been considered as short duration pulses (10 - 20 microseconds), the electrostatic changes after the main bipolar pulse ranged from 0.7 ms to 34 ms and associated charge moments were calculated. The total duration of the electrostatic E-change was strongly dependent on the distance to the sensors. In this presentation, we will present data for these electrostatic changes, some statistics, and physical background and reasoning for the electrostatic changes.

  11. 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.

  12. Electrostatic Focusing Lens

    NASA Astrophysics Data System (ADS)

    Thomas, Eric; Hopkins, Demitri

    2011-10-01

    We developed an electrostatic focusing lens capable of generating DD reactions, by focusing deuterium ions generated from a pointed emitter at a frozen heavy water target. Due to difficulty with the pointed emitter, we later switched to a hollow cathode design. To model the lenses, chamber, and calculate the dimensions for the design that would maximize ion energy and density, the program SIMION was used. During stable operation, vacuum was hand adjusted around 10-13 mTorr. To keep stable beam, DC voltage generator was varied between 15-25 kV. Hand adjusting was necessary, because at points in the operation the frozen heavy water would release vapor at an increased rate. This caused the pressure to rise and the beam current to spike, creating instabilities and an arc to the lens. Three methods were used to determine successful DD production. (1) Two differently shielded Geiger counters (unshielded and UHMW-PE insulated tube), (2) Spectrophotometer comparing control peaks with heavy water tests, and (3) a calibrated bubble dosimeter specific to neutrons. Analysis of the results suggest the neutrons flux varied from 532 to 1.4 × 106 neutrons/sec, and require further tests to plot and narrow results.

  13. 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.

  14. Teacher Education: A Continuum.

    ERIC Educational Resources Information Center

    Momentum, 1990

    1990-01-01

    This document is a theme issue of the journal "Momentum", devoted to the topic "Teacher Education: A Continuum." It contains 15 articles in the central section and 7 articles in a special section subtitled "The Multicultural Challenge." The following articles on the central theme are presented: (1) "Closing the Gap" concerns fusing the college and…

  15. Extragalactic continuum sources.

    NASA Astrophysics Data System (ADS)

    Valtaoja, E.

    1989-09-01

    As with most other high-frequency radio telescopes, continuum work occupies only a small fraction - currently about 5% - of SEST's total time. The importance of these observations in increasing our understanding of quasars and other extragalactic sources is, however, large.

  16. 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.…

  17. 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

  18. Electrostatic Field Invisibility Cloak

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

    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.

  19. Studying Electrostatic Levitator Specimen

    NASA Technical Reports Server (NTRS)

    2000-01-01

    Kevin Croat of Washington University in St. Louis, MO, examines samples processed in NASA/Marshall Space Flight Center's (MSFC)Electrostatic Levitator Facility. Croat is working with Prof. Kerneth Kelton in investigating undercooling of polytetrahedral phase-forming liquids.

  20. 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.

  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 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.

  3. 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.

  4. 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.

  5. Electrostatic Levitator Layout

    NASA Technical Reports Server (NTRS)

    1998-01-01

    Electrostatic Levitator (ESL) general layout with captions. The ESL uses static electricity to suspend an object (about 2-3 mm in diameter) inside a vacuum chamber while a laser heats the sample until it melts. This lets scientists record a wide range of physical properties without the sample contacting the container or any instruments, conditions that would alter the readings. The Electrostatic Levitator is one of several tools used in NASA's microgravity materials science program.

  6. 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.

  7. 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.

  8. Electrostatics in molecular phenomena

    NASA Astrophysics Data System (ADS)

    Náray-Szabó, G.

    1995-04-01

    Molecular electrostatic potentials (MEP) and fields (MEF) became very popular in the last two decades since they offer a pictorial modeling of complicated molecular events. In this paper we give an overview on applications. We can discuss chemical reactivity in terms of MEP maps: negative and positive regions are preferred by electrophilic and nucleophilic reagents, respectively. We may define the concept of electrostatic enzyme catalysis. In cases when the ground-state polarity of the active site essentially increases in the transition state the catalytic rate enhancement is due to electrostatic stabilization by the polar protein and solvent environment. Crystal surfaces provide strong MEF, thus enhanced reactivity, in their vicinity. Hydration depends also on the electrostatic behaviour. It is possible to define the average MEF of a molecule that is an appropriate descriptor of hydration ability to be used in quantitative structure-activity relationships. Molecular recognition has also important electrostatic aspects. Complementarity and similarity are determined beside steric aspects by electrostatic and hydrophobic factors, as well. We may define hydrophilic and hydrophobic regions around a molecule in terms of the MEF and apply this representation to the study of host-guest complementarity, as well as crystal packing.

  9. 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.

  10. 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(+).

  11. 3D holography: from discretum to continuum

    NASA Astrophysics Data System (ADS)

    Bonzom, Valentin; Dittrich, Bianca

    2016-03-01

    We study the one-loop partition function of 3D gravity without cosmological constant on the solid torus with arbitrary metric fluctuations on the boundary. To this end we employ the discrete approach of (quantum) Regge calculus. In contrast with similar calculations performed directly in the continuum, we work with a boundary at finite distance from the torus axis. We show that after taking the continuum limit on the boundary — but still keeping finite distance from the torus axis — the one-loop correction is the same as the one recently found in the continuum in Barnich et al. for an asymptotically flat boundary. The discrete approach taken here allows to identify the boundary degrees of freedom which are responsible for the non-trivial structure of the one-loop correction. We therefore calculate also the Hamilton-Jacobi function to quadratic order in the boundary fluctuations both in the discrete set-up and directly in the continuum theory. We identify a dual boundary field theory with a Liouville type coupling to the boundary metric. The discrete set-up allows again to identify the dual field with degrees of freedom associated to radial bulk edges attached to the boundary. Integrating out this dual field reproduces the (boundary diffeomorphism invariant part of the) quadratic order of the Hamilton-Jacobi functional. The considerations here show that bulk boundary dualities might also emerge at finite boundaries and moreover that discrete approaches are helpful in identifying such dualities.

  12. 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.

  13. A new constituent of electrostatic energy in semiconductors. An attempt to reformulate electrostatic energy in matter

    NASA Astrophysics Data System (ADS)

    Sallese, Jean-Michel

    2016-06-01

    The concept of electric energy is revisited in detail for semiconductors. We come to the conclusion that the main relationship used to calculate the energy related to the penetration of the electric field in semiconductors is missing a fundamental term. For instance, spatial derivate of the electrostatic energy using the traditional formula fails at giving the correct electrostatic force between semiconductor based capacitor plates, and reveals unambiguously the existence of an extra contribution to the standard electrostatic free energy. The additional term is found to be related to the generation of space charge regions which are predicted when combining electrostatics with semiconductor physics laws, such as for accumulation and inversion layers. On the contrary, no such energy is needed when relying on electrostatics only, as for instance when adopting the so-called full depletion approximation. The same holds for neutral and charged insulators that are still consistent with the customary definition, but these two examples are in fact singular cases. In semiconductors for instance, this additional energy can largely exceed the energy gained by the dipoles, thus becoming the dominant term. This unexpected result clearly asks for a generalization of electrostatic energy in matter in order to reconcile basic concepts of electrostatic energy in the framework of classical physics.

  14. 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.

  15. 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.

  16. Dual excitation multiphase electrostatic drive

    SciTech Connect

    Niino, Toshiki; Higuchi, Toshiro |; Egawa, Saku

    1995-12-31

    A novel electrostatic drive technology named Dual Excitation Multiphase Electrostatic Drive (DEMED) was presented. A basic DEMED consisted of two plastic films in which 3-phase parallel electrodes were embedded and was driven by a 3-phase ac excitation to the electrodes. Static characteristics of DEMED were calculated and tested and the results agreed very well. Three prototype motors of DEMED were fabricated using commercially available technique. The first prototype consisted of a single slider and stator and generated a linear motion with a slider`s motion range of about 5mm. It weighed 7g and generated a power of 1.6W and a thrust force of 4.4N. The second prototype consisted of 50 layer stack of linear motors, summing their outputs. It weighed 3.6kg and generated a propulsive force of 310N being powered with boosted commercial 3-phase electricity. The third prototype consisted of a rotor and a stator in which electrodes were arranged radially and generated rotational motion. The maximum power of 36mW was generated by the prototype weighing only 260mg for its rotor and stator. From the results of the numerical calculation, a practical design methodology for the motor was determined. An optimal design for a motor employing currently available material and fabrication techniques is provided as an example. Analyses predict that force generation over the interfacial area between the slider and stator of this motor would be 3,900N/m{sup 2}.

  17. Screened Electrostatic Interactions in Molecular Mechanics.

    PubMed

    Wang, Bo; Truhlar, Donald G

    2014-10-14

    In a typical application of molecular mechanics (MM), the electrostatic interactions are calculated from parametrized partial atomic charges treated as point charges interacting by radial Coulomb potentials. This does not usually yield accurate electrostatic interactions at van der Waals distances, but this is compensated by additional parametrized terms, for example Lennard-Jones potentials. In the present work, we present a scheme involving radial screened Coulomb potentials that reproduces the accurate electrostatics much more accurately. The screening accounts for charge penetration of one subsystem's charge cloud into that of another subsystem, and it is incorporated into the interaction potential in a way similar to what we proposed in a previous article (J. Chem. Theory Comput. 2010, 6, 3330) for combined quantum mechanical and molecular mechanical (QM/MM) simulations, but the screening parameters are reoptimized for MM. The optimization is carried out with electrostatic-potential-fitted partial atomic charges, but the optimized parameters should be useful with any realistic charge model. In the model we employ, the charge density of an atom is approximated as the sum of a point charge representing the nucleus and inner electrons and a smeared charge representing the outermost electrons; in particular, for all atoms except hydrogens, the smeared charge represents the two outermost electrons in the present model. We find that the charge penetration effect can cause very significant deviations from the popular point-charge model, and by comparison to electrostatic interactions calculated by symmetry-adapted perturbation theory, we find that the present results are considerably more accurate than point-charge electrostatic interactions. The mean unsigned error in electrostatics for a large and diverse data set (192 interaction energies) decreases from 9.2 to 3.3 kcal/mol, and the error in the electrostatics for 10 water dimers decreases from 1.7 to 0.5 kcal

  18. Screened Electrostatic Interactions in Molecular Mechanics.

    PubMed

    Wang, Bo; Truhlar, Donald G

    2014-10-14

    In a typical application of molecular mechanics (MM), the electrostatic interactions are calculated from parametrized partial atomic charges treated as point charges interacting by radial Coulomb potentials. This does not usually yield accurate electrostatic interactions at van der Waals distances, but this is compensated by additional parametrized terms, for example Lennard-Jones potentials. In the present work, we present a scheme involving radial screened Coulomb potentials that reproduces the accurate electrostatics much more accurately. The screening accounts for charge penetration of one subsystem's charge cloud into that of another subsystem, and it is incorporated into the interaction potential in a way similar to what we proposed in a previous article (J. Chem. Theory Comput. 2010, 6, 3330) for combined quantum mechanical and molecular mechanical (QM/MM) simulations, but the screening parameters are reoptimized for MM. The optimization is carried out with electrostatic-potential-fitted partial atomic charges, but the optimized parameters should be useful with any realistic charge model. In the model we employ, the charge density of an atom is approximated as the sum of a point charge representing the nucleus and inner electrons and a smeared charge representing the outermost electrons; in particular, for all atoms except hydrogens, the smeared charge represents the two outermost electrons in the present model. We find that the charge penetration effect can cause very significant deviations from the popular point-charge model, and by comparison to electrostatic interactions calculated by symmetry-adapted perturbation theory, we find that the present results are considerably more accurate than point-charge electrostatic interactions. The mean unsigned error in electrostatics for a large and diverse data set (192 interaction energies) decreases from 9.2 to 3.3 kcal/mol, and the error in the electrostatics for 10 water dimers decreases from 1.7 to 0.5 kcal

  19. The Response Continuum

    SciTech Connect

    Caltagirone, Sergio; Frincke, Deborah A.

    2005-06-17

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

  20. Electrostatically shaped membranes

    NASA Technical Reports Server (NTRS)

    Silverberg, Larry M. (Inventor)

    1994-01-01

    Disclosed is a method and apparatus for electrostatically shaping a membrane suitable for use in antennas or the like, comprising an electrically conductive thin membrane where the periphery of said membrane is free to move in at least one direction, a first charge on the electrically conductive thin membrane to electrostatically stiffen the membrane, a second charge which shapes the electrostatically stiffened thin membrane and a restraint for limiting the movement of at least one point of the thin membrane relative to the second charge. Also disclosed is a method and apparatus for adaptively controlling the shape of the thin membrane by sensing the shape of the membrane and selectively controlling the first and second charge to achieve a desired performance characteristic of the membrane.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. Electrostatic Levitator Operations

    NASA Technical Reports Server (NTRS)

    1998-01-01

    Dr. Jan Rogers and Dr. Michael Robinson operate 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.

  7. 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.

  8. Electrostatic Exclusion of Neutral Solutes from Condensed DNA and Other Charged Phases

    PubMed Central

    Todd, Brian A.

    2009-01-01

    Abstract Motivated by experiments on condensed DNA phases in binary mixtures of water and a low-dielectric solute, we develop a theory for the electrostatic contribution to solute exclusion from a highly charged phase, within the continuum approximation of the medium. Because the electric field is maximum at the surface of each ion, the electrostatic energy is dominated by the Born energy; interactions between charges are of secondary importance. Neglecting interactions and considering only the competition between the Born energy and the free energy of mixing, we predict that low dielectric solutes are excluded from condensed DNA phases in water-cosolvent mixtures. This suggests that the traditional continuum electrostatic approach of modeling binary mixtures with a uniform dielectric constant needs to be modified. The linking of solute exclusion to solute dielectric properties also suggests a mechanism for predicting the electrostatic contribution to preferential hydration of polar and charged surfaces. PMID:19619468

  9. The electrostatic surface term: (I) periodic systems.

    PubMed

    Herce, Henry David; Garcia, Angel Enrique; Darden, Thomas

    2007-03-28

    The authors propose a new approach to understand the electrostatic surface contributions to the interactions of large but finite periodic distributions of charges. They present a simple method to derive and interpret the surface contribution to any electrostatic field produced by a periodic distribution of charges. They discuss the physical and mathematical interpretations of this term. They present several examples and physical details associated with the calculation of the surface term. Finally, they provide a simple derivation of the surface contribution to the virial. This term does not disappear even if tinfoil boundary conditions are applied.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. Studying Electrostatic Levitator Specimen

    NASA Technical Reports Server (NTRS)

    2000-01-01

    Prof. Kerneth Kelton of Washington University in St. Lous, MO, (L) and Dr. Michael Robinson of NASA's Marshall Space Flight Center (MSFC) examine a titanium-iron silicate (TiFeSiO)sample processed in MSFC's Electrostatic Levitator (ESL) Facility (background). Kelton is investigating undercooling of polytetrahedral phase-forming liquids.

  15. 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.

  16. Electrostatic and Allosteric Cooperativity in Ion-Pair Binding: A Quantitative and Coupled Experiment-Theory Study with Aryl-Triazole-Ether Macrocycles.

    PubMed

    Qiao, Bo; Sengupta, Arkajyoti; Liu, Yun; McDonald, Kevin P; Pink, Maren; Anderson, Joseph R; Raghavachari, Krishnan; Flood, Amar H

    2015-08-01

    Cooperative binding of ion pairs to receptors is crucial for the manipulation of salts, but a comprehensive understanding of cooperativity has been elusive. To this end, we combine experiment and theory to quantify ion-pair binding and to separate allostery from electrostatics to understand their relative contributions. We designed aryl-triazole-ether macrocycles (MC) to be semiflexible, which allows ion pairs (NaX; X = anion) to make contact, and to be monocyclic to simplify analyses. A multiequilibrium model allows us to quantify, for the first time, the experimental cooperativity, α, for the equilibrium MC·Na(+) + MC·X(-) ⇌ MC·NaX + MC, which is associated with contact ion-pair binding of NaI (α = 1300, ΔGα = -18 kJ mol(-1)) and NaClO4 (α = 400, ΔGα = -15 kJ mol(-1)) in 4:1 dichloromethane-acetonitrile. We used accurate energies from density functional theory to deconvolute how the electrostatic effects and the allosteric changes in receptor geometry individually contribute to cooperativity. Computations, using a continuum solvation model (dichloromethane), show that allostery contributes ∼30% to overall positive cooperativity. The calculated trend of electrostatic cooperativity using pairs of spherical ions (NaCl > NaBr > NaI) correlates to experimental observations (NaI > NaClO4). We show that intrinsic ionic size, which dictates charge separation distance in contact ion pairs, controls electrostatic cooperativity. This finding supports the design principle that semiflexible receptors can facilitate optimal electrostatic cooperativity. While Coulomb's law predicts the size-dependent trend, it overestimates electrostatic cooperativity; we suggest that binding of the individual anion and cation to their respective binding sites dilutes their effective charge. This comprehensive understanding is critical for rational designs of ion-pair receptors for the manipulation of salts. PMID:26207611

  17. Electrostatic Interactions in Aminoglycoside-RNA Complexes

    PubMed Central

    Kulik, Marta; Goral, Anna M.; Jasiński, Maciej; Dominiak, Paulina M.; Trylska, Joanna

    2015-01-01

    Electrostatic interactions often play key roles in the recognition of small molecules by nucleic acids. An example is aminoglycoside antibiotics, which by binding to ribosomal RNA (rRNA) affect bacterial protein synthesis. These antibiotics remain one of the few valid treatments against hospital-acquired infections by Gram-negative bacteria. It is necessary to understand the amplitude of electrostatic interactions between aminoglycosides and their rRNA targets to introduce aminoglycoside modifications that would enhance their binding or to design new scaffolds. Here, we calculated the electrostatic energy of interactions and its per-ring contributions between aminoglycosides and their primary rRNA binding site. We applied either the methodology based on the exact potential multipole moment (EPMM) or classical molecular mechanics force field single-point partial charges with Coulomb formula. For EPMM, we first reconstructed the aspherical electron density of 12 aminoglycoside-RNA complexes from the atomic parameters deposited in the University at Buffalo Databank. The University at Buffalo Databank concept assumes transferability of electron density between atoms in chemically equivalent vicinities and allows reconstruction of the electron densities from experimental structural data. From the electron density, we then calculated the electrostatic energy of interaction using EPMM. Finally, we compared the two approaches. The calculated electrostatic interaction energies between various aminoglycosides and their binding sites correlate with experimentally obtained binding free energies. Based on the calculated energetic contributions of water molecules mediating the interactions between the antibiotic and rRNA, we suggest possible modifications that could enhance aminoglycoside binding affinity. PMID:25650932

  18. Electrostatic interactions in aminoglycoside-RNA complexes.

    PubMed

    Kulik, Marta; Goral, Anna M; Jasiński, Maciej; Dominiak, Paulina M; Trylska, Joanna

    2015-02-01

    Electrostatic interactions often play key roles in the recognition of small molecules by nucleic acids. An example is aminoglycoside antibiotics, which by binding to ribosomal RNA (rRNA) affect bacterial protein synthesis. These antibiotics remain one of the few valid treatments against hospital-acquired infections by Gram-negative bacteria. It is necessary to understand the amplitude of electrostatic interactions between aminoglycosides and their rRNA targets to introduce aminoglycoside modifications that would enhance their binding or to design new scaffolds. Here, we calculated the electrostatic energy of interactions and its per-ring contributions between aminoglycosides and their primary rRNA binding site. We applied either the methodology based on the exact potential multipole moment (EPMM) or classical molecular mechanics force field single-point partial charges with Coulomb formula. For EPMM, we first reconstructed the aspherical electron density of 12 aminoglycoside-RNA complexes from the atomic parameters deposited in the University at Buffalo Databank. The University at Buffalo Databank concept assumes transferability of electron density between atoms in chemically equivalent vicinities and allows reconstruction of the electron densities from experimental structural data. From the electron density, we then calculated the electrostatic energy of interaction using EPMM. Finally, we compared the two approaches. The calculated electrostatic interaction energies between various aminoglycosides and their binding sites correlate with experimentally obtained binding free energies. Based on the calculated energetic contributions of water molecules mediating the interactions between the antibiotic and rRNA, we suggest possible modifications that could enhance aminoglycoside binding affinity. PMID:25650932

  19. Electrostatic interactions in aminoglycoside-RNA complexes.

    PubMed

    Kulik, Marta; Goral, Anna M; Jasiński, Maciej; Dominiak, Paulina M; Trylska, Joanna

    2015-02-01

    Electrostatic interactions often play key roles in the recognition of small molecules by nucleic acids. An example is aminoglycoside antibiotics, which by binding to ribosomal RNA (rRNA) affect bacterial protein synthesis. These antibiotics remain one of the few valid treatments against hospital-acquired infections by Gram-negative bacteria. It is necessary to understand the amplitude of electrostatic interactions between aminoglycosides and their rRNA targets to introduce aminoglycoside modifications that would enhance their binding or to design new scaffolds. Here, we calculated the electrostatic energy of interactions and its per-ring contributions between aminoglycosides and their primary rRNA binding site. We applied either the methodology based on the exact potential multipole moment (EPMM) or classical molecular mechanics force field single-point partial charges with Coulomb formula. For EPMM, we first reconstructed the aspherical electron density of 12 aminoglycoside-RNA complexes from the atomic parameters deposited in the University at Buffalo Databank. The University at Buffalo Databank concept assumes transferability of electron density between atoms in chemically equivalent vicinities and allows reconstruction of the electron densities from experimental structural data. From the electron density, we then calculated the electrostatic energy of interaction using EPMM. Finally, we compared the two approaches. The calculated electrostatic interaction energies between various aminoglycosides and their binding sites correlate with experimentally obtained binding free energies. Based on the calculated energetic contributions of water molecules mediating the interactions between the antibiotic and rRNA, we suggest possible modifications that could enhance aminoglycoside binding affinity.

  20. Intermolecular electrostatic energies using density fitting.

    PubMed

    Cisneros, G Andrés; Piquemal, Jean-Philip; Darden, Thomas A

    2005-07-22

    A method is presented to calculate the electron-electron and nuclear-electron intermolecular Coulomb interaction energy between two molecules by separately fitting the unperturbed molecular electron density of each monomer. This method is based on the variational Coulomb fitting method which relies on the expansion of the ab initio molecular electron density in site-centered auxiliary basis sets. By expanding the electron density of each monomer in this way the integral expressions for the intermolecular electrostatic calculations are simplified, lowering the operation count as well as the memory usage. Furthermore, this method allows the calculation of intermolecular Coulomb interactions with any level of theory from which a one-electron density matrix can be obtained. Our implementation is initially tested by calculating molecular properties with the density fitting method using three different auxiliary basis sets and comparing them to results obtained from ab initio calculations. These properties include dipoles for a series of molecules, as well as the molecular electrostatic potential and electric field for water. Subsequently, the intermolecular electrostatic energy is tested by calculating ten stationary points on the water dimer potential-energy surface. Results are presented for electron densities obtained at four different levels of theory using two different basis sets, fitted with three auxiliary basis sets. Additionally, a one-dimensional electrostatic energy surface scan is performed for four different systems (H2O dimer, Mg2+-H2O, Cu+-H2O, and n-methyl-formamide dimer). Our results show a very good agreement with ab initio calculations for all properties as well as interaction energies.

  1. Electrostatic doping in oxide heterostructures.

    NASA Astrophysics Data System (ADS)

    Demkov, Alexander A.; Lee, Jaekwang; Sai, Na

    2009-03-01

    Recent experiments on perovskite heterostructures grown by methods ranging from molecular beam epitaxy to pulsed laser deposition suggest the existence of two dimensional electron gas of high mobility at the oxide/oxide interface, and even a possibility of a superconducting state. Both p-type and n-type interfaces have been reported. However, the origin of charge in these insulating materials is still under debate. We report a first-principles study of several heterostructures where we employ the internal filed in a polar oxide LaAlO3 to demonstrate the possibility of the electrostatic doping, an effect similar to a well known polar catastrophe in e.g., III-V semiconductors. We use density functional theory at the LDA+U level. We mainly focus on the electronic structure of the oxide/oxide junctions. The results of our calculations suggest that once the critical thickness of the aluminate layer is reached the internal electric field is sufficient to produce the electrostatic doping. We will discuss simple estimates for the temperature of the superconducting transition and the role of oxygen-related defects such as vacancies in the electronic structure and thermodynamic stability of these fascinating oxide structures.

  2. Electrostatics in sandstorms and earthquakes

    NASA Astrophysics Data System (ADS)

    Shinbrot, Troy; Thyagu, Nirmal; Paehtz, Thomas; Herrmann, Hans

    2010-11-01

    We present new data demonstrating (1) that electrostatic charging in sandstorms is a necessary outcome in a class of rapid collisional flows, and (2) that electrostatic precursors to slip events - long reported in earthquakes - can be reproduced in the laboratory.

  3. A new finite element and finite difference hybrid method for computing electrostatics of ionic solvated biomolecule

    NASA Astrophysics Data System (ADS)

    Ying, Jinyong; Xie, Dexuan

    2015-10-01

    The Poisson-Boltzmann equation (PBE) is one widely-used implicit solvent continuum model for calculating electrostatics of ionic solvated biomolecule. In this paper, a new finite element and finite difference hybrid method is presented to solve PBE efficiently based on a special seven-overlapped box partition with one central box containing the solute region and surrounded by six neighboring boxes. In particular, an efficient finite element solver is applied to the central box while a fast preconditioned conjugate gradient method using a multigrid V-cycle preconditioning is constructed for solving a system of finite difference equations defined on a uniform mesh of each neighboring box. Moreover, the PBE domain, the box partition, and an interface fitted tetrahedral mesh of the central box can be generated adaptively for a given PQR file of a biomolecule. This new hybrid PBE solver is programmed in C, Fortran, and Python as a software tool for predicting electrostatics of a biomolecule in a symmetric 1:1 ionic solvent. Numerical results on two test models with analytical solutions and 12 proteins validate this new software tool, and demonstrate its high performance in terms of CPU time and memory usage.

  4. 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.

  5. 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.

  6. Electrostatic Levitator Vacuum Chamber

    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 (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.

  7. Electrostatic Levitator Vaccum 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 (the beam passes through the window at left), positioning 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.

  8. 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

  9. 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.

  10. 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.

  11. Electrostatic containerless processing system

    NASA Astrophysics Data System (ADS)

    Rulison, Aaron J.; Watkins, John L.; Zambrano, Brian

    1997-07-01

    We introduce a materials science tool for investigating refractory solids and melts: the electrostatic containerless processing system (ESCAPES). ESCAPES maintains refractory specimens of materials in a pristine state by levitating and heating them in a vacuum chamber, thereby avoiding the contaminating influences of container walls and ambient gases. ESCAPES is designed for the investigation of thermophysical properties, phase equilibria, metastable phase formation, undercooling and nucleation, time-temperature-transformation diagrams, and other aspects of materials processing. ESCAPES incorporates several design improvements over prior electrostatic levitation technology. It has an informative and responsive computer control system. It has separate light sources for heating and charging, which prevents runaway discharging. Both the heating and charging light sources are narrow band, which allows the use of optical pyrometry and other diagnostics at all times throughout processing. Heat is provided to the levitated specimens by a 50 W Nd:YAG laser operating at 1.064 μm. A deuterium arc lamp charges the specimen through photoelectric emission. ESCAPES can heat metals, ceramics, and semiconductors to temperatures exceeding 2300 K; specimens range in size from 1 to 3 mm diam. This article describes the design, capabilities, and applications of ESCAPES, focusing on improvements over prior electrostatic levitation technology.

  12. Electrostatic modeling for LISA

    NASA Astrophysics Data System (ADS)

    Shaul, Diana N.; Sumner, Timothy J.

    2003-03-01

    LISA employs a capacitive sensing and positioning system to maintain the drag free environment of the test masses acting as interferometer mirror elements. The need for detailed electrostatic modelling of the test mass environment arises because any electric field gradient or variation associated with test mass motion can couple the test mass to its housing, and ultimately the spacecraft. Cross-couplings between components in the system can introduce direct couplings between sensing signals, sensing axes and the drive signal. A variation in cross-couplings or asymmetry in the system can introduce capacitance gradients and second derivatives, giving rise to unwanted forces and spring constant modifications. These effects will vary dependent on the precise geometry of the system and will also tend to increase the sensitivity to accumulated charge on the test-mass. Presented are the results of a systematic study of the effect of the principal geometry elements (e.g. machining imperfections, the caging mechanism) on the test mass electrostatic environment, using the finite element code ANSYS. This work is part of an ongoing ESA study into drag-free control for LISA and the LTP on SMART 2 and ultimately aims to eliminate geometries that introduce too large a disturbance and optimise the electrostatic design.

  13. 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.

  14. 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.

  15. Rethinking Electrostatic Solvers in Particle Simulations for the Exascale Era

    NASA Astrophysics Data System (ADS)

    Deca, Jan; Markidis, Stefano; Lapenta, Giovanni; Járleberg, Erik; Apostolov, Rossen; Laure, Erwin

    2012-10-01

    In preparation to the exascale era, an alternative approach to calculate the electrostatic forces in Particle Mesh (PM) methods is proposed. While the traditional techniques are based on the calculation of the electrostatic potential by solving the Poisson equation, in the new approach the electric field is calculated by solving Ampère's law. When the Ampere's law is discretized explicitly in time, the electric field values on the mesh are simply updated from the previous values. In this way, the electrostatic solver becomes an embarrassingly parallel problem, making the algorithm extremely scalable and suitable for exascale computing platforms. An implementation PM code with the new electrostatic solver is presented to show that the proposed method produces correct results. It is a very promising algorithm for exascale PM simulations.

  16. Electrostatic contribution to the bending of DNA.

    PubMed

    Sivolob, A; Khrapunov, S N

    1997-09-01

    A model is derived that accounts for the short-range electrostatic contribution to the bending of DNA molecule in solution and in complexes with proteins in terms of the non-linear Poisson-Boltzmann equation. We defined that the short-range electrostatic interactions depend on the changes of the polyion surface charge density under deformation, while the long-range interactions depend on the bending-induced changes in distances between each two points along the polyion axis. After an appropriate simplification of the Poisson-Boltzmann equation, the short-range term is calculated separately giving the lower limit for the electrostatic contribution to the DNA persistence length. The result is compared with the theoretical approaches developed earlier [M. Fixman, J. Chem. Phys. 76 (1982) 6346; M. Le Bret, J. Chem. Phys. 76 (1982) 6243] and with the experimental data. The conclusion is made that the results of Fixman-Le Bret, which took into account both types of the electrostatic interactions for a uniformly bent polyion, give the upper limit for the electrostatic persistence length at low ionic strength, and the actual behavior of the DNA persistence length lies between two theoretical limits. Only the short-range term is significant at moderate-to-high ionic strength where our results coincide with the predictions of Fixman-Le Bret. The bending of DNA on the protein surface that is accompanied by an asymmetric neutralization of the DNA charge is also analyzed. In this case, the electrostatic bending energy gives a significant favorite contribution to the total bending energy of DNA. Important implications to the mechanisms of DNA-protein interactions, particularly in the nucleosome particle, are discussed.

  17. 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

  18. 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

  19. 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

  20. The virial theorem for the Polarizable Continuum Model.

    PubMed

    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.

  1. The virial theorem for the Polarizable Continuum Model.

    PubMed

    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. PMID:24588153

  2. On the proper formulation of Maxwellian electrodynamics for continuum mechanics

    NASA Astrophysics Data System (ADS)

    Weile, Daniel S.; Hopkins, David A.; Gazonas, George A.; Powers, Brian M.

    2014-05-01

    Despite the importance of electromagnetomechanical physics to processes ranging from piezoelectricity to the dynamics of electron beams, confusion abounds in the continuum mechanics literature as to how Maxwell's equations of electrodynamics should be formulated in the material frame of continuum mechanics. Current formulations in the literature conflict as to the manner in which the authors define fields, derive constitutive relations, and interpret contradictory formulations. The difficulties persist even when the phenomena described are electrostatic. This paper will demonstrate that the perplexity arises from two sources: a misunderstanding of the limitations of material frame descriptions, and the failure to appreciate the centrality of relativity theory to the formulation of electrodynamic equations in the vicinity of mechanical motion. Two new formulations of Maxwell's equations are provided that avoid the paradoxes of earlier formulations and thus describe the physics clearly and without self-contradiction.

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. Brownian dynamics simulations of ions channels: A general treatment of electrostatic reaction fields for molecular pores of arbitrary geometry

    NASA Astrophysics Data System (ADS)

    Im, Wonpil; Roux, Benoît

    2001-09-01

    A general method has been developed to include the electrostatic reaction field in Brownian dynamics (BD) simulations of ions diffusing through complex molecular channels of arbitrary geometry. Assuming that the solvent is represented as a featureless continuum dielectric medium, a multipolar basis-set expansion is developed to express the reaction field Green's function. A reaction field matrix, which provides the coupling between generalized multipoles, is calculated only once and stored before the BD simulations. The electrostatic energy and forces are calculated at each time step by updating the generalized multipole moments. The method is closely related to the generalized solvent boundary potential [Im et al., J. Chem. Phys. 114, 2924 (2001)] which was recently developed to include the influence of distant atoms on a small region part of a large macromolecular system in molecular dynamics simulations. It is shown that the basis-set expansion is accurate and computationally inexpensive for three simple models such as a spherical ionic system, an impermeable membrane system, and a cylindrical pore system as well as a realistic system such as OmpF porin with all atomic details. The influence of the static field and the reaction field on the ion distribution and conductance in the OmpF channel is studied and discussed.

  11. Electrostatic particle precipitator

    SciTech Connect

    Uchiya, T.; Hikizi, S.; Yabuta, H.

    1984-04-03

    An electrostatic particle precipitator for removing dust particles from a flue gas. The precipitator includes a plurality of collecting electrodes in the shape of plates mounted on endless chains and moving between a first region through which flue gas to be treated flows and a second region where the flow of gas is extremely scarce. A dust removal mechanism is positioned in the second region to remove dust which accumulates on the electrode plates. The moving speed of the collecting electrodes is controlled within a certain range to maintain a prescribed thickness of dust on the electrodes whereby the ocurrence of reverse ionization phenomenon is prevented.

  12. 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

  13. Physics of electrostatic lens

    NASA Astrophysics Data System (ADS)

    1981-09-01

    The purpose of this program was to study the physics of the ion-energy boosting electrostatic lens for collective ion acceleration in the Luce diode. Extensive work was done in preparation for experiments on the PI Pulserad 1150. Analytic work was done on the orbit of protons in a mass spectrometer and a copper stack for nuclear activation analysis of proton energy spectrum has been designed. Unfortunately, a parallel program which would provide the Luce diode for the collective ion acceleration experiment never materialized. As a result no experiments were actually performed on the Pulserad 1150.

  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. 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.

  16. Electrostatic Suspension Using Variable Capacitors

    NASA Astrophysics Data System (ADS)

    Kato, Takaaki; Tsukada, Shinya; Ishino, Yuji; Takasaki, Masaya; Mizuno, Takeshi

    A new control system for electrostatic actuators was applied to electrostatic suspension. This control system was designed to use a variable capacitor connected with an electrostatic actuator in series. A high voltage was applied to this connection. The voltage applied to the actuator was controlled by varying the capacitance of the variable capacitor. An experimental apparatus was fabricated in order to study the controllability of electrostatic force using this control system. The experimental results show that electrostatic force can be controlled both statically and dynamically. Another experimental apparatus was fabricated for demonstrating the feasibility of electrostatic suspension. This apparatus was able to control the 3-DOF vertical motions of the suspended object. Non-contact suspension was achieved with the developed control system using variable capacitors.

  17. Wave-particle transport by weak electrostatic flow shear fluctuations

    NASA Technical Reports Server (NTRS)

    Gary, S. P.; Schwartz, S. J.

    1981-01-01

    A description is presented of the first consistent theoretical treatment of transport due to weak electrostatic fluctuations from microinstabilities driven by a shear in plasma flow parallel to a uniform magnetic field. The model used considers electrostatic fluctuations in a Vlasov plasma with sheared bulk velocity parallel to a uniform magnetic field. The linear stability theory for the model has been studied by Gary and Schwartz (1980). In the current investigation, a calculation is performed of the wave-particle transport associated with the electrostatic flow shear instability.

  18. The Intraprofessional Continuum and Cleft.

    PubMed

    Jensen, Clyde B

    2016-08-01

    The continuum cleft is a costly and precarious gap that divides professions on the health professions' continuum. It is an interprofessional phenomenon that is encouraged because health care professions protect their members in professional silos and isolate competing professions in professional cysts. This article uses case studies of the allopathic, osteopathic, naturopathic, and chiropractic professions to contemplate the existence, consequences, and possible mitigation of intraprofessional silos, cysts, and clefts. PMID:27574493

  19. 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

  20. 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.

  1. 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.

  2. Fast Analytical Methods for Macroscopic Electrostatic Models in Biomolecular Simulations*

    PubMed Central

    Xu, Zhenli; Cai, Wei

    2013-01-01

    We review recent developments of fast analytical methods for macroscopic electrostatic calculations in biological applications, including the Poisson–Boltzmann (PB) and the generalized Born models for electrostatic solvation energy. The focus is on analytical approaches for hybrid solvation models, especially the image charge method for a spherical cavity, and also the generalized Born theory as an approximation to the PB model. This review places much emphasis on the mathematical details behind these methods. PMID:23745011

  3. Cluster-continuum quantum mechanical models to guide the choice of anions for Li{sup +}-conducting ionomers

    SciTech Connect

    Shiau, Huai-Suen; Janik, Michael J.; Liu, Wenjuan; Colby, Ralph H.

    2013-11-28

    A quantum-mechanical investigation on Li poly(ethylene oxide)-based ionomers was performed in the cluster-continuum solvation model (CCM) that includes specific solvation in the first shell surrounding the cation, all surrounded by a polarizable continuum. A four-state model, including a free Li cation, Li{sup +}-anion pair, triple ion, and quadrupole was used to represent the states of Li{sup +} within the ionomer in the CCM. The relative energy of each state was calculated for Li{sup +} with various anions, with dimethyl ether representing the ether oxygen solvation. The population distribution of Li{sup +} ions among states was estimated by applying Boltzmann statistics to the CCM energies. Entropy difference estimates are needed for populations to better match the true ionomer system. The total entropy change is considered to consist of four contributions: translational, rotational, electrostatic, and solvent immobilization entropies. The population of ion states is reported as a function of Bjerrum length divided by ion-pair separation with/without entropy considered to investigate the transition between states. Predicted concentrations of Li{sup +}-conducting states (free Li{sup +} and positive triple ions) are compared among a series of anions to indicate favorable features for design of an optimal Li{sup +}-conducting ionomer; the perfluorotetraphenylborate anion maximizes the conducting positive triple ion population among the series of anions considered.

  4. Electrostatic precipitator having apparatus for sensing electrostatic field strengths

    SciTech Connect

    Perryman, J.W.

    1984-03-27

    An electrostatic precipitator (10) of the type having a casing (12) defining a precipitation chamber (6) wherein a plurality of discharge electrode frames (32) are disposed alternately between a plurality of collecting electrode plates (20). Paired probe devices (50) are mounted on the collecting electrode plates for sensing the strength of the electrostatic field generated by at least one discharge electrode wire (36) at at least one location on each of the collecting electrode plates (20) disposed adjacent thereto. The electrostatic field strength sensed by the paired probe devices are compared with each other to provide an indication of the degree of imbalance, if any, existing between the sensed electrostatic fields experienced by the bounding electrode plates. The existence of an imbalance and the strength of the electrostatic fields on the bounding collecting electrode plates and the degree of any such imbalance provide an indication of whether or not the discharge electrode frame is properly positioned within the assembly of collecting electrode plates.

  5. Edge gyrokinetic theory and continuum simulations

    NASA Astrophysics Data System (ADS)

    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.

    2007-08-01

    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 plateau 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.

  6. 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.

  7. 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.

  8. Pcetk: A pDynamo-based Toolkit for Protonation State Calculations in Proteins.

    PubMed

    Feliks, Mikolaj; Field, Martin J

    2015-10-26

    Pcetk (a pDynamo-based continuum electrostatic toolkit) is an open-source, object-oriented toolkit for the calculation of proton binding energetics in proteins. The toolkit is a module of the pDynamo software library, combining the versatility of the Python scripting language and the efficiency of the compiled languages, C and Cython. In the toolkit, we have connected pDynamo to the external Poisson-Boltzmann solver, extended-MEAD. Our goal was to provide a modern and extensible environment for the calculation of protonation states, electrostatic energies, titration curves, and other electrostatic-dependent properties of proteins. Pcetk is freely available under the CeCILL license, which is compatible with the GNU General Public License. The toolkit can be found on the Web at the address http://github.com/mfx9/pcetk. The calculation of protonation states in proteins requires a knowledge of pKa values of protonatable groups in aqueous solution. However, for some groups, such as protonatable ligands bound to protein, the pKa aq values are often difficult to obtain from experiment. As a complement to Pcetk, we revisit an earlier computational method for the estimation of pKa aq values that has an accuracy of ± 0.5 pKa-units or better. Finally, we verify the Pcetk module and the method for estimating pKa aq values with different model cases.

  9. 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)

  10. Electrostatic forces in the Poisson-Boltzmann systems.

    PubMed

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

    2013-09-01

    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. PMID:24028101

  11. 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. PMID:24920153

  12. 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

  13. 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

    2009-05-01

    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

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. Ligand Affinities Estimated by Quantum Chemical Calculations.

    PubMed

    Söderhjelm, Pär; Kongsted, Jacob; Ryde, Ulf

    2010-05-11

    We present quantum chemical estimates of ligand-binding affinities performed, for the first time, at a level of theory for which there is a hope that dispersion and polarization effects are properly accounted for (MP2/cc-pVTZ) and at the same time effects of solvation, entropy, and sampling are included. We have studied the binding of seven biotin analogues to the avidin tetramer. The calculations have been performed by the recently developed PMISP approach (polarizable multipole interactions with supermolecular pairs), which treats electrostatic interactions by multipoles up to quadrupoles, induction by anisotropic polarizabilities, and nonclassical interactions (dispersion, exchange repulsion, etc.) by explicit quantum chemical calculations, using a fragmentation approach, except for long-range interactions that are treated by standard molecular-mechanics Lennard-Jones terms. In order to include effects of sampling, 10 snapshots from a molecular dynamics simulation are studied for each biotin analogue. Solvation energies are estimated by the polarized continuum model (PCM), coupled to the multipole-polarizability model. Entropy effects are estimated from vibrational frequencies, calculated at the molecular mechanics level. We encounter several problems, not previously discussed, illustrating that we are first to apply such a method. For example, the PCM model is, in the present implementation, questionable for large molecules, owing to the use of a surface definition that gives numerous small cavities in a protein. PMID:26615702

  1. 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

  2. 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.

  3. 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.

  4. Using visualizations to teach electrostatics

    NASA Astrophysics Data System (ADS)

    Casperson, Janet M.; Linn, Marcia C.

    2006-04-01

    We investigate the effect of visualizations of electrostatics phenomena on students' ability to integrate microscopic and macroscopic views of electrostatics in the context of a technology-enhanced inquiry project that features particle interactions. We used knowledge integration instructional design patterns to determine activity sequences. A pretest/post-test design was used to assess the students' overall gains. The results from the implementation of the project in two classes demonstrate that it helped students form a more integrated understanding of electrostatics. An analysis of student responses to prompts embedded with the visualizations reveals that interactions with the visualizations played a significant role in increasing understanding.

  5. Electrostatic Tractor Analysis for GEO Debris Remediation

    NASA Astrophysics Data System (ADS)

    Hogan, Erik A.

    work, eccentric orbits and plane changes are also considered. Requirements on relative positioning of the tug and debris for various orbit corrections are identified for the different orbit corrections. In some cases, the tug must maneuver around the debris at particular locations in the orbit, but the incurred performance losses during this repositioning are minimal. Co-planar reorbiting maneuvers with corrections of several kilometers per day are achievable, but large scale plane changes are not. A first-order analytic current model is used to calculate the charging on tug debris during the charge transfer process. The model includes plasma currents, photoelectron current, secondary electron emission, and electron beam current. The effects of nominal changes (as a function of local time) in GEO space weather conditions on tractor performance are characterized. While the electron beam current can be modified to compensate for these changes, maintaining a fixed beam current achieves similar performance. The impacts of the relative sizes of tug and deputy are studied to determine thresholds where charge transfer is no longer possible, and the effects on tractor performance are considered. The simultaneous emission of an electron beam (onto the debris) and an ion beam (into space) is considered as a means for improving tractor performance. For smaller tug vehicles, this simultaneous emission allows for significant performance increases, enabling the tug to tow larger debris objects. The benefits are not as pronounced for larger tug vehicles. The debris object emits photoelectrons and secondary electrons that may be recaptured by the positively charged tug. NASCAP-2K is used to provide an estimate about the severity of this back flux. It is not found to hinder performance of the electrostatic tractor. Overall, the study supports the feasibility of the electrostatic tractor for GEO debris remediation, and helps to identify areas for further research.

  6. 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.

  7. 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. PMID:25135067

  8. Population transfer through the continuum

    SciTech Connect

    Nakajima, T.; Elk, M.; Zhang, J.; Lambropoulos, P. Foundation of Research and Technology Hellas, Institute of Electronic Structure and Laser and Department of Physics, University of Crete, P.O. Box 1527, Heraklion 711 10, Crete Department of Physics, University of Southern California, Los Angeles, California 90089-0484 )

    1994-08-01

    We show that complete population transfer is not in general possible through continuum intermediate states. We present a formal theoretical argument and supporting numerical results. In addition, the behavior of the system is compared with the well-known [Lambda] system.

  9. Parameter identification in continuum models

    NASA Technical Reports Server (NTRS)

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

    1983-01-01

    Approximation techniques for use in numerical schemes for estimating spatially varying coefficients in continuum models such as those for Euler-Bernoulli beams are discussed. The techniques are based on quintic spline state approximations and cubic spline parameter approximations. Both theoretical and numerical results are presented. Previously announced in STAR as N83-28934

  10. Parameter identification in continuum models

    NASA Technical Reports Server (NTRS)

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

    1983-01-01

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

  11. A continuum of care model.

    PubMed

    Godchaux, C W; Travioli, J; Hughes, L A

    1997-11-01

    An interdisciplinary documentation tool provides a composite of all of the planning activities that occur relative to each individual patient and his/her family before discharge. In response to the Joint Commission on Accreditation of Healthcare Organization's mandate, this tool evolved into a "Continuum of Care" model. Now, all disciplines maintain a patient's continuity of care. PMID:9385163

  12. Fabrication of a New Electrostatic Linear Actuator

    NASA Astrophysics Data System (ADS)

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

    2000-12-01

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

  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. 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.

  15. 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.

  16. Characterization of electrostatic glass actuators

    NASA Astrophysics Data System (ADS)

    Moser, R.; Wüthrich, R.; Sache, L.; Higuchi, T.; Bleuler, H.

    2003-06-01

    Electrostatic glass actuators are a promising concept for various applications. The use of the interaction between glassy substances and electrostatic fields allows synchronous propulsion akin to the electret actuator. Even though some properties of electrostatic glass motors have been observed and described, a characterization is still missing. The authors would like to present the experimental work leading to the determination of the optimal glass blend and to the optimal electrode pattern in order to maximize the exploitable forces. An analytical model is also presented, satisfactorily close to the measured data. These measurements and models constitute a tool to design electrostatic glass actuators such as, for example, a miniature disk drive, which is presented as one of several promising applications.

  17. 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

  18. 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.

  19. 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.

  20. Resonant behavior of dielectric objects (electrostatic resonances).

    PubMed

    Fredkin, D R; Mayergoyz, I D

    2003-12-19

    Resonant behavior of dielectric objects occurs at certain frequencies for which the object permittivity is negative and the free-space wavelength is large in comparison with the object dimensions. Unique physical features of these resonances are studied and a novel technique for the calculation of resonance values of permittivity, and hence resonance frequencies, is proposed. Scale invariance of resonance frequencies, unusually strong orthogonality properties of resonance modes, and a two-dimensional phenomenon of "twin" spectra are reported. The paper concludes with brief discussions of optical controllability of these resonances in semiconductor nanoparticles and a plausible, electrostatic resonance based, mechanism for nucleation and formation of ball lightning.

  1. Resonant behavior of dielectric objects (electrostatic resonances).

    PubMed

    Fredkin, D R; Mayergoyz, I D

    2003-12-19

    Resonant behavior of dielectric objects occurs at certain frequencies for which the object permittivity is negative and the free-space wavelength is large in comparison with the object dimensions. Unique physical features of these resonances are studied and a novel technique for the calculation of resonance values of permittivity, and hence resonance frequencies, is proposed. Scale invariance of resonance frequencies, unusually strong orthogonality properties of resonance modes, and a two-dimensional phenomenon of "twin" spectra are reported. The paper concludes with brief discussions of optical controllability of these resonances in semiconductor nanoparticles and a plausible, electrostatic resonance based, mechanism for nucleation and formation of ball lightning. PMID:14754117

  2. 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.

  3. 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.

  4. Unusually strong attraction in the presence of continuum bound state

    SciTech Connect

    Delfino, A.; Adhikari, S.K.; Tomio, L.; Frederico, T. Departamento de Fisica, Universidade Federal Fluminense, 24210 Niteroi, Rio de Janeiro Instituto de Fisica Teorica, Universidade Estadual Paulista, 01405 Sao Paulo, SP School of Physical Sciences, The Flinders University of South Australia, Bedford Park, SA 5042 Instituto de Estudos Avancados, Centro Tecnico Aeroespacial, 12231 Sao Jose dos Campos, SP )

    1992-11-01

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

  5. Differential Complexes in Continuum Mechanics

    NASA Astrophysics Data System (ADS)

    Angoshtari, Arzhang; Yavari, Arash

    2015-04-01

    We study some differential complexes in continuum mechanics that involve both symmetric and non-symmetric second-order tensors. In particular, we show that the tensorial analogue of the standard grad-curl-div complex can simultaneously describe the kinematics and the kinetics of motion of a continuum. The relation between this complex and the de Rham complex allows one to readily derive the necessary and sufficient conditions for the compatibility of displacement gradient and the existence of stress functions on non-contractible bodies.We also derive the local compatibility equations in terms of the Green deformation tensor for motions of 2D and 3D bodies, and shells in curved ambient spaces with constant curvatures.

  6. A continuum of misidentification symptoms.

    PubMed

    Sno, H N

    1994-01-01

    A case study of a schizophrenic patient with differing forms of experiences of inappropriate familiarity is described. Reduplicative paramnesia is redefined as a delusion of familiarity related to a reduplication of time, place or person. The author proposes the concept of a continuum of positive and negative misidentification symptoms. The positive pole of the continuum ranges from the minor form of déjà vu experience to reduplicative paramnesia. The negative pole ranges from depersonalisation to nihilistic delusions. Differentiation is based on the severity of the disturbance of reality testing. The argumentation is based on the fact that both déjà vu experiences and depersonalisation occurring in pathological as well as non-pathological conditions are phenomenologically uniform.

  7. 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.

  8. Continuum modelling of granular flows

    NASA Astrophysics Data System (ADS)

    Staron, L.; Lagrée, P.-Y.

    2011-10-01

    The continuum modelling of transient granular flows is of primary importance in the context of predicting the behaviour of many natural systems involving granular matter. In this perspective, the granular column collapse experiment provides an interesting benchmark due to its challenging complexity (Lajeunesse et al 2004, Lube et al 2004), and form a trying test for candidate rheological models. In this contribution, we present 2D continuum simulations of granular column collapse using Navier-Stokes solver Gerris (Popinet 2003). The rheology implemented to model the granular media is the so-called μ(I)-rheology, relating the frictional properties and the viscosity of the material to the pressure and shear rate. In addition, discrete simulations using the Contact Dynamics method are performed for systematic comparison between the granular flow dynamics and its continuum counterpart (Staron & Hinch 2005). We find a good agreement, recovering the shape of the flow in the course of time as well as experimental scaling laws for the run-out. A systematic underestimation of the latter is nevertheless observed, and discussed in terms of physical and numerical modeling.

  9. 77 FR 45367 - Continuum of Care Homeless Assistance Grant Application; Continuum of Care Application

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-31

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

  10. Human Mobility in a Continuum Approach

    PubMed Central

    Simini, Filippo; Maritan, Amos; Néda, Zoltán

    2013-01-01

    Human mobility is investigated using a continuum approach that allows to calculate the probability to observe a trip to any arbitrary region, and the fluxes between any two regions. The considered description offers a general and unified framework, in which previously proposed mobility models like the gravity model, the intervening opportunities model, and the recently introduced radiation model are naturally resulting as special cases. A new form of radiation model is derived and its validity is investigated using observational data offered by commuting trips obtained from the United States census data set, and the mobility fluxes extracted from mobile phone data collected in a western European country. The new modeling paradigm offered by this description suggests that the complex topological features observed in large mobility and transportation networks may be the result of a simple stochastic process taking place on an inhomogeneous landscape. PMID:23555885

  11. Developments and trends in continuum plasticity

    NASA Astrophysics Data System (ADS)

    Becker, Richard

    2002-05-01

    Multiscale modeling applied to meso and macro scale continuum calculations is a broad field with a long history. It encompasses hardening relations based on dislocation density, porosity related ductile failure models, crystal plasticity, composite media and numerous other general topics dating back more than half a century. There are also a myriad of more recent activities that can be grouped under this subject heading. Emphasis will be placed on efforts described at the Bodega Bay workshop aimed at bridging length scales rather than focusing on model developments at any particular length scale. Also, areas will be highlighted where additional connections should be possible with available tools; methods exist but need to be exercised; and critical experiments are needed for validation.

  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

    SciTech Connect

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

    2009-04-30

    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

  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. PMID:26636074

  14. 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. PMID:26443128

  15. 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

  16. 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.

  17. 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.

  18. An alternative Laplacian electrostatic field finite element formulation

    SciTech Connect

    Barber, P.F.; Lauber, T.S.

    1987-01-01

    An alternative finite element method for calculating three-dimensional electrostatic fields is described. The matrix equation is assembled using linear tetrahedral elements and an electrical network solution techniques known as impedance matrix building with axis discarding. The solutions of sample problems are described.

  19. 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

  20. Electrostatic precipitator construction having spacers

    SciTech Connect

    Jonelis, J.A.

    1984-10-23

    The present invention relates to an improved construction for an electrostatic precipitator. The electrostatic precipitator collects solid particles carried by a flue gas from a source of combustion. The precipitator includes a plurality of spaced plates for collecting solid particles from the flue gas by electrostatic attraction of the solid particles to the plates. A plurality of elongated electrodes is positioned among the plates. Each of the electrodes is mounted between a pair of adjacent plates. Each of the electrodes is parallel to the other electrodes and is parallel to the plates. A plurality of identical spacers is positioned between adjacent plates to hold the plates in a flat attitude and to maintain adjacent surfaces of adjacent plates equidistantly spaced from one another. Each of the spacers is an elongated single unitary member and has one end fixed to a surface of one of a pair of adjacent surfaces of the plates and the other end abutting the other of the adjacent surfaces.

  1. Electrostatic attraction between overall neutral surfaces

    NASA Astrophysics Data System (ADS)

    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.

  2. Electrostatic attraction between overall neutral surfaces.

    PubMed

    Adar, Ram M; Andelman, David; Diamant, Haim

    2016-08-01

    Two overall neutral surfaces with positively and negatively charged domains ("patches") have been shown in recent experiments to exhibit long-range attraction when immersed in an ionic solution. Motivated by the experiments, we calculate analytically the osmotic pressure between such surfaces within the Poisson-Boltzmann framework, using a variational principle for the surface-averaged free energy. The electrostatic potential, calculated beyond the linear Debye-Hückel theory, yields an overall attraction at large intersurface separations, over a wide range of the system's controlled length scales. In particular, the attraction is stronger and occurs at smaller separations for surface patches of larger size and charge density. In this large patch limit, we find that the attraction-repulsion crossover separation is inversely proportional to the square of the patch-charge density and to the Debye screening length. PMID:27627373

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

    PubMed

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

    2007-09-01

    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. PMID:17691837

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

    PubMed Central

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

    2010-01-01

    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 to 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. PMID:17691837

  5. 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.

  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. 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.

  8. 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.

  9. Electrostatic probe disruption of drift waves in magnetized microdischarges

    SciTech Connect

    Ito, T.; Cappelli, M. A.

    2009-05-25

    Ultrahigh speed images of ExB discharges are collected during electrostatic probing of magnetized microdischarges. Two azimuthally separated floating micro-Langmuir probes inserted into an axisymmetric microscale magnetically confined plasma are used to characterize azimuthal drift waves. The images reveal features associated with probe intrusion, showing how the electrostatic probes may disrupt the otherwise coherent azimuthal waves. The resulting wave dispersion calculated from the probe signals is consistent with the disruptions seen in the images. These images demonstrate how probe measurements of fluctuations and turbulence, even when probe dimensions are much smaller than characteristic discharge scales, must be interpreted with caution.

  10. 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.

  11. Continuum theory of contractile fibres

    NASA Astrophysics Data System (ADS)

    Kruse, K.; Zumdieck, A.; Jülicher, F.

    2003-12-01

    The generation of contractile forces by living cells often involves linear arrangements of actively interacting polar filaments. We develop a physical description of the dynamics of active fibers based on a general expression for the tension in terms of the filament density and the bundle polarisation. We discuss the long-time behaviour of oriented and of nonpolar fibres, discuss effects of polymerization and depolymerization, and relate this continuum theory to nonlocal descriptions of filament-motor systems. We show that a nonpolar arrangement of filaments suppresses oscillatory instabilities which could be relevant for muscle fibers.

  12. 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.

  13. Electrostatic Precipitator (ESP) TRAINING MANUAL

    EPA Science Inventory

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

  14. Electrostatic precipitator with precipitator electrodes

    SciTech Connect

    Junkers, G.

    1980-12-16

    The invention relates to an electrostatic precipitator with collecting electrodes which are arranged in rows adjacent to each other and in respective pairs at equal distances from a respective discharge electrode with which they cooperate. Spring elements are provided between the collecting electrodes and influence the stiffness and oscillating properties of the array of the collecting electrodes.

  15. 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.

  16. 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)

  17. 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.

  18. 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.

  19. 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.

  20. Plastic dislocation motion via nonequilibrium molecular and continuum dynamics

    SciTech Connect

    Hoover, W.G.; Ladd, A.J.C.; Hoover, N.E.

    1980-09-29

    The classical two-dimensional close-packed triangular lattice, with nearest-neighbor spring forces, is a convenient standard material for the investigation of dislocation motion and plastic flow. Two kinds of calculations, based on this standard material, are described here: (1) Molecular Dynamics simulations, incorporating adiabatic strains described with the help of Doll's Tensor, and (2) Continuum Dynamics simulations, incorporating periodic boundaries and dislocation interaction through stress-field superposition.

  1. Magnetohydrodynamic theory of the global structure and magnetic components of the geodesic acoustic continuum modes in tokamaks

    NASA Astrophysics Data System (ADS)

    Wahlberg, C.; Graves, J. P.

    2016-07-01

    Ideal magnetohydrodynamic (MHD) theory is used to investigate some of the fundamental properties of the geodesic acoustic continuum modes (GAMs) in tokamaks, including their global structure, their associated magnetic components both inside and outside the plasma, and effects of a non-circular cross section of the plasma. In addition to the well-known m=1 side-bands in the perturbed density and pressure of the (electrostatic) GAM, the MHD continuum GAM also includes a m=1 side-band in the perturbed toroidal magnetic field as well as m=2 side-bands in the perturbed density, pressure, poloidal flow and in the magnetic components δ {{B}r} and δ {{B}θ} (m is the poloidal mode number). These m=2 side-bands exist within the whole plasma and the magnetic components also outside the plasma, and the magnitudes of these components in the vacuum region are calculated in the paper. It is shown that, for plasmas with a conducting wall not too far from the plasma surface, the perturbed magnetic field in the vacuum region is dominated by its poloidal component δ {{B}θ} , with poloidal dependence \\sin 2θ , in agreement with experiments. Aspects of the plasma equilibrium that affect the magnitude of the perturbed magnetic field in the vacuum region are discussed in the paper. Furthermore, the influence of a non-circular plasma cross section on the GAM frequency and on the spectrum of the global, perturbed magnetic field is analysed. It is found that the only significant effect of a non-circular cross section on the GAM frequency comes from elongation and its variation across the plasma radius. However, higher-order shaping effects, as well as finite aspect ratio, induce other Fourier components than m=2 in the magnetic halo that surrounds the GAM surface.

  2. Vibrating diaphragm measures high electrostatic field strengths

    NASA Technical Reports Server (NTRS)

    1965-01-01

    Meter with flexible conductive diaphragm measures electrostatic charge density on a conducting surface in a vacuum. The diaphragm is supported from an insulated conductive support ring rigidly attached to the conductive surface whose electrostatic charge density is to be measured.

  3. 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)

  4. 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.

  5. 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.

  6. 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. PMID:26352781

  7. 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

  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. 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.

  10. 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

  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. An atomistically validated continuum model for strain relaxation and misfit dislocation formation

    NASA Astrophysics Data System (ADS)

    Zhou, X. W.; Ward, D. K.; Zimmerman, J. A.; Cruz-Campa, J. L.; Zubia, D.; Martin, J. E.; van Swol, F.

    2016-06-01

    In this paper, molecular dynamics (MD) calculations have been used to examine the physics behind continuum models of misfit dislocation formation and to assess the limitations and consequences of approximations made within these models. Without compromising the physics of misfit dislocations below a surface, our MD calculations consider arrays of dislocation dipoles constituting a mirror imaged "surface". This allows use of periodic boundary conditions to create a direct correspondence between atomistic and continuum representations of dislocations, which would be difficult to achieve with free surfaces. Additionally, by using long-time averages of system properties, we have essentially reduced the errors of atomistic simulations of large systems to "zero". This enables us to deterministically compare atomistic and continuum calculations. Our work results in a robust approach that uses atomistic simulation to accurately calculate dislocation core radius and energy without the continuum boundary conditions typically assumed in the past, and the novel insight that continuum misfit dislocation models can be inaccurate when incorrect definitions of dislocation spacing and Burgers vector in lattice-mismatched systems are used. We show that when these insights are properly incorporated into the continuum model, the resulting energy density expression of the lattice-mismatched systems is essentially indistinguishable from the MD results.

  13. Electrostatic Persistence Length in Polymeric and Biological Systems

    NASA Astrophysics Data System (ADS)

    Carrillo, Jan-Michael; Dobrynin, Andrey; Cao, Zhen

    2014-03-01

    Electrostatic interactions play an important role in controlling properties of polyelectrolytes and biological objects, such as DNA and filamentous viruses. The change in the ionic environment in such systems can influence their conformational properties. Using molecular dynamics simulations and theoretical calculations we have developed a model of swelling of semiflexible polyelectrolytes in salt solutions. Our approach is based on separation of length scales which allowed us to split a chain's electrostatic energy into two parts that describe local and remote along the polymer backbone interactions. The local part takes into account interactions between charged monomers that are separated by distances shorter than the persistence length. These electrostatic interactions renormalize chain persistence length. The second part includes electrostatic interactions between remote charged pairs located at distances larger than the persistence length. These interactions are responsible for chain swelling. In the framework of this approach we calculated effective chain persistence length and chain size as a function of the Debye screening length, chain degree of ionization, bare persistence length and chain degree of polymerization. Our crossover expression for the effective chain's persistence length is in a good quantitative agreement with the experimental data on DNA. We have been able to fit experimental data sets by using two adjustable parameters: DNA ionization degree (α = 0 . 15 +/- 0 . 17) and a bare persistence length (lp = 40 +/- 44 nm) . NSF-DMR-1004576.

  14. 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.

  15. Electrostatic discharge effects on EBW detonators

    SciTech Connect

    Lee, R S; Lee, R E

    1991-04-01

    With appropriate circuit resistance and inductance and sufficient stored energy, discharging a charged human body or component through an exploding bridgewire (EBW) detonator may cause the detonator to function or may damage the detonator. We have studied the effects of electrostatic discharge (ESD) on a number of exploding bridgewire detonators which were subjected to discharges which passed directly through the bridgewires (pin-to-pin), as well as discharges which passed from the bridge to the metal case of the detonator (pin-to-case). We have performed calculations to determine the values of inductance and resistance for which burst and melt may occur for given ESD sources, using a phenomenological model of bridgewire burst in a computer code called FIRESET. Bridge melt was computed using the same computer code, but using experimental values of bridge resistivity and specific heat up to melt. 13 refs., 5 figs.

  16. Universal method for computation of electrostatic potentials.

    PubMed

    Sundholm, D

    2005-05-15

    A computational approach to determine electrostatic interaction and gravitational potentials by performing direct numerical integration is presented. The potential is expanded using finite-element functions of arbitrary order. The method does not involve any solutions of systems of linear equations. The potential is instead obtained as a sum of differential contributions. Thus, no boundary conditions for the potential are needed. It is computationally efficient and well suited for parallel computers, since the innermost loops constitute matrix multiplications and the outer ones can be used as parallel indices. Without using prescreening or other computational tricks to speed up the calculation, the algorithm scales as N4/3 where N denotes the grid size.

  17. 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.

  18. 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.

  19. 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.

  20. Electrostatic Interactions Between Glycosaminoglycan Molecules

    NASA Astrophysics Data System (ADS)

    Song, Fan; Moyne, Christian; Bai, Yi-Long

    2005-02-01

    The electrostatic interactions between nearest-neighbouring chondroitin sulfate glycosaminoglycan (CS-GAG) molecular chains are obtained on the bottle brush conformation of proteoglycan aggrecan based on an asymptotic solution of the Poisson-Boltzmann equation the CS-GAGs satisfy under the physiological conditions of articular cartilage. The present results show that the interactions are associated intimately with the minimum separation distance and mutual angle between the molecular chains themselves. Further analysis indicates that the electrostatic interactions are not only expressed to be purely exponential in separation distance and decrease with the increasing mutual angle but also dependent sensitively on the saline concentration in the electrolyte solution within the tissue, which is in agreement with the existed relevant conclusions.

  1. Electrostatic waves in the magnetosphere.

    NASA Technical Reports Server (NTRS)

    Scarf, F. L.; Fredricks, R. W.

    1972-01-01

    Electric dipole antennas on magnetospheric spacecraft measure E field components of many kinds of electromagnetic waves. In addition, lower hybrid resonance emissions are frequently observed well above the ionosphere. The Ogo 5 plasma wave experiment has also detected new forms of electrostatic emissions that appear to interact very strongly with the local plasma particles. Greatly enhanced wave amplitudes have been found during the expansion phases of substorms, and analysis indicates that these emissions produce strong pitch angle diffusion. Intense broadband electrostatic turbulence is also detected at current layers containing steep magnetic field gradients. This current-driven instability is operative at the bow shock and also at field null regions just within the magnetosheath, and at the magnetopause near the dayside polar cusp. The plasma turbulence appears to involve ion acoustic waves, and the wave particle scattering provides an important collisionless dissipation mechanism for field merging.

  2. 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.

  3. 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.

  4. 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.

  5. Electrostatic generator/motor configurations

    SciTech Connect

    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.

  6. 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.

  7. 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

    2015-11-01

    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. PMID:26228582

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Neoclassical orbit calculations with a full-f code for tokamak edge plasmas

    NASA Astrophysics Data System (ADS)

    Rognlien, T. D.; Cohen, R. H.; Dorr, M.; Hittinger, J.; Xu, X. Q.; Collela, P.; Martin, D.

    2008-11-01

    Ion distribution function modifications are considered for the case of neoclassical orbit widths comparable to plasma radial-gradient scale-lengths. Implementation of proper boundary conditions at divertor plates in the continuum TEMPEST code, including the effect of drifts in determining the direction of total flow, enables such calculations in single-null divertor geometry, with and without an electrostatic potential. The resultant poloidal asymmetries in densities, temperatures, and flows are discussed. For long-time simulations, a slow numerical instability develops, even in simplified (circular) geometry with no endloss, which aids identification of the mixed treatment of parallel and radial convection terms as the cause. The new Edge Simulation Laboratory code, expected to be operational, has algorithmic refinements that should address the instability. We will present any available results from the new code on this problem as well as geodesic acoustic mode tests.

  13. Optical continuum generation on a silicon chip

    NASA Astrophysics Data System (ADS)

    Jalali, Bahram; Boyraz, Ozdal; Koonath, Prakash; Raghunathan, Varun; Indukuri, Tejaswi; Dimitropoulos, Dimitri

    2005-08-01

    Although the Raman effect is nearly two orders of magnitude stronger than the electronic Kerr nonlinearity in silicon, under pulsed operation regime where the pulse width is shorter than the phonon response time, Raman effect is suppressed and Kerr nonlinearity dominates. Continuum generation, made possible by the non-resonant Kerr nonlinearity, offers a technologically and economically appealing path to WDM communication at the inter-chip or intra-chip levels. We have studied this phenomenon experimentally and theoretically. Experimentally, a 2 fold spectral broadening is obtained by launching ~4ps optical pulses with 2.2GW/cm2 peak power into a conventional silicon waveguide. Theoretical calculations, that include the effect of two-photon-absorption, free carrier absorption and refractive index change indicate that up to >30 times spectral broadening is achievable in an optimized device. The broadening is due to self phase modulation and saturates due to two photon absorption. Additionally, we find that free carrier dynamics also contributes to the spectral broadening and cause the overall spectrum to be asymmetric with respect to the pump wavelength.

  14. 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.

  15. 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.

  16. Lattice continuum and diffusional creep

    NASA Astrophysics Data System (ADS)

    Mesarovic, Sinisa Dj.

    2016-04-01

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

  17. A continuum, O(N) Monte Carlo algorithm for charged particles

    NASA Astrophysics Data System (ADS)

    Rottler, Jörg; Maggs, A. C.

    2004-02-01

    We introduce a Monte Carlo algorithm for the simulation of charged particles moving in the continuum. Electrostatic interactions are not instantaneous as in conventional approaches, but are mediated by a constrained, diffusing electric field on an interpolating lattice. We discuss the theoretical justifications of the algorithm and show that it efficiently equilibrates model electrolytes and polar fluids. In order to reduce lattice artifacts that arise from the interpolation of charges to the grid we implement a local, dynamic subtraction algorithm. This dynamic scheme is completely general and can also be used with other Coulomb codes, such as multigrid based methods.

  18. Kinesin motor protein as an electrostatic ratchet machine

    NASA Astrophysics Data System (ADS)

    Tsironis, George; Ciudad, Aleix; Sancho, Jose Maria

    2008-03-01

    Kinesin and related motor proteins utilize ATP fuel to propel themselves along the external surface of microtubules in a processive and directional fashion. We show that the observed step-like motion is possible through time varying charge distributions furnished by the ATP hydrolysis circle while the static charge configuration on the microtuble provides the guide for motion. Thus, while the chemical hydrolysis energy induces appropriate local conformational changes, the motor translational energy is fundamentally electrostatic. Numerical simulations of the mechanical equations of motion show that processivity and directionality are direct consequences of the ATP-dependent electrostatic interaction between the different charge distributions of kinesin and microtubule. Treating proterins as continuous dielectric media and using a Green's function formalism we find analytical expressions for the electrostatic energy in the vicinity of the protein surfaces. We calculate the Bjerrum length in the interior of the protein and analyze its dependence on the charge proximity to the protein interface. We apply these results to kinesin and estimate the pure electrostatic ATP-ADP interaction to be larger than 2k T.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  20. 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.

  1. Is it possible to observe biological macromolecules by electrostatic force microscopy?

    PubMed

    Bergasa, F; Sáenz, J J

    1992-07-01

    Biological macromolecules such as proteins are charged species in solution. The exact charge depends upon the pH, temperature and ionic strength of the medium in general. This suggests the possibility of employing electrostatic force microscopy as a useful tool for the observation of these macromolecules. Our calculations show that electrostatic forces could be used for this purpose, thus helping to remove ambiguities in the location and identification of proteins. The long-range nature of electrostatic forces could make them useful to locate these macromolecules on the appropriate substrate while, at the same time, overcoming important disturbing effects such as lateral displacement of the macromolecules or destructive contact with the sample.

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

    PubMed Central

    Chen, Duan; Wei, Guo-Wei

    2012-01-01

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

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

    PubMed

    Chen, Duan; Wei, Guo-Wei

    2012-04-01

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

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

    PubMed

    Chen, Duan; Wei, Guo-Wei

    2012-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Chen, Duan; Wei, Guo-Wei

    2012-04-01

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

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

    PubMed

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

    2013-01-01

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

  7. 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.

  8. 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.

  9. 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).

  10. Electrostatics of deformable lipid membranes.

    PubMed

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

    2010-06-16

    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 (approximately 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.

  11. 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.

  12. Preventing Electrostatic-Discharge Damage to Electronics

    NASA Technical Reports Server (NTRS)

    Read, W. S.; Dozois, P. C.; Lonborg, J. O.

    1986-01-01

    Booklet discusses damage to electronic components caused by electrostatic discharges during assembly. Describes procedure for setting up static-free workplace for handling and assembling electronic components.

  13. Periodic amplitude variations in Jovian continuum radiation

    NASA Technical Reports Server (NTRS)

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

    1986-01-01

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

  14. Characterization of Continuum Coma features in Comets

    NASA Astrophysics Data System (ADS)

    Mueller, Beatrice E. A.; Samarasinha, Nalin H.; Hergenrother, Carl W.

    2016-10-01

    We will present the results of an analysis of continuum coma features of comets belonging to different dynamical classes at geocentric distances less than 1.5 AU. Our analysis focusses on groundbased visible observations of over a dozen comets. The position angles of the continuum features close to the nucleus, the curvatures, and extents of radial features will be determined, and the dynamics of dust grains will be investigated. We will also use the change in position angles (if relevant) to place constraints on the periodicity of the repeatability of the features. The prevalence of the features in the sunward direction compared to other orientations will be investigated. We will further compare continuum features with CN features when available. This investigation will eventually lead to the discrimination between hemispherical and localized outgassing for the sunward continuum features seen in comets.We acknowledge support from the NASA SSW and PAST programs.

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

    PubMed

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

    2016-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Voit, G. Mark

    1990-01-01

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

  17. Geometric continuum regularization of quantum field theory

    SciTech Connect

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

    1989-11-08

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

  18. Electrostatic contributions to protein-protein interactions: fast energetic filters for docking and their physical basis.

    PubMed

    Norel, R; Sheinerman, F; Petrey, D; Honig, B

    2001-11-01

    The methods of continuum electrostatics are used to calculate the binding free energies of a set of protein-protein complexes including experimentally determined structures as well as other orientations generated by a fast docking algorithm. In the native structures, charged groups that are deeply buried were often found to favor complex formation (relative to isosteric nonpolar groups), whereas in nonnative complexes generated by a geometric docking algorithm, they were equally likely to be stabilizing as destabilizing. These observations were used to design a new filter for screening docked conformations that was applied, in conjunction with a number of geometric filters that assess shape complementarity, to 15 antibody-antigen complexes and 14 enzyme-inhibitor complexes. For the bound docking problem, which is the major focus of this paper, native and near-native solutions were ranked first or second in all but two enzyme-inhibitor complexes. Less success was encountered for antibody-antigen complexes, but in all cases studied, the more complete free energy evaluation was able to identify native and near-native structures. A filter based on the enrichment of tyrosines and tryptophans in antibody binding sites was applied to the antibody-antigen complexes and resulted in a native and near-native solution being ranked first and second in all cases. A clear improvement over previously reported results was obtained for the unbound antibody-antigen examples as well. The algorithm and various filters used in this work are quite efficient and are able to reduce the number of plausible docking orientations to a size small enough so that a final more complete free energy evaluation on the reduced set becomes computationally feasible. PMID:11604522

  19. Liquid-Structure Forces and Electrostatic Modulation of Biomolecular Interactions in Solution

    PubMed Central

    Hassan, Sergio A.

    2008-01-01

    Molecular interactions in solution are controlled by the bulk medium and by the forces originating in the structured region of the solvent close to the solutes. In this paper, a model of electrostatic and liquid-structure forces for dynamics simulations of biomolecules is presented. The model introduces information on the microscopic nature of the liquid in the vicinity of polar and charged groups and the associated non-pairwise character of the forces, thus improving upon conventional continuum representations. The solvent is treated as a polar and polarizable medium, with dielectric properties described by an inhomogeneous version of the Onsager theory. This treatment leads to an effective position-dependent dielectric permittivity that incorporates saturation effects of the electric field and the spatial variation of the liquid density. The non-pairwise additivity of the liquid-structure forces is represented by centers of force located at specific points in the liquid phase. These out-of-the-solute centers are positioned at the peaks of liquid density and exert local, external forces on the atoms of the solute. The density is calculated from a barometric law, using a Lennard-Jones-type solute–liquid effective interaction potential. The conceptual aspects of the model and its exact numerical solutions are discussed for single alkali and halide ions and for ion-pair interactions. The practical aspects of the model and the simplifications introduced for efficient computation of forces in molecular solutes are discussed in the context of polar and charged amino acid dimers. The model reproduces the contact and solvent-separated minima and the desolvation barriers of intermolecular potentials of mean force of amino acid dimers, as observed in atomistic dynamics simulations. Possible refinements based on an improved treatment of molecular correlations are discussed. PMID:17201447

  20. Stabilization of protein crystals by electrostatic interactions as revealed by a numerical approach.

    PubMed

    Takahashi, T; Endo, S; Nagayama, K

    1993-11-20

    We developed a novel algorithm to solve numerically the Poisson-Boltzmann equations under a periodic boundary condition. By employing this algorithm to calculate the electrostatic potentials in two different types of protein crystals, a bovine pancreatic trypsin inhibitor (BPTI) orthorhombic crystal and a pig-insulin cubic crystal, the energy contributions of the electrostatic interactions to the crystals' stability were evaluated. At a high ionic strength, the condensed state of proteins in the crystal was stabilized electrostatically compared with that isolated in dilute solution because the attractive electrostatic interactions between neighboring protein molecules overcame the repulsive forces that originated from the same net charges of the equivalent protein molecules. On the other hand, at a low ionic strength the electrostatic interactions destabilized the crystalline state of both proteins, although a different dependence on the ionic strength was found between them. Here, the insulin crystal was more stable than the BPTI one because of the higher charge density in the BPTI crystal. In all of the solvent ionic strengths investigated, the attractive electrostatic interactions between charge pairs separated by less than 5 A on the respective protein molecules prominently stabilize the protein crystals. Therefore, two protein molecules in the crystals are oriented to compensate each other for their opposite charges on the surfaces. We also found a specific role for bound phosphate ions in the stabilization of the BPTI crystal, based on comparison of the electrostatic energies of the two crystals with and without the ions. By determining the contribution of each atomic charge in the crystals to the electrostatic energy, it was revealed that several electrostatic pairs specifically contributed to the crystal's stability. On the basis of our numerical calculation results, we propose a new method to design protein molecules that adopt stable crystals by replacing

  1. Influence of temperature fluctuations on continuum spectra of cosmic objects

    NASA Astrophysics Data System (ADS)

    Silant'ev, N. A.; Alekseeva, G. A.; Novikov, V. V.

    2012-12-01

    The presence of convective and turbulent motions, and the evolution of magnetic fields give rise to existence of temperature fluctuations in stellar atmospheres, active galactic nuclei and other cosmic objects. We observe the time and surface averaged radiation fluxes from these objects. These fluxes depend on both the mean temperature and averaged temperature fluctuations. The usual photosphere models do not take into account the temperature fluctuations and use only the distribution of the mean temperature into surface layers of stars. We investigate how the temperature fluctuations change the spectra in continuum assuming that the degree of fluctuations (the ratio of mean temperature fluctuation to the mean temperature) is small. We suggest the procedure of calculation of continuum spectra, which takes into account the temperature fluctuations. As a first step one uses the usual model of a photosphere without fluctuations. The observed spectrum is presented as a part depending on mean temperature and the additional part proportional to quadratic value of fluctuation degree. It is shown that for some forms of absorption factor the additional part in Wien's region of spectrum can be evaluated directly from observed spectrum. This part depends on the first and second wavelength derivatives, which can be calculated numerically from the observed spectrum. Our estimates show that the temperature dependence of absorption factors is very important by calculation of continuum spectra corrections. As the examples we present the estimates for a few stars from Pulkovo spectrophotometric catalog and for the Sun. The influence of temperature fluctuations on color indices of observed cosmic objects is also investigated.

  2. Anisotropy of electrostatic interaction in smectic-C^{*} liquid crystals.

    PubMed

    Romanov, V P; Ulyanov, S V

    2014-11-01

    The contribution to the free energy of distortion of the ferroelectric smectic-C^{*} due to the electrostatic interaction of polarization charges is calculated. These calculations are performed by accounting for the anisotropy of the permittivity, which is essential for smectic-C^{*}. Fluctuations of the c director in an external electric field are considered. It is shown that the anisotropy of the permittivity strongly affects the interaction of the polarization charges, the spectrum orientation fluctuations, and the angular dependence of the light scattering intensity.

  3. Bound and continuum vibrational states of the bifluoride anion

    NASA Astrophysics Data System (ADS)

    Špirko, V.; Šindelka, M.; Shirsat, R. N.; Leszczynski, J.

    2003-07-01

    The energies of the bound vibrational states and energy density spectra of the continuum vibrational states of FHF - are calculated, 'exactly' and 'adiabatically', using a new ab initio (CCSD(T)) potential energy surface. Statistical properties of the bound states are probed in terms of the density of states and nearest neighbor level spacing distributions (NNSD). Importantly, the approximate 'adiabatic' densities coincide nearly quantitatively with their 'exact' counterparts. A quantitative fitting of the NNSDs is achieved with a new empirical modification of the Wigner distribution.

  4. Vertical electrostatic force in MEMS cantilever IR sensor

    NASA Astrophysics Data System (ADS)

    Rezadad, Imen; Boroumand Azad, Javaneh; Smith, Evan M.; Alhasan, Ammar; Peale, Robert E.

    2014-06-01

    A MEMS cantilever IR detector that repetitively lifts from the surface under the influence of a saw-tooth electrostatic force, where the contact duty cycle is a measure of the absorbed IR radiation, is analyzed. The design is comprised of three parallel conducting plates. Fixed buried and surface plates are held at opposite potential. A moveable cantilever is biased the same as the surface plate. Calculations based on energy methods with position-dependent capacity and electrostatic induction coefficients demonstrate the upward sign of the force on the cantilever and determine the force magnitude. 2D finite element method calculations of the local fields confirm the sign of the force and determine its distribution across the cantilever. The upward force is maximized when the surface plate is slightly larger than the other two. The electrostatic repulsion is compared with Casimir sticking force to determine the maximum useful contact area. MEMS devices were fabricated and the vertical displacement of the cantilever was observed in a number of experiments. The approach may be applied also to MEMS actuators and micromirrors.

  5. Theory of the water vapor continuum and validations

    NASA Technical Reports Server (NTRS)

    Tipping, Richard H.; Ma, Q.

    1995-01-01

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

  6. Electrostatic generator/motor configurations

    SciTech Connect

    Post, Richard Freeman

    2012-09-11

    Electrostatic generators/motors designs are provided that include a stator fixedly connected to a first central support centered about a central axis. The stator elements are attached to the first central support. Similarly, a second stator is connected to a central support centered about the central axis, and the second stator has stator elements attached to the second central support. A rotor is located between the first stator and the second stator and includes an outer support, where the rotor is rotatably centered about the central axis, the rotor having elements in contact with the outer support, each rotor element having an extending rotor portion that extends radially from the outer support toward the axis of rotation.

  7. Galileo internal electrostatic discharge program

    NASA Technical Reports Server (NTRS)

    Leung, P. L.; Plamp, G. H.; Robinson, P. A., Jr.

    1985-01-01

    The Galileo spacecraft which will orbit Jupiter in 1988 will encounter a very harsh environment of energetic electrons. These electrons will have sufficient energy to penetrate the spacecraft shielding, consequently depositing charges in the dielectric insulating materials or ungrounded conductors. The resulting electric field could exceed the breakdown strength of the insulating materials, producing discharges. The transients produced from these Internal Electrostatic Discharges (IESD) could, depending on their relative location, be coupled to nearby cables and circuits. These transients could change the state of logic circuits or degrade or even damage spacecraft components, consequently disrupting the operation of subsystems and systems of the Galileo spacecraft during its expected mission life. An extensive testing program was initiated for the purpose of understanding the potential threats associated with these IESD events. Data obtained from these tests were used to define design guidelines.

  8. Microencapsulation and Electrostatic Processing Method

    NASA Technical Reports Server (NTRS)

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

    2000-01-01

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

  9. SUPER ESP: Ultimate electrostatic precipitation

    SciTech Connect

    Plaks, N.

    1991-01-01

    The paper discusses SUPER ESP, a new electrostatic precipitator (ESP) concept, enabling high collection efficiencies with considerably smaller collection areas than has previously been possible. The new concept allows a major reduction in ESP size by using an alternating sequence of prechargers and short collector sections. The length of the collection section in each precharger/collector pair (module) dominates the optimization. The size reduction is greater for ESPs operating with high resistivity particulate matter than with low resistivity particulate matter. The relationship in number of modules, collector section size, and overall ESP collection is presented and discussed. Comparisons are given of ESP size for both conventional and SUPER ESP technology operating with either high or low resistivity particulate matter. Because of the size reduction, the cost of the SUPER ESP is projected to be lower than that of a conventional ESP of comparable efficiencY. The paper is based on an ESP model, ESPVI 4.0.

  10. An electrostatically rebalanced micromechanical accelerometer

    NASA Astrophysics Data System (ADS)

    Boxenhorn, Burton; Greiff, Paul

    The design and test performance of a low-cost micromechanical accelerometer (MA) with integral electrodes, developed for use with the vibratory micromechanical gyro described by Boxenhorn and Greiff (1988), are reported. The MA is a monolithic Si device of size 300 x 600 microns and comprises a torsional pendulum with capacitive readout and an electrostatic torquer. Data from 360-deg sweep tests performed in a g-field are presented in tables and graphs and discussed in detail. Results include bandwidth about 1 Hz, scale-factor error 480 ppm, stable bias of 260 microg over 203 min, and temperature effect 2100 microg/C on bias and -123 ppm/C on scale factor.

  11. Large Aperture Electrostatic Dust Detector

    SciTech Connect

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

    2007-10-09

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

  12. Portable liquid collection electrostatic precipitator

    DOEpatents

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

    2005-10-18

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

  13. Review on the modeling of electrostatic MEMS.

    PubMed

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

    2010-01-01

    Electrostatic-driven microelectromechanical systems devices, in most cases, consist of couplings of such energy domains as electromechanics, optical electricity, thermoelectricity, and electromagnetism. Their nonlinear working state makes their analysis complex and complicated. This article introduces the physical model of pull-in voltage, dynamic characteristic analysis, air damping effect, reliability, numerical modeling method, and application of electrostatic-driven MEMS devices. PMID:22219707

  14. Review on the Modeling of Electrostatic MEMS

    PubMed Central

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

    2010-01-01

    Electrostatic-driven microelectromechanical systems devices, in most cases, consist of couplings of such energy domains as electromechanics, optical electricity, thermoelectricity, and electromagnetism. Their nonlinear working state makes their analysis complex and complicated. This article introduces the physical model of pull-in voltage, dynamic characteristic analysis, air damping effect, reliability, numerical modeling method, and application of electrostatic-driven MEMS devices. PMID:22219707

  15. Ionic electrostatic excitations along biological membranes

    NASA Astrophysics Data System (ADS)

    Moradi, Afshin

    2011-02-01

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

  16. Electrostatics experiments with sharp metal points

    NASA Astrophysics Data System (ADS)

    Ivanov, Dragia; Nikolov, Stefan

    2016-11-01

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

  17. Electrostatic Propulsion Using C60 Molecules

    NASA Technical Reports Server (NTRS)

    Leifer, Stephanie D.; Saunders, Winston A.

    1993-01-01

    Report proposes use of C60 as propellant material in electrostatic propulsion system of spacecraft. C60, C70, and similar molecules, have recently been found to have characteristics proving advantageous in electrostatic propulsion. Report discusses these characteristics and proposes experiments to determine feasibility of concept.

  18. Electrostatics with Computer-Interfaced Charge Sensors

    ERIC Educational Resources Information Center

    Morse, Robert A.

    2006-01-01

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

  19. Preliminary tests of the electrostatic plasma accelerator

    NASA Technical Reports Server (NTRS)

    Aston, G.; Acker, T.

    1990-01-01

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

  20. A bridge between two important problems in optics and electrostatics

    NASA Astrophysics Data System (ADS)

    Capelli, R.; Pozzi, G.

    2008-09-01

    It is shown how the same physically appealing method can be applied to find analytic solutions for two difficult and apparently unrelated problems in optics and electrostatics. They are: (i) the diffraction of a plane wave at a perfectly conducting thin half-plane and (ii) the electrostatic field associated with a parallel array of stripes held at opposite potentials and lying in a half-plane. In the latter case, the solution of the problem is essential in order to calculate the electron optical phase shift experienced by the electron beam in electron microscopy experiments, where the model mimics an array of reverse biased p-n junctions. This paper is intended, in particular, for the undergraduate student who has completed his programme of calculus and electromagnetism, but it can also be of interest to the general physicist.

  1. 34 CFR 300.115 - Continuum of alternative placements.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 34 Education 2 2012-07-01 2012-07-01 false Continuum of alternative placements. 300.115 Section... Continuum of alternative placements. (a) Each public agency must ensure that a continuum of alternative... services. (b) The continuum required in paragraph (a) of this section must— (1) Include the...

  2. 34 CFR 300.115 - Continuum of alternative placements.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 34 Education 2 2013-07-01 2013-07-01 false Continuum of alternative placements. 300.115 Section... Continuum of alternative placements. (a) Each public agency must ensure that a continuum of alternative... services. (b) The continuum required in paragraph (a) of this section must— (1) Include the...

  3. Control of electrostatic damage to electronic circuits

    SciTech Connect

    Kirk, W.J. Jr.

    1980-03-01

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

  4. Electrostatic thin film chemical and biological sensor

    DOEpatents

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

    2010-01-19

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

  5. Assessment and control of electrostatic charges. [hazards to space missions

    NASA Technical Reports Server (NTRS)

    Barrett, M.

    1974-01-01

    The experience is described of NASA and DOD with electrostatic problems, generation mechanisms, and type of electrostatic hazards. Guidelines for judging possible effects of electrostatic charges on space missions are presented along with mathematical formulas and definitions.

  6. Electrostatic comb drive for vertical actuation

    SciTech Connect

    Lee, A. P., LLNL

    1997-07-10

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

  7. Microstructural and continuum evolution modeling of sintering.

    SciTech Connect

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

    2003-12-01

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

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

    SciTech Connect

    Koenies, Axel; Kleiber, Ralf

    2012-12-15

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

  9. Semiclassical calculations of observable cross sections in breakup reactions

    SciTech Connect

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

    2008-09-15

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

  10. Internal electrostatic discharge hazard risk assessment to the Galileo orbiter

    NASA Technical Reports Server (NTRS)

    Schmidt, R. E.; Andrews, J. C.; Treadaway, M. J.; Leadon, R. E.

    1980-01-01

    A worst case assessment was performed on the Command Data System (CDS) multilayer printed circuit board and an output power transformer module in the power subsystem. An estimate of the Jovian environment during the 35 hour orbit insertion was supplied by JPL and used as an input to calculate the electron transport into the Galileo components. A radiation shielding analysis computer code, CHARGE, calculated the electron transport deposition trapped in the anticipated sensitive areas of the multilayer board and transformer module. Based on these trapped charge calculations electric fields were calculated between the identified isolated areas and the spacecraft ground. The results of the assessment of electrostatic discharge (DSD) in the CDS multilayer printed circuit board indicate that the probability of ESD in the FR4 is low. The probability of ESD in the components attached to the multilayer board, however, is uncertain based on a lack of prior experimental data.

  11. ELECTROSTATICALLY ENHANCED BARRIER FILTER COLLECTION

    SciTech Connect

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

    2003-06-01

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

  12. Electrostatic Charged Two-Phase Flow Equations

    NASA Astrophysics Data System (ADS)

    Wang, Zhentao; Wen, Jianlong; Wang, Junfeng; Tang, Zhihua; Luo, Tiqian

    2007-06-01

    Electrostatic charged two-phase flows exit in electrostatic spray crop-dusting and fuel spray and so on. Electrostatic charged spray applying to FGD scrubber can improve desulfurization efficiency, decrease water usage. For the complexity of two-phase flow's structure in FGD scrubber, and there exit coupled action between non-uniform electric and flow field, also exit phase interaction between charged particles and continuous phase, which makes the flow more complex. So the complete theory has not formed at present. This paper adopts Lagrange and Euler method of combining together and takes the dispersed particle as fluid, and applies the Reynolds transport principle to set up a Reynolds transport equation, which suit electrostatic charged particle and liquid phase. Then based on Reynolds transport equation, equations for the volume average and instantaneous state of the electrostatic charged two-phase flow are obtained. Similar to equations for single phase turbulent flow, this paper applies Reynolds-average method, and develops equations for Reynolds-average equations for electrostatic charged two-phase flow. Finally, according to the model of single phase turbulent flow, equations for electrostatic charged two-phase flows has been closed. So the k - ɛ - kp model is obtained. Contrast of result by PIV and simulation has been finished.

  13. Intrinsic electrostatic effects in nanostructured ceramics

    SciTech Connect

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

    2009-01-01

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

  14. Orion Aerodynamics for Hypersonic Free Molecular to Continuum Conditions

    NASA Technical Reports Server (NTRS)

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

    2006-01-01

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

  15. Internal Electrostatic Discharge Monitor - IESDM

    NASA Technical Reports Server (NTRS)

    Kim, Wousik; Goebel, Dan M.; Jun, Insoo; Garrett, Henry B.

    2011-01-01

    A document discusses an innovation designed to effectively monitor dielectric charging in spacecraft components to measure the potential for discharge in order to prevent damage from internal electrostatic discharge (IESD). High-energy electrons penetrate the structural materials and shielding of a spacecraft and then stop inside dielectrics and keep accumulating. Those deposited charges generate an electric field. If the electric field becomes higher than the breakdown threshold (approx. =2 x 10(exp 5) V/cm), discharge occurs. This monitor measures potentials as a function of dielectric depth. Differentiation of potential with respect to the depth yields electric field. Direct measurement of the depth profile of the potential in a dielectric makes real-time electronic field evaluation possible without simulations. The IESDM has been designed to emulate a multi-layer circuit board, to insert very thin metallic layers between the dielectric layers. The conductors serve as diagnostic monitoring locations to measure the deposited electron-charge and the charge dynamics. Measurement of the time-dependent potential of the metal layers provides information on the amount of charge deposited in the dielectrics and the movement of that charge with time (dynamics).

  16. Feedback controlled electrostatic and electromagnetic sample positioners

    NASA Technical Reports Server (NTRS)

    Rhim, Won-Kyu; Elleman, D. D.

    1990-01-01

    Four different sample positioners are discussed. The four systems share a common operating principle in that the sample positioning is achieved by feedback controlled forces which can be electrostatic, dielectrophoretic, or electromagnetic. The first system is the electrostatic liquid drop positioner which operates at the near ambient position. The second system is the tetrahedral electrostatic positioner which is being developed for the high temperature materials processing in vacuum. The third system is essentially the the same tetrahedral system above except that the position control is achieved by dielectrophoretic forces in the pressurized gas environment. Finally, the feasibility of a feedback controlled electromagnetic positioner is discussed.

  17. Electrostatic Stabilization Of Growing Protein Crystals

    NASA Technical Reports Server (NTRS)

    Shlichta, Paul J.

    1991-01-01

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

  18. Electrostatic precipitator control for high resistivity particulate

    SciTech Connect

    Bibbo, P.P.; Hankins, F.E.; Jakoplic, R.

    1982-01-19

    A method and apparatus are described for optimizing the operating efficiency of an electrostatic precipitator based on controlling the average input power of the precipitator electrodes in response to control signals derived by sensing changes in specific instantaneous peak voltages associated with the average electrode voltages. The method is particularly well suited for electrostatic precipitators processing high resistivity fly ash and exhibiting an inflection region in its kvmin electrode voltage characteristic. The apparatus is organized to serve as a stand alone control system, or as an adjunct to existing electrostatic precipitator control systems.

  19. High-order continuum kinetic Vlasov-Poisson simulations of magnetized plasmas

    NASA Astrophysics Data System (ADS)

    Vogman, G. V.; Colella, P.; Shumlak, U.

    2014-10-01

    Continuum methods offer a high-fidelity means of simulating plasma kinetics as modeled by the Boltzmann-Maxwell equation system. These methods are advantageous because they can be cast in conservation law form, are not susceptible to noise, and can be implemented using high-order numerical methods. Thereby the methods can conserve mass, momentum, and energy to a high degree. A fourth-order accurate finite volume method has been developed to solve the continuum kinetic Vlasov-Poisson equation system in one spatial and two velocity dimensions. The method is validated in cartesian coordinates using the Dory-Guest-Harris instability, which is a special case of a perpendicularly-propagating kinetic electrostatic wave in a warm uniformly magnetized plasma. The instability dispersion relation, and its generalization to arbitrary distribution functions, are demonstrated to be well-suited benchmarks for continuum algorithms in higher-dimensional phase space. The numerical method has also been extended to two spatial dimensions, and has been implemented in cylindrical coordinates to simulate axisymmetric configurations such as a Z-pinch. This work was supported by the DOE SCGF fellowship, and grants from DOE ASCR and AFOSR.

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

    PubMed

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

    2013-12-01

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

  1. Electrostatic interaction of heterogeneously charged surfaces with semipermeable membranes.

    PubMed

    Maduar, Salim R; Lobaskin, Vladimir; Vinogradova, Olga I

    2013-01-01

    In this paper we study the electrostatic interaction of a heterogeneously charged wall with a neutral semipermeable membrane. The wall consists of periodic stripes, where the charge density varies in one direction. The membrane is in contact with a bulk reservoir of an electrolyte solution and separated from the wall by a thin film of salt-free liquid. One type of ions (small counterions) permeates into the gap. This gives rise to a distance-dependent membrane potential, which translates into a repulsive electrostatic disjoining pressure due to an overlap of counterion clouds in the gap. To quantify it we use two complementary approaches. First, we propose a mean-field theory based on a linearized Poisson-Boltzmann equation and Fourier analysis. These calculations allow us to estimate the effect of a heterogeneous charge pattern at the wall on the induced heterogeneous membrane potential, and the value of the disjoining pressure as a function of the gap. Second, we perform Langevin dynamics simulations of the same system with explicit ions. The results of the two approaches are in good agreement with each other at low surface charges and small gaps, but differ due to nonlinearity at higher charges. These results demonstrate that a heterogeneity of the wall charge can lead to a huge reduction in the electrostatic repulsion, which could dramatically facilitate self-assembly in complex synthetic and biological systems.

  2. Modeling of particle trajectories in an electrostatically charged channel

    NASA Astrophysics Data System (ADS)

    Wu, Mengbai; Kuznetsov, Andrey V.; Jasper, Warren J.

    2010-04-01

    Modeling and analyses of filtration efficiency in electrostatically charged monolith filters are important for evaluating and designing this class of filters. Unlike traditional fibrous filters which comprise external flow around a fiber, monolith filters are modeled as internal flow through small channels. Analogous to single fiber theory for external flows, single channel theory is used to analyze basic fluid mechanics in monolith filters and predict filtration efficiencies. The model incorporates three forces: hydrodynamic forces, electrostatic forces, and Brownian motion. Fluid velocity within the channels is calculated by using an analytical solution for circular channel flow, within which the slip boundary condition is considered because of small length scales. This velocity field is then used to evaluate the drag force on the particle according to Stokes's law. For this model, a one-way coupling between the fluid flow and the particle motion is assumed due to the fact that the relaxation time for the particles simulated in this paper is very small compared to the time the particles spend in the channel. The electrostatic field is computed assuming a uniform charge distribution on the inner surface of a cylindrical channel of finite length. Using a Monte Carlo simulation, particles are randomly injected into a single channel to determine the filtration efficiency.

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

    SciTech Connect

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

    2015-11-15

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    SciTech Connect

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

    2014-07-15

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

  7. Continuum and line emission of flares on red dwarf stars

    NASA Astrophysics Data System (ADS)

    Morchenko, E.; Bychkov, K.; Livshits, M.

    2015-06-01

    The emission spectrum has been calculated of a homogeneous pure hydrogen layer, which parameters are typical for a flare on a red dwarf. The ionization and excitation states were determined by the solution of steady-state equations taking into account the continuum and all discrete hydrogen levels. We consider the following elementary processes: electron-impact transitions, spontaneous and induced radiative transitions, and ionization by the bremsstrahlung and recombination radiation of the layer itself. The Biberman-Holstein approximation was used to calculate the scattering of line radiation. Asymptotic formulae for the escape probability are obtained for a symmetric line profile taking into account the Stark and Doppler effects. The approximation for the core of the H- α line by a Gaussian curve has been substantiated.

  8. Electrostatic forces on two almost touching nonspherical charged conductors

    NASA Astrophysics Data System (ADS)

    Khair, Aditya S.

    2013-10-01

    Analytical expressions are derived for the electrostatic forces on two almost touching nonspherical conductors held at unequal voltages or carrying dissimilar charges in an insulating medium. Each conductor is a body of revolution whose surface is defined by the equation rn+zn=an, where r and z are radial and axial cylindrical co-ordinates, respectively, 2a is the equatorial width, and n is a parameter that controls the particle shape. The two objects are of identical shape and placed in a coaxial configuration, in which case the electrostatic forces are solely along their line of centers. The calculation of the forces is performed via a local analysis of the electrostatics in the thin gap region separating the particles. At a fixed potential difference, the magnitude of the attractive force F on the particles scales with the minimum gap height h0 as F ˜h02(1/n-1) for n > 1 and F ˜ln h0 for n = 1, to leading order as h0/a→0. The force increases as the gap region becomes flatter (increasing n), due to the intense electric field in the gap acting over a larger surface area. The opposite is found for particles carrying fixed charges: here, F ˜h0-2/n for n > 2 and F ˜h0-1[ln(a/h0)]-2 for n = 2. In this case, the potential difference between the conductors diminishes as the gap region becomes flatter, which overpowers the increase in gap area. Our results demonstrate that like-charge attraction occurs for a broad class of nonspherical conductors at close separations. The predicted sensitivity of the electrostatic force to particle shape is relevant to probe-based microscopy: specifically, to quantify the influence of tip-geometry on the force experienced by a charged probe near a conducting surface.

  9. Electrostatic correlations near charged planar surfaces

    PubMed Central

    Deng, Mingge; Em Karniadakis, George

    2014-01-01

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

  10. Electrostatic interactions in gas-solid chromatography.

    NASA Technical Reports Server (NTRS)

    Benson, S. W.; King, J., Jr.

    1966-01-01

    Electrostatic theory of physical adsorption applied to gas-solid chromatography, discussing chromatographic inseparability of argon and oxygen at room temperature, prediction of elution order of many gases, etc

  11. The Electrocardiogram as an Example of Electrostatics

    ERIC Educational Resources Information Center

    Hobbie, Russell K.

    1973-01-01

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

  12. Electrostatic discharge control for STDN stations

    NASA Technical Reports Server (NTRS)

    Mckiernan, J.

    1983-01-01

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

  13. Electrostatic Liquid-Drop-Levitation System

    NASA Technical Reports Server (NTRS)

    Rhim, Won Kyu; Chung, San Kun; Hyson, Michael T.; Elleman, Daniel D.

    1988-01-01

    Electrostatic levitator has levitated drops of liquid up to 4 mm in diameter while maintaining spherical drop shapes. Stable levitation of spherical drops valuable in experiments involving super-cooling, solidification, and crystal growth.

  14. Stochastic ion acceleration by beating electrostatic waves.

    PubMed

    Jorns, B; Choueiri, E Y

    2013-01-01

    A study is presented of the stochasticity in the orbit of a single, magnetized ion produced by the particle's interaction with two beating electrostatic waves whose frequencies differ by the ion cyclotron frequency. A second-order Lie transform perturbation theory is employed in conjunction with a numerical analysis of the maximum Lyapunov exponent to determine the velocity conditions under which stochasticity occurs in this dynamical system. Upper and lower bounds in ion velocity are found for stochastic orbits with the lower bound approximately equal to the phase velocity of the slower wave. A threshold condition for the onset of stochasticity that is linear with respect to the wave amplitudes is also derived. It is shown that the onset of stochasticity occurs for beating electrostatic waves at lower total wave energy densities than for the case of a single electrostatic wave or two nonbeating electrostatic waves. PMID:23410446

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

    NASA Technical Reports Server (NTRS)

    Kim, Sang-Wook

    1996-01-01

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

  16. Modal kinematics for multisection continuum arms.

    PubMed

    Godage, Isuru S; Medrano-Cerda, Gustavo A; Branson, David T; Guglielmino, Emanuele; Caldwell, Darwin G

    2015-05-13

    This paper presents a novel spatial kinematic model for multisection continuum arms based on mode shape functions (MSF). Modal methods have been used in many disciplines from finite element methods to structural analysis to approximate complex and nonlinear parametric variations with simple mathematical functions. Given certain constraints and required accuracy, this helps to simplify complex phenomena with numerically efficient implementations leading to fast computations. A successful application of the modal approximation techniques to develop a new modal kinematic model for general variable length multisection continuum arms is discussed. The proposed method solves the limitations associated with previous models and introduces a new approach for readily deriving exact, singularity-free and unique MSF's that simplifies the approach and avoids mode switching. The model is able to simulate spatial bending as well as straight arm motions (i.e., pure elongation/contraction), and introduces inverse position and orientation kinematics for multisection continuum arms. A kinematic decoupling feature, splitting position and orientation inverse kinematics is introduced. This type of decoupling has not been presented for these types of robotic arms before. The model also carefully accounts for physical constraints in the joint space to provide enhanced insight into practical mechanics and impose actuator mechanical limitations onto the kinematics thus generating fully realizable results. The proposed method is easily applicable to a broad spectrum of continuum arm designs.

  17. Modal kinematics for multisection continuum arms.

    PubMed

    Godage, Isuru S; Medrano-Cerda, Gustavo A; Branson, David T; Guglielmino, Emanuele; Caldwell, Darwin G

    2015-06-01

    This paper presents a novel spatial kinematic model for multisection continuum arms based on mode shape functions (MSF). Modal methods have been used in many disciplines from finite element methods to structural analysis to approximate complex and nonlinear parametric variations with simple mathematical functions. Given certain constraints and required accuracy, this helps to simplify complex phenomena with numerically efficient implementations leading to fast computations. A successful application of the modal approximation techniques to develop a new modal kinematic model for general variable length multisection continuum arms is discussed. The proposed method solves the limitations associated with previous models and introduces a new approach for readily deriving exact, singularity-free and unique MSF's that simplifies the approach and avoids mode switching. The model is able to simulate spatial bending as well as straight arm motions (i.e., pure elongation/contraction), and introduces inverse position and orientation kinematics for multisection continuum arms. A kinematic decoupling feature, splitting position and orientation inverse kinematics is introduced. This type of decoupling has not been presented for these types of robotic arms before. The model also carefully accounts for physical constraints in the joint space to provide enhanced insight into practical mechanics and impose actuator mechanical limitations onto the kinematics thus generating fully realizable results. The proposed method is easily applicable to a broad spectrum of continuum arm designs. PMID:25969947

  18. Aims, Modes, and the Continuum of Discourse.

    ERIC Educational Resources Information Center

    Beale, Walter H.

    A framework for the study of discourse, based on the analysis of three superordinate features of discourse (asymmetry, hierarchy, and continuum), is proposed in this paper. The paper begins by noting the confusion in terminology that exists in the world of composition pedagogy and theory; pointing to the need for a framework for testing,…

  19. Radio continuum from FU Orionis stars

    SciTech Connect

    Rodriguez, L.F.; Hartmann, L.W.; Chavira, E. Harvard-Smithsonian Center for Astrophysics, Cambridge, MA Instituto Nacional de Astrofisica, Optica y Electronica, Puebla )

    1990-12-01

    Using the very large array a sensitive search is conducted for 3.6-cm continuum emission toward four FU Orionis objects: FU Ori, V1515 Cyg, V1057 Cyg, and Elias 1-12. V1057 Cyg and Elias 1-12 at the level of about 0.1 mJy is detected. The association of radio continuum emission with these FU Ori objects strengthens a possible relation between FU Ori stars and objects like L 1551 IRS 5 and Z CMa that are also sources of radio continuum emission and have been proposed as post-FU Ori objects. Whether the radio continuum emission is caused by free-free emission from ionized ejecta or if it is optically thin emission from a dusty disk is discussed. It was determined that, in the archives of the Tonantzintla Observatory, a plate taken in 1957 does not show Elias 1-12. This result significantly narrows the time range for the epoch of the outburst of this source to between 1957 and 1965. 38 refs.

  20. Parental Involvement to Parental Engagement: A Continuum

    ERIC Educational Resources Information Center

    Goodall, Janet; Montgomery, Caroline

    2014-01-01

    Based on the literature of the field, this article traces a continuum between parental involvement with schools, and parental engagement with children's learning. The article seeks to shed light on an area of confusion; previous research has shown that different stakeholder groups understand "parental engagement" in different ways.…

  1. Clinical Integration Managing across the care continuum.

    PubMed

    Karash, Julius A; Larson, Laurie

    2016-06-01

    In the changing world of health care, the traditional boundaries are vanishing and hospitals and others must integrate care within their own organizations, as well as externally, across the care continuum. Here are three approaches to accomplishing just that. PMID:27468454

  2. Construction of the energy matrix for complex atoms. Part V: Electrostatically correlated spin-orbit and electrostatically correlated hyperfine interactions

    NASA Astrophysics Data System (ADS)

    Elantkowska, Magdalena; Ruczkowski, Jarosław; Dembczyński, Jerzy

    2016-02-01

    The continuation of the previous series of papers related to the construction of the energy matrix for complex atoms is presented. The contributions from the second-order perturbation theory concerning electrostatically correlated spin-orbit interactions (CSO), as well as electrostatically correlated hyperfine interactions (CHFS) to the atomic structure of nlN, nlNn1l1^{N_1} and nlNn1l1^{N_1}n2l2^{N_2} configurations, are considered. This theory assumes that the electron excitation n0l0→ nl affects spin-orbit splitting and magnetic dipole and electric quadrupole hyperfine structure in the same way which will be discussed below. Part I of the series presented, in general terms, a method allowing the analysis of complex electronic systems. Parts II, III and IV provided a description of an electrostatic interaction up to second-order perturbation theory; they constitute the basis for the design of an efficient computer program package for large-scale calculations of accurate wave functions. Analyses presented in the entire series of our papers clearly demonstrate that obtaining the precise wave functions is impossible without considering the contribution from the second-order effects into fine and hyperfine atomic structure.

  3. Calculation of Electron Trajectories

    1982-06-01

    EGUN, the SLAC Electron Trajectory Program, computes trajectories of charged particles in electrostatic and magnetostatic focusing systems including the effects of space charge and self-magnetic fields. Starting options include Child''s Law conditions on cathodes of various shapes, user-specified initial conditions for each ray, and a combination of Child''s Law conditions and user specifications. Either rectangular or cylindrically symmetric geometry may be used. Magnetic fields may be specified using arbitrary configuration of coils, or the outputmore » of a magnet program, such as Poisson, or by an externally calculated array of the axial fields.« less

  4. Continuum modeling of large lattice structures: Status and projections

    NASA Technical Reports Server (NTRS)

    Noor, Ahmed K.; Mikulas, Martin M., Jr.

    1988-01-01

    The status and some recent developments of continuum modeling for large repetitive lattice structures are summarized. Discussion focuses on a number of aspects including definition of an effective substitute continuum; characterization of the continuum model; and the different approaches for generating the properties of the continuum, namely, the constitutive matrix, the matrix of mass densities, and the matrix of thermal coefficients. Also, a simple approach is presented for generating the continuum properties. The approach can be used to generate analytic and/or numerical values of the continuum properties.

  5. Electrostatic Beneficiation of Lunar Simulant

    NASA Technical Reports Server (NTRS)

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

    2006-01-01

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

  6. Miniature Bipolar Electrostatic Ion Thruster

    NASA Technical Reports Server (NTRS)

    Hartley, Frank T.

    2006-01-01

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

  7. Electrostatic Levitation Furnace for the ISS

    NASA Technical Reports Server (NTRS)

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

    2012-01-01

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

  8. Improved Electronic Control for Electrostatic Precipitators

    NASA Technical Reports Server (NTRS)

    Johnston, D. F.

    1986-01-01

    Electrostatic precipitators remove particulate matter from smoke created by burning refuse. Smoke exposed to electrostatic field, and particles become electrically charged and migrate to electrically charged collecting surfaces. New microprocessor-based electronic control maintains precipitator power at maximum particulate-collection level. Control automatically senses changes in smoke composition due to variations in fuel or combustion and adjusts precipitator voltage and current accordingly. Also, sensitive yet stable fault detection provided.

  9. Electrostatic breakup in a misty plasma.

    PubMed

    Coppins, M

    2010-02-12

    A misty plasma is defined as a plasma containing small liquid droplets. In such a system, the droplets will undergo total electrostatic breakup if their charge exceeds the well-known Rayleigh limit. This imposes a minimum size on the droplets. Electrostatic breakup is a significant mechanism limiting droplet survival in a wide range of plasma applications, including plasma-enhanced chemical vapor deposition and fusion tokamaks. PMID:20366826

  10. Electrostatic camera system functional design study

    NASA Technical Reports Server (NTRS)

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

    1972-01-01

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

  11. Miniature Electrostatic Ion Thruster With Magnet

    NASA Technical Reports Server (NTRS)

    Hartley, Frank T.

    2006-01-01

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

  12. Electrostatic Breakup in a Misty Plasma

    SciTech Connect

    Coppins, M.

    2010-02-12

    A misty plasma is defined as a plasma containing small liquid droplets. In such a system, the droplets will undergo total electrostatic breakup if their charge exceeds the well-known Rayleigh limit. This imposes a minimum size on the droplets. Electrostatic breakup is a significant mechanism limiting droplet survival in a wide range of plasma applications, including plasma-enhanced chemical vapor deposition and fusion tokamaks.

  13. Analytical theory of the shear Alfvén continuum in the presence of a magnetic island

    SciTech Connect

    Cook, C. R. Hegna, C. C.

    2015-04-15

    The effect of a magnetic island chain on the shear Alfvén continuum is calculated analytically. Using a WKB approximation of the linearized ideal MHD equations, the island is shown to cause an upshift in the continuum accumulation point frequency. This minimum of the frequency spectrum is shifted from the rational surface to the island separatrix. The structure of the eigenmodes is also presented.

  14. On the electrostatic properties of homodimeric proteins

    PubMed Central

    Campbell, Brandon; Petukh, Marharyta; Alexov, Emil

    2014-01-01

    A large fraction of proteins function as homodimers, but it is not always clear why the dimerization is important for functionality since frequently each monomer possesses a distinctive active site. Recent work (PLoS Computational Biology, 9(2), e1002924) indicates that homodimerization may be important for forming an electrostatic funnel in the spermine synthase homodimer which guides changed substrates toward the active centers. This prompted us to investigate the electrostatic properties of a large set of homodimeric proteins and resulted in an observation that in a vast majority of the cases the dimerization indeed results in specific electrostatic features, although not necessarily in an electrostatic funnel. It is demonstrated that the electrostatic dipole moment of the dimer is predominantly perpendicular to the axis connecting the centers of the mass of the monomers. In addition, the surface points with highest potential are located in the proximity of the interfacial plane of the homodimeric complexes. These findings indicate that frequently homodimerization provides specific electrostatic features needed for the function of proteins. PMID:25419028

  15. Relativistic mean field calculations in neutron-rich nuclei

    SciTech Connect

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

    2014-08-14

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

  16. Observations of continuum depression in warm dense matter with x-ray Thomson scattering.

    PubMed

    Fletcher, L B; Kritcher, A L; Pak, A; Ma, T; Döppner, T; Fortmann, C; Divol, L; Jones, O S; Landen, O L; Scott, H A; Vorberger, J; Chapman, D A; Gericke, D O; Mattern, B A; Seidler, G T; Gregori, G; Falcone, R W; Glenzer, S H

    2014-04-11

    Detailed measurements of the electron densities, temperatures, and ionization states of compressed CH shells approaching pressures of 50 Mbar are achieved with spectrally resolved x-ray scattering. Laser-produced 9 keV x-rays probe the plasma during the transient state of three-shock coalescence. High signal-to-noise x-ray scattering spectra show direct evidence of continuum depression in highly degenerate warm dense matter states with electron densities ne>1024  cm-3. The measured densities and temperatures agree well with radiation-hydrodynamic modeling when accounting for continuum lowering in calculations that employ detailed configuration accounting.

  17. A semi-continuum model on vibration frequency of silicon nanowires in <111> orientation

    NASA Astrophysics Data System (ADS)

    Yu, Hong; Chen, Hong-Bo

    2016-06-01

    In this article, a new semi-continuum model is built to describe the fundamental vibration frequency of the silicon nanowires in <111> orientation. The Keating potential model and the discrete nature in the width and the thickness direction of the silicon nanowires in <111> orientation are applied in the new semi-continuum model. Based on the Keating model and the principle of conservation of energy, the vibration frequency of the silicon nanowires with the triangle, the rhombus, and the hexagon cross sections are derived. It is indicated that the calculation results based on this new model are accordant with the simulation results of the software based on molecular dynamics (MD).

  18. Polarizable continuum model study of solvent effects on electronic circular dichroism parameters

    NASA Astrophysics Data System (ADS)

    Pecul, Magdalena; Marchesan, Domenico; Ruud, Kenneth; Coriani, Sonia

    2005-01-01

    We present an implementation of the polarizable continuum model for the calculation of solvent effects on electronic circular dichroism spectra. The computational model used is density functional theory in the length-gauge formulation, and gauge-origin independence is ensured through the use of London atomic orbitals. Results of calculations carried out for methyloxirane and bicyclic ketones, camphor, norcamphor, norbornenone, and fenchone are presented, and the theoretically obtained solvent effects are compared with experimental observations.

  19. The Switching/gaussian Method for Polarizable Continuum Models with Applications to Aqueous Molecular Dynamics and Vibrational Spectra

    NASA Astrophysics Data System (ADS)

    Lange, Adrian W. G.; Herbert, John M.

    2010-06-01

    We describe the recently-developed Switching/Gaussian (SWIG) formalism for polarizable continuum models (PCMs) in electronic structure theory and QM/MM calculations. Existing PCM implementations are well-established, yet still exhibit Coulomb singularities and/or discontinuities in potential energy surfaces, which result from the finite-element discretization of the solute--continuum interface. Our revised implementation eliminates these problems. We illustrate the robustness this approach using ab initio molecular dynamics and vibrational spectra calculations, for which existing PCM implementations fail. Furthermore, we present the extension of SWIG to unprecedentedly large systems, making it a viable implicit solvation method even for molecular mechanics calculations of biological macromolecules.

  20. Continuum Damping of Free-boundary TAE with AEGIS

    NASA Astrophysics Data System (ADS)

    Chen, Eugene; Berk, Herb; Breizman, Boris; Zheng, Linjin

    2010-11-01

    An extension has been added to the ideal MHD code AEGIS (Adaptive EiGenfunction Independent Solutions) to estimate continuum damping of an Alfvenic mode. In our scheme we analyze the determinant arising from attempting to match solutions at the surface of the plasma vacuum interface. A zero of the determinant corresponds to an eigenvalue of the system. When continuum damping exists in a stable system, the eigenmode cannot be calculated by an integration along the real axis (in principle integration in deformed regions of the complex plane is required). The approach we take here is to scan the value of the determinant as a function of complex frequency where the imaginary part of the frequency is positive. The analytic continuation of the determinant gives an estimate of the root in the lower half plane, from which the damping rate is extracted. A complicating factor in our procedure is that the positions of a pole and zero of a determinant is frequently comparable to the damping rate. Hence, the search procedure must account for both the zero and pole structure of the determinant. It is interesting to note that the root of the pole corresponds to the eigenvalue of the problem where an ideal conducting wall is placed on the plasma vacuum interface. We are attempting to apply our new subroutine to realistic equilibria, such as C-Mod.

  1. Self-consistent continuum solvation for optical absorption of complex molecular systems in solution

    SciTech Connect

    Timrov, Iurii; Biancardi, Alessandro; Andreussi, Oliviero; Marzari, Nicola; Baroni, Stefano

    2015-01-21

    We introduce a new method to compute the optical absorption spectra of complex molecular systems in solution, based on the Liouville approach to time-dependent density-functional perturbation theory and the revised self-consistent continuum solvation model. The former allows one to obtain the absorption spectrum over a whole wide frequency range, using a recently proposed Lanczos-based technique, or selected excitation energies, using the Casida equation, without having to ever compute any unoccupied molecular orbitals. The latter is conceptually similar to the polarizable continuum model and offers the further advantages of allowing an easy computation of atomic forces via the Hellmann-Feynman theorem and a ready implementation in periodic-boundary conditions. The new method has been implemented using pseudopotentials and plane-wave basis sets, benchmarked against polarizable continuum model calculations on 4-aminophthalimide, alizarin, and cyanin and made available through the QUANTUM ESPRESSO distribution of open-source codes.

  2. Self-consistent continuum solvation for optical absorption of complex molecular systems in solution.

    PubMed

    Timrov, Iurii; Andreussi, Oliviero; Biancardi, Alessandro; Marzari, Nicola; Baroni, Stefano

    2015-01-21

    We introduce a new method to compute the optical absorption spectra of complex molecular systems in solution, based on the Liouville approach to time-dependent density-functional perturbation theory and the revised self-consistent continuum solvation model. The former allows one to obtain the absorption spectrum over a whole wide frequency range, using a recently proposed Lanczos-based technique, or selected excitation energies, using the Casida equation, without having to ever compute any unoccupied molecular orbitals. The latter is conceptually similar to the polarizable continuum model and offers the further advantages of allowing an easy computation of atomic forces via the Hellmann-Feynman theorem and a ready implementation in periodic-boundary conditions. The new method has been implemented using pseudopotentials and plane-wave basis sets, benchmarked against polarizable continuum model calculations on 4-aminophthalimide, alizarin, and cyanin and made available through the Quantum ESPRESSO distribution of open-source codes. PMID:25612693

  3. Progress toward bridging from atomistic to continuum modeling to predict nuclear waste glass dissolution.

    SciTech Connect

    Zapol, Peter; Bourg, Ian; Criscenti, Louise Jacqueline; Steefel, Carl I.; Schultz, Peter Andrew

    2011-10-01

    This report summarizes research performed for the Nuclear Energy Advanced Modeling and Simulation (NEAMS) Subcontinuum and Upscaling Task. The work conducted focused on developing a roadmap to include molecular scale, mechanistic information in continuum-scale models of nuclear waste glass dissolution. This information is derived from molecular-scale modeling efforts that are validated through comparison with experimental data. In addition to developing a master plan to incorporate a subcontinuum mechanistic understanding of glass dissolution into continuum models, methods were developed to generate constitutive dissolution rate expressions from quantum calculations, force field models were selected to generate multicomponent glass structures and gel layers, classical molecular modeling was used to study diffusion through nanopores analogous to those in the interfacial gel layer, and a micro-continuum model (K{mu}C) was developed to study coupled diffusion and reaction at the glass-gel-solution interface.

  4. SYSTEMATIC CONTINUUM ERRORS IN THE Ly{alpha} FOREST AND THE MEASURED TEMPERATURE-DENSITY RELATION

    SciTech Connect

    Lee, Khee-Gan

    2012-07-10

    Continuum fitting uncertainties are a major source of error in estimates of the temperature-density relation (usually parameterized as a power-law, T {proportional_to} {Delta}{sup {gamma}-1}) of the intergalactic medium through the flux probability distribution function (PDF) of the Ly{alpha} forest. Using a simple order-of-magnitude calculation, we show that few percent-level systematic errors in the placement of the quasar continuum due to, e.g., a uniform low-absorption Gunn-Peterson component could lead to errors in {gamma} of the order of unity. This is quantified further using a simple semi-analytic model of the Ly{alpha} forest flux PDF. We find that under(over)estimates in the continuum level can lead to a lower (higher) measured value of {gamma}. By fitting models to mock data realizations generated with current observational errors, we find that continuum errors can cause a systematic bias in the estimated temperature-density relation of ({delta}({gamma})) Almost-Equal-To -0.1, while the error is increased to {sigma}{sub {gamma}} Almost-Equal-To 0.2 compared to {sigma}{sub {gamma}} Almost-Equal-To 0.1 in the absence of continuum errors.

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

    PubMed

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

    2015-02-17

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

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

    SciTech Connect

    Kato, Tsunehiko N.; Takabe, Hideaki

    2010-03-15

    A two-dimensional electromagnetic particle-in-cell simulation with the realistic ion-to-electron mass ratio of 1836 is carried out to investigate the electrostatic collisionless shocks in relatively high-speed (approx3000 km s{sup -1}) plasma flows and also the influence of both electrostatic and electromagnetic instabilities, which can develop around the shocks, on the shock dynamics. It is shown that the electrostatic ion-ion instability can develop in front of the shocks, where the plasma is under counterstreaming condition, with highly oblique wave vectors as was shown previously. The electrostatic potential generated by the electrostatic ion-ion instability propagating obliquely to the shock surface becomes comparable with the shock potential and finally the shock structure is destroyed. It is also shown that in front of the shock the beam-Weibel instability gradually grows as well, consequently suggesting that the magnetic field generated by the beam-Weibel instability becomes important in long-term evolution of the shock and the Weibel-mediated shock forms long after the electrostatic shock vanished. It is also observed that the secondary electrostatic shock forms in the reflected ions in front of the primary electrostatic shock.

  7. Modeling the elastic energy of alloys: Potential pitfalls of continuum treatments

    NASA Astrophysics Data System (ADS)

    Baskaran, Arvind; Ratsch, Christian; Smereka, Peter

    2015-12-01

    Some issues that arise when modeling elastic energy for binary alloys are discussed within the context of a Keating model and density-functional calculations. The Keating model is a simplified atomistic formulation based on modeling elastic interactions of a binary alloy with harmonic springs whose equilibrium length is species dependent. It is demonstrated that the continuum limit for the strain field are the usual equations of linear elasticity for alloys and that they correctly capture the coarse-grained behavior of the displacement field. In addition, it is established that Euler-Lagrange equation of the continuum limit of the elastic energy will yield the same strain field equation. This is the same energy functional that is often used to model elastic effects in binary alloys. However, a direct calculation of the elastic energy atomistic model reveals that the continuum expression for the elastic energy is both qualitatively and quantitatively incorrect. This is because it does not take atomistic scale compositional nonuniformity into account. Importantly, this result also shows that finely mixed alloys tend to have more elastic energy than segregated systems, which is the exact opposite of predictions made by some continuum theories. It is also shown that for strained thin films the traditionally used effective misfit for alloys systematically underestimate the strain energy. In some models, this drawback is handled by including an elastic contribution to the enthalpy of mixing, which is characterized in terms of the continuum concentration. The direct calculation of the atomistic model reveals that this approach suffers serious difficulties. It is demonstrated that elastic contribution to the enthalpy of mixing is nonisotropic and scale dependent. It is also shown that such effects are present in density-functional theory calculations for the Si-Ge system. This work demonstrates that it is critical to include the microscopic arrangements in any elastic

  8. Modeling the elastic energy of alloys: Potential pitfalls of continuum treatments.

    PubMed

    Baskaran, Arvind; Ratsch, Christian; Smereka, Peter

    2015-12-01

    Some issues that arise when modeling elastic energy for binary alloys are discussed within the context of a Keating model and density-functional calculations. The Keating model is a simplified atomistic formulation based on modeling elastic interactions of a binary alloy with harmonic springs whose equilibrium length is species dependent. It is demonstrated that the continuum limit for the strain field are the usual equations of linear elasticity for alloys and that they correctly capture the coarse-grained behavior of the displacement field. In addition, it is established that Euler-Lagrange equation of the continuum limit of the elastic energy will yield the same strain field equation. This is the same energy functional that is often used to model elastic effects in binary alloys. However, a direct calculation of the elastic energy atomistic model reveals that the continuum expression for the elastic energy is both qualitatively and quantitatively incorrect. This is because it does not take atomistic scale compositional nonuniformity into account. Importantly, this result also shows that finely mixed alloys tend to have more elastic energy than segregated systems, which is the exact opposite of predictions made by some continuum theories. It is also shown that for strained thin films the traditionally used effective misfit for alloys systematically underestimate the strain energy. In some models, this drawback is handled by including an elastic contribution to the enthalpy of mixing, which is characterized in terms of the continuum concentration. The direct calculation of the atomistic model reveals that this approach suffers serious difficulties. It is demonstrated that elastic contribution to the enthalpy of mixing is nonisotropic and scale dependent. It is also shown that such effects are present in density-functional theory calculations for the Si-Ge system. This work demonstrates that it is critical to include the microscopic arrangements in any elastic

  9. Modeling the elastic energy of alloys: Potential pitfalls of continuum treatments.

    PubMed

    Baskaran, Arvind; Ratsch, Christian; Smereka, Peter

    2015-12-01

    Some issues that arise when modeling elastic energy for binary alloys are discussed within the context of a Keating model and density-functional calculations. The Keating model is a simplified atomistic formulation based on modeling elastic interactions of a binary alloy with harmonic springs whose equilibrium length is species dependent. It is demonstrated that the continuum limit for the strain field are the usual equations of linear elasticity for alloys and that they correctly capture the coarse-grained behavior of the displacement field. In addition, it is established that Euler-Lagrange equation of the continuum limit of the elastic energy will yield the same strain field equation. This is the same energy functional that is often used to model elastic effects in binary alloys. However, a direct calculation of the elastic energy atomistic model reveals that the continuum expression for the elastic energy is both qualitatively and quantitatively incorrect. This is because it does not take atomistic scale compositional nonuniformity into account. Importantly, this result also shows that finely mixed alloys tend to have more elastic energy than segregated systems, which is the exact opposite of predictions made by some continuum theories. It is also shown that for strained thin films the traditionally used effective misfit for alloys systematically underestimate the strain energy. In some models, this drawback is handled by including an elastic contribution to the enthalpy of mixing, which is characterized in terms of the continuum concentration. The direct calculation of the atomistic model reveals that this approach suffers serious difficulties. It is demonstrated that elastic contribution to the enthalpy of mixing is nonisotropic and scale dependent. It is also shown that such effects are present in density-functional theory calculations for the Si-Ge system. This work demonstrates that it is critical to include the microscopic arrangements in any elastic

  10. Modeling and analysis of electrostatic adhesion force for climbing robot on dielectric wall materials

    NASA Astrophysics Data System (ADS)

    Mao, Jiu-Bing; Qin, Lan; Zhang, Wan-Xiong; Xie, Li; Wang, Yong

    2015-01-01

    In recent years, electrostatic adhesion technology on the wall climbing robots has attracted many researchers interest for its outstanding characteristics. In this paper, a theoretical analytical model is derived from the electrostatic adhesion field between the dielectric wall and a coplanar array of parallel strip electrodes called inter-digital electrodes (IDE). Due to the polarization on the different dielectric being complicated, the field is divided into four layers in order to obtain corresponding boundaries. Besides, the roughness of the wall surface, alternately polarities applied voltages and different dielectric parameter with different layer, all of which are also taken into account in the model since they have a significant influence on the electrostatic adhesion field. Based on this model, the electrostatic adhesion force (EAF) is calculated utilizing the Maxwell stress tensor (MST) formulation. As we all known, EAF is vital to the climbing robot design. Specially, it is possible for us to optimize the load to weight ratio in next step. Through comparing the finite element method (FEM) simulation with theoretical computation, the simulation and calculated data show that our proposed scheme can achieve desired results. Moreover, experiments of electrostatic adhesion performance for the adhesive on some different dielectric materials are also implemented.

  11. 34 CFR 300.115 - Continuum of alternative placements.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 34 Education 2 2014-07-01 2013-07-01 true Continuum of alternative placements. 300.115 Section 300... alternative placements. (a) Each public agency must ensure that a continuum of alternative placements is...) The continuum required in paragraph (a) of this section must— (1) Include the alternative...

  12. Continuum of Collaboration: Little Steps for Little Feet

    ERIC Educational Resources Information Center

    Powell, Gwynn M.

    2013-01-01

    This mini-article outlines a continuum of collaboration for faculty within a department of the same discipline. The goal of illustrating this continuum is showcase different stages of collaboration so that faculty members can assess where they are as a collective and consider steps to collaborate more. The separate points along a continuum of…

  13. Continuum Statistics of the Airy2 Process

    NASA Astrophysics Data System (ADS)

    Corwin, Ivan; Quastel, Jeremy; Remenik, Daniel

    2013-01-01

    We develop an exact determinantal formula for the probability that the Airy_2 process is bounded by a function g on a finite interval. As an application, we provide a direct proof that {sup({A}2(x)-x^2)} is distributed as a GOE random variable. Both the continuum formula and the GOE result have applications in the study of the end point of an unconstrained directed polymer in a disordered environment. We explain Johansson's (Commun. Math. Phys. 242(1-2):277-329, 2003) observation that the GOE result follows from this polymer interpretation and exact results within that field. In a companion paper (Moreno Flores et al. in Commun. Math. Phys. 2012) these continuum statistics are used to compute the distribution of the endpoint of directed polymers.

  14. A continuum model of transcriptional bursting

    PubMed Central

    Corrigan, Adam M; Tunnacliffe, Edward; Cannon, Danielle; Chubb, Jonathan R

    2016-01-01

    Transcription occurs in stochastic bursts. Early models based upon RNA hybridisation studies suggest bursting dynamics arise from alternating inactive and permissive states. Here we investigate bursting mechanism in live cells by quantitative imaging of actin gene transcription, combined with molecular genetics, stochastic simulation and probabilistic modelling. In contrast to early models, our data indicate a continuum of transcriptional states, with a slowly fluctuating initiation rate converting the gene between different levels of activity, interspersed with extended periods of inactivity. We place an upper limit of 40 s on the lifetime of fluctuations in elongation rate, with initiation rate variations persisting an order of magnitude longer. TATA mutations reduce the accessibility of high activity states, leaving the lifetime of on- and off-states unchanged. A continuum or spectrum of gene states potentially enables a wide dynamic range for cell responses to stimuli. DOI: http://dx.doi.org/10.7554/eLife.13051.001 PMID:26896676

  15. Models of Uranium continuum radio emission

    NASA Technical Reports Server (NTRS)

    Romig, Joseph H.; Evans, David R.; Sawyer, Constance B.; Schweitzer, Andrea E.; Warwick, James W.

    1987-01-01

    Uranium continuum radio emission detected by the Voyager 2 Planetary Radio Astronomy experiment during the January 1986 encounter is considered. The continuum emissions comprised four components (equatorial emissions, anomaly emissions, strong nightside emissions, and weak nightside emissions) associated with different sources. The equatorial emissions appeared most prominently during the days before closest approach and extended from 40 kHz or below to about 120 kHz. The anomaly emissions were seen about 12 hours before closest approach and extended to about 250 kHz. The agreement found between Miranda's phase and strong radio emission at 20.4 kHz, just after closest approach, suggests intense dynamic activity on the Miranda L shell.

  16. Driving Forces for Oppositely Charged Polyion Association in Aqueous Solutions: Enthalpic, Entropic, but Not Electrostatic.

    PubMed

    Fu, Jingcheng; Schlenoff, Joseph B

    2016-01-27

    Driving forces for association between oppositely charged biological or synthetic polymers in aqueous solution have long been identified as electrostatic in origin. This attraction is broken down into an entropic component, due to loss of counterions, and an enthalpic component, stemming from Coulombic attraction between opposite charges. While the balance between entropic and enthalpic contributions shifts according to the conditions, the presence of exotherms or endotherms on mixing, though small, are viewed as signatures of Coulombic interactions which support theories of polyelectrolyte association rooted in continuum electrostatics. Here, a head-to-head comparison is made between mechanisms based on electrostatics and those based on specific ion pairing, or ion exchange. Using a Hofmeister series of counterions for a common polycation, poly(diallyldimethylammonium), enthalpy changes on association with poly(styrenesulfonate) are shown to derive from changes in water perturbation, revealed by Raman scattering studies of water O-H vibrations. The free energy for complexation is almost completely entropic over all salt concentrations. PMID:26771205

  17. Spatiotemporal dynamics of continuum neural fields

    NASA Astrophysics Data System (ADS)

    Bressloff, Paul C.

    2012-01-01

    We survey recent analytical approaches to studying the spatiotemporal dynamics of continuum neural fields. Neural fields model the large-scale dynamics of spatially structured biological neural networks in terms of nonlinear integrodifferential equations whose associated integral kernels represent the spatial distribution of neuronal synaptic connections. They provide an important example of spatially extended excitable systems with nonlocal interactions and exhibit a wide range of spatially coherent dynamics including traveling waves oscillations and Turing-like patterns.

  18. Electrostatic effects on hyaluronic acid configuration

    NASA Astrophysics Data System (ADS)

    Berezney, John; Saleh, Omar

    2015-03-01

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

  19. Study on electrostatic resonance of nanoprisms with sharp corners

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  20. Bipotential continuum models for granular mechanics

    NASA Astrophysics Data System (ADS)

    Goddard, Joe

    2014-03-01

    Most currently popular continuum models for granular media are special cases of a generalized Maxwell fluid model, which describes the evolution of stress and internal variables such as granular particle fraction and fabric,in terms of imposed strain rate. It is shown how such models can be obtained from two scalar potentials, a standard elastic free energy and a ``dissipation potential'' given rigorously by the mathematical theory of Edelen. This allows for a relatively easy derivation of properly invariant continuum models for granular media and fluid-particle suspensions within a thermodynamically consistent framework. The resulting continuum models encompass all the prominent regimes of granular flow, ranging from the quasi-static to rapidly sheared, and are readily extended to include higher-gradient or Cosserat effects. Models involving stress diffusion, such as that proposed recently by Kamrin and Koval (PRL 108 178301), provide an alternative approach that is mentioned in passing. This paper provides a brief overview of a forthcoming review articles by the speaker (The Princeton Companion to Applied Mathematics, and Appl. Mech. Rev.,in the press, 2013).

  1. A Continuum Theory of Thermal Transpiration

    NASA Astrophysics Data System (ADS)

    Bielenberg, James; Brenner, Howard

    2003-11-01

    A rational, continuum mechanical description is given for the pressure drop that develops in a closed capillary tube subject to an imposed temperature gradient. This phenomenon, termed thermal transpiration, has been experimentally demonstrated in systems at vanishing Knudsen numbers, yet no purely continuum mechanical description has, until now, been given. Previous hybrid solutions (dating back to Maxwell in 1879) have utilized the classical, incompressible flow equations along with molecularly derived slip boundary conditions. This solution approach will be briefly discussed and shown to be dynamically consistent yet energetically flawed. Subsequently, we will apply a novel reformulation of continuum-mechanics and -thermodynamics, which clearly distinguishes between the Lagrangian (tracer) and the barycentric velocities, to generate a solution for the thermal pressure drop developed in a closed system. Explicitly, the phenomena at hand will be shown to be entirely analogous to Poiseuille flow in tube, albeit with the tacit recognition that the ``flow'' we are speaking of is defined in a dynamic sense rather than in the more traditional, kinematic mass-flux based sense. This solution will be show to be free of ad hoc parameters, consistent with experimental results, and in accordance with classical macroscopic thermodynamics. Beyond its purely scientific importance, this phenomenon may find applications in the emerging area of micro-fluidic pumping.

  2. Polymer Fluid Dynamics: Continuum and Molecular Approaches.

    PubMed

    Bird, R B; Giacomin, A J

    2016-06-01

    To solve problems in polymer fluid dynamics, one needs the equations of continuity, motion, and energy. The last two equations contain the stress tensor and the heat-flux vector for the material. There are two ways to formulate the stress tensor: (a) One can write a continuum expression for the stress tensor in terms of kinematic tensors, or (b) one can select a molecular model that represents the polymer molecule and then develop an expression for the stress tensor from kinetic theory. The advantage of the kinetic theory approach is that one gets information about the relation between the molecular structure of the polymers and the rheological properties. We restrict the discussion primarily to the simplest stress tensor expressions or constitutive equations containing from two to four adjustable parameters, although we do indicate how these formulations may be extended to give more complicated expressions. We also explore how these simplest expressions are recovered as special cases of a more general framework, the Oldroyd 8-constant model. Studying the simplest models allows us to discover which types of empiricisms or molecular models seem to be worth investigating further. We also explore equivalences between continuum and molecular approaches. We restrict the discussion to several types of simple flows, such as shearing flows and extensional flows, which are of greatest importance in industrial operations. Furthermore, if these simple flows cannot be well described by continuum or molecular models, then it is not necessary to lavish time and energy to apply them to more complex flow problems. PMID:27276553

  3. Line and continuum variability in active galaxies

    NASA Astrophysics Data System (ADS)

    Rashed, Y. E.; Eckart, A.; Valencia-S., M.; García-Marín, M.; Busch, G.; Zuther, J.; Horrobin, M.; Zhou, H.

    2015-12-01

    We compared optical spectroscopic and photometric data for 18 active galactic nuclei (AGN) galaxies over two to three epochs, with time intervals of typically 5 to 10 yr. We used the multi-object double spectrograph (MODS) at the Large Binocular Telescope (LBT) and compared the spectra with data taken from the SDSS data base and the literature. We found variations in the forbidden oxygen lines as well as in the hydrogen recombination lines of these sources. For four of the sources we found that, within the calibration uncertainties, the variations in continuum and line spectra of the sources are very small. We argue that it is mainly the difference in black hole mass between the samples that is responsible for the different degree of continuum variability. In addition, we found that for an otherwise constant accretion rate the total line variability (dominated by the narrow line contributions) reverberates in a similar way to the continuum variability with a dependence ΔLline ∝ (ΔLcont)3/2. Because this dependence is predominantly expressed in the narrow line emission, the implication is that the part of the source that dominates the luminosity in the narrow line region must be very compact, with a diameter of the order of at least 10 light-years. A comparison with data from the literature shows that these findings describe the variability characteristics of a total of 61 broad and narrow line sources.

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

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

  5. Electrostatic beneficiation of coal. Quarterly technical progress report, April 1, 1996--June 30, 1996

    SciTech Connect

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

    1996-07-01

    Progress reports are presented for the following: modification to the electrostatic separator; review of DOE specifications for minimum beneficiation and calculations of grinding requirements based on washability; two-pass beneficiation; analysis of different sieve fractions; measurement of charge to mass ratio as a function of height of deposition; and charging of coal against different materials.

  6. Densities of Si Determined by an Image Digitizing Technique in Combination with an Electrostatic Levitator

    NASA Technical Reports Server (NTRS)

    Ohsaka, K.; Chung, S. K.; Rhim, W. K.

    1996-01-01

    We have determined the densities of Si in the liquid, rho1(T), and solid,rho s(T), states as a function of temperature,T, by employing an image digitizing technique and numerical calculation methods in combination with an electrostatic levitator.

  7. Pairing resonances and the continuum spectroscopy of 10Li

    NASA Astrophysics Data System (ADS)

    Orrigo, S. E. A.; Lenske, H.

    2009-06-01

    Pairing across the particle emission threshold and the properties of corresponding quasiparticle strength functions are discussed in an extended mean-field approach. This particular type of dynamical correlations gives rise to a unique class of sharp low-lying resonances close to the particle emission threshold. Spectral functions for particle and hole states are discussed. They are explored theoretically by single-nucleon transfer reactions, populating the low energy continuum with respect to a core nucleus. The cross sections of the reaction d(9Li, 10Li)p at Tlab = 2.36 AMeV, recently measured at REX-ISOLDE, are well reproduced by our calculations including a pairing resonance in the 3 /2- partial wave of purely coupled channels nature.

  8. Diffuse continuum gamma rays from the Galaxy observed by COMPTEL

    NASA Technical Reports Server (NTRS)

    Strong, A. W.; Bennett, K.; Bloemen, H.; Diehl, R.; Hermsen, W.; Morris, D.; Schonfelder, V.; Stacy, J. G.; De Vries, C.; Varendorff, M.

    1994-01-01

    The diffuse Galactic continuum gamma-ray emission has been studied using the full Sky Survey from COMPTEL on the Compton Observatory CGRO. The diffuse emission appears to be visible in the whole 0.75-30 MeV range covered by the instrument, although a considerable contribution from unresolved point sources cannot be excluded. A correlation analysis using HI and CO surveys of the Galaxy is used to derive the Galactic emissivity spectrum, and this is consistent with a smooth continuation to the spectrum at higher energies derived by a similar analysis of COS-B data. The apparent conversion factor from integrated CO temperature to molecular hydrogen column density can also be determined from the correlation analysis. The value obtained is consistent with results from COS-B and other non-gamma-ray methods. Calculations of the emissivity spectrum from bremsstrahlung from a cosmic-ray electron spectrum based on propagation models are compared with the observations.

  9. A new approach to solve inverse kinematics of a planar flexible continuum robot

    NASA Astrophysics Data System (ADS)

    Amouri, Ammar; Mahfoudi, Chawki; Zaatri, Abdelouahab; Merabti, Halim

    2014-10-01

    Research on the modeling of continuum robots, focused on ways to constrain the geometrical models, while maintaining maximum specificities and mechanical properties of the robot. In this paper we propose a new numerical solution for solving the inverse geometric model of a planar flexible continuum robot, we assuming that each section is curved in an arc of a circle, while having the central axis of the inextensible structure. The inverse geometric model for one section is calculated geometrically, whereas the extreme points, of each section, used in calculating the inverse geometric model for multi-section is calculated numerically using a particle swarm optimization (PSO) method. Simulation examples of this method are carried to validate the proposed approach.

  10. Electrostatic coating technologies for food processing.

    PubMed

    Barringer, Sheryl A; Sumonsiri, Nutsuda

    2015-01-01

    The application of electrostatics in both powder and liquid coating can improve the quality of food, such as its appearance, aroma, taste, and shelf life. Coatings can be found most commonly in the snack food industry, as well as in confectionery, bakery, meat and cheese processing. In electrostatic powder coating, the most important factors influencing coating quality are powder particle size, density, flowability, charge, and resistivity, as well as the surface properties and characteristics of the target. The most important factors during electrostatic liquid coating, also known as electrohydrodynamic coating, include applied voltage and electrical resistivity and viscosity of the liquid. A good understanding of these factors is needed for the design of optimal coating systems for food processing. PMID:25648420

  11. Electrostatic micromotor based on ferroelectric ceramics

    NASA Astrophysics Data System (ADS)

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

    2004-11-01

    A new electrostatic micromotor is described that utilizes the electromechanical energy conversion principle earlier described by the authors. The electromechanical energy conversion is based on reversible electrostatic rolling of thin metallic films (petals) on a ferroelectric surface. The motor's active media are layers of ferroelectric ceramics (about 100 µm in thickness). The characteristics of the electrostatic rolling of the petals on different ceramic surfaces are studied, as well as the dynamic characteristics of the micromotors. It is shown that the use of antiferroelectric material allows one to reach a specific energy capacitance comparable to that of the micromotors based on ferroelectric films and to achieve a specific power of 30-300 µW mm-2.

  12. Art and the science of electrostatic precipitation

    SciTech Connect

    White, H.J.

    1984-11-01

    An essay on the art and science of electrostatic precipitation was presented by Harry J. White in November 1982 at a symposium in Tokyo for the Institute of Electrostatics Japan. The paper is written in a philosophic rather than a scientific vein in order to express a personal viewpoint distilled over many years on the subject. In examining the roles of art and science in electrostatic precipitation it has been shown how both are operative and essential. The long-term trend is for less dependence on the art phase, and more on the science. But there is no indication that art and intuition will not continue to be very important. This is especially true in precipitator design which even today is almost as much an art as it is a science.

  13. Analytical expressions for electrostatics of graphene structures

    NASA Astrophysics Data System (ADS)

    Georgantzinos, S. K.; Giannopoulos, G. I.; Fatsis, A.; Vlachakis, N. V.

    2016-10-01

    This study focuses on electrostatics of various graphene structures as graphene monolayer, graphene nanoribbons, as well as multi-layer graphene or graphene flakes. An atomistic moment method based on classical electrostatics is utilized in order to evaluate the charge distribution in each nanostructure. Assuming a freestanding graphene structure in an infinite or in a semi-infinite space limited by a grounded infinite plane, the effect of the length, width, number of layers and position of the nanostructure on its electrostatic charge distributions and total charge and capacitance is examined through a parametric analysis. The results of the present show good agreement with corresponding available data in the literature, obtained from different theoretical approaches. Performing nonlinear regression analysis on the numerical results, where it is possible, simple analytical expressions are proposed for the total charge and charge distribution prediction based on structure geometry.

  14. Nonlinear parallel momentum transport in strong electrostatic turbulence

    NASA Astrophysics Data System (ADS)

    Wang, Lu; Wen, Tiliang; Diamond, P. H.

    2015-05-01

    Most existing theoretical studies of momentum transport focus on calculating the Reynolds stress based on quasilinear theory, without considering the nonlinear momentum flux- ⟨ v ˜ r n ˜ u ˜ ∥ ⟩ . However, a recent experiment on TORPEX found that the nonlinear toroidal momentum flux induced by blobs makes a significant contribution as compared to the Reynolds stress [Labit et al., Phys. Plasmas 18, 032308 (2011)]. In this work, the nonlinear parallel momentum flux in strong electrostatic turbulence is calculated by using a three dimensional Hasegawa-Mima equation, which is relevant for tokamak edge turbulence. It is shown that the nonlinear diffusivity is smaller than the quasilinear diffusivity from Reynolds stress. However, the leading order nonlinear residual stress can be comparable to the quasilinear residual stress, and so may be important to intrinsic rotation in tokamak edge plasmas. A key difference from the quasilinear residual stress is that parallel fluctuation spectrum asymmetry is not required for nonlinear residual stress.

  15. Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory

    NASA Astrophysics Data System (ADS)

    Wang, Hao; Yang, Weitao

    2016-06-01

    We developed a new method to calculate the atomic polarizabilities by fitting to the electrostatic potentials (ESPs) obtained from quantum mechanical (QM) calculations within the linear response theory. This parallels the conventional approach of fitting atomic charges based on electrostatic potentials from the electron density. Our ESP fitting is combined with the induced dipole model under the perturbation of uniform external electric fields of all orientations. QM calculations for the linear response to the external electric fields are used as input, fully consistent with the induced dipole model, which itself is a linear response model. The orientation of the uniform external electric fields is integrated in all directions. The integration of orientation and QM linear response calculations together makes the fitting results independent of the orientations and magnitudes of the uniform external electric fields applied. Another advantage of our method is that QM calculation is only needed once, in contrast to the conventional approach, where many QM calculations are needed for many different applied electric fields. The molecular polarizabilities obtained from our method show comparable accuracy with those from fitting directly to the experimental or theoretical molecular polarizabilities. Since ESP is directly fitted, atomic polarizabilities obtained from our method are expected to reproduce the electrostatic interactions better. Our method was used to calculate both transferable atomic polarizabilities for polarizable molecular mechanics' force fields and nontransferable molecule-specific atomic polarizabilities.

  16. Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory.

    PubMed

    Wang, Hao; Yang, Weitao

    2016-06-14

    We developed a new method to calculate the atomic polarizabilities by fitting to the electrostatic potentials (ESPs) obtained from quantum mechanical (QM) calculations within the linear response theory. This parallels the conventional approach of fitting atomic charges based on electrostatic potentials from the electron density. Our ESP fitting is combined with the induced dipole model under the perturbation of uniform external electric fields of all orientations. QM calculations for the linear response to the external electric fields are used as input, fully consistent with the induced dipole model, which itself is a linear response model. The orientation of the uniform external electric fields is integrated in all directions. The integration of orientation and QM linear response calculations together makes the fitting results independent of the orientations and magnitudes of the uniform external electric fields applied. Another advantage of our method is that QM calculation is only needed once, in contrast to the conventional approach, where many QM calculations are needed for many different applied electric fields. The molecular polarizabilities obtained from our method show comparable accuracy with those from fitting directly to the experimental or theoretical molecular polarizabilities. Since ESP is directly fitted, atomic polarizabilities obtained from our method are expected to reproduce the electrostatic interactions better. Our method was used to calculate both transferable atomic polarizabilities for polarizable molecular mechanics' force fields and nontransferable molecule-specific atomic polarizabilities.

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

    PubMed Central

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

    2013-01-01

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

  18. A continuum model of docking of synaptic vesicle to plasma membrane

    PubMed Central

    Liu, Tianshu; Singh, Pankaj; Jenkins, James T.; Jagota, Anand; Bykhovskaia, Maria; Hui, Chung-Yuen

    2015-01-01

    Neurotransmitter release from neuronal terminals is governed by synaptic vesicle fusion. Vesicles filled with transmitters are docked at the neuronal membrane by means of the SNARE machinery. After a series of events leading up to the fusion pore formation, neurotransmitters are released into the synaptic cleft. In this paper, we study the mechanics of the docking process. A continuum model is used to determine the deformation of a spherical vesicle and a plasma membrane, under the influence of SNARE-machinery forces and electrostatic repulsion. Our analysis provides information on the variation of in-plane stress in the membranes, which is known to affect fusion. Also, a simple model is proposed to study hemifusion. PMID:25551140

  19. Simplified continuum solvent model with a smooth cavity based on volumetric data.

    PubMed

    Held, Alexander; Walter, Michael

    2014-11-01

    We present a continuum solvent model (CSM) with a smooth cavity for the application in grid-based electronic structure methods. The cavity is identified with the inherently smooth distribution function of a binary mixture at infinite dilution. We obtain a cavity model based on atomic van der Waals radii and one free parameter controlling the overall size. This single parameter is sufficient to adequately reproduce experimental partial molar volumes. The CSM based on this cavity is of similar accuracy in the prediction of aqueous solvation Gibbs energies of small neutral molecules and ions as other CSMs with a smooth cavity. We apply the model to systems in non-aqueous solution, i.e., spiropyran/merocyanin energetics, a proton transfer reaction in dimethyl sulfoxide, and the electrostatic screening of charged gold clusters in an ionic liquid. PMID:25381503

  20. Simplified continuum solvent model with a smooth cavity based on volumetric data

    SciTech Connect

    Held, Alexander; Walter, Michael

    2014-11-07

    We present a continuum solvent model (CSM) with a smooth cavity for the application in grid-based electronic structure methods. The cavity is identified with the inherently smooth distribution function of a binary mixture at infinite dilution. We obtain a cavity model based on atomic van der Waals radii and one free parameter controlling the overall size. This single parameter is sufficient to adequately reproduce experimental partial molar volumes. The CSM based on this cavity is of similar accuracy in the prediction of aqueous solvation Gibbs energies of small neutral molecules and ions as other CSMs with a smooth cavity. We apply the model to systems in non-aqueous solution, i.e., spiropyran/merocyanin energetics, a proton transfer reaction in dimethyl sulfoxide, and the electrostatic screening of charged gold clusters in an ionic liquid.