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Sample records for additive all-atom force

  1. CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol

    PubMed Central

    Hatcher, Elizabeth; Guvench, Olgun; MacKerell, Alexander D.

    2009-01-01

    Parametrization of the additive all-atom CHARMM force field for acyclic polyalcohols, acyclic carbohydrates and inositol is conducted. Initial parameters were transferred from the alkanes and hexopyranose carbohydrates, with subsequent development and optimization of parameters unique to the molecules considered in this study. Using the model compounds acetone and acetaldehyde, nonbonded parameters for carbonyls were optimized targeting quantum mechanical interaction data for solute-water pairs and pure solvent thermodynamic data. Bond and angle parameters were adjusted by comparing optimized geometries to small molecule crystal survey data and by performing vibrational analyses on acetone, acetaldehyde and glycerol. C-C-C-C, C-C-C-O, C-C-OH and O-C-C-O torsional parameters for polyol chains were fit to quantum mechanical dihedral potential energy scans comprising over 1500 RIMP2/cc-pVTZ//MP2/6-31G(d) conformations using an automated Monte Carlo simulated annealing procedure. Comparison of computed condensed-phase data, including crystal lattice parameters and densities, NMR proton-proton couplings, densities and diffusion coefficients of aqueous solutions, to experimental data validated the optimized parameters. Parameter development for these compounds proved particularly challenging because of the flexibility of the acyclic sugars and polyalcohols as well as the intramolecular hydrogen bonding between vicinal hydroxyls for all of the compounds. The newly optimized additive CHARMM force field parameters are anticipated to be of utility for atomic level of detail simulations of acyclic polyalcohols, acyclic carbohydrates and inositol in solution. PMID:20160980

  2. CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates

    PubMed Central

    Mallajosyula, Sairam S.; Guvench, Olgun; Hatcher, Elizabeth; MacKerell, Alexander D.

    2012-01-01

    Presented is an extension of the CHARMM additive all-atom carbohydrate force field to enable the modeling of phosphate and sulfate linked to carbohydrates. The parameters are developed in a hierarchical fashion using model compounds containing the key atoms in the full carbohydrates. Target data for parameter optimization included full two-dimensional energy surfaces defined by the glycosidic dihedral angle pairs in the phosphate/sulfate model compound analogs of hexopyranose monosaccharide phosphates and sulfates, as determined by quantum mechanical (QM) MP2/cc-pVTZ single point energies on MP2/6-31+G(d) optimized structures. In order to achieve balanced, transferable dihedral parameters for the dihedral angles, surfaces for all possible anomeric and conformational states were included during the parametrization process. In addition, to model physiologically relevant systems both the mono- and di-anionic charged states were studied for the phosphates. This resulted in over 7000 MP2/cc-pVTZ//MP2/6-31G+(d) model compound conformational energies which, supplemented with QM geometries, were the main target data for the parametrization. Parameters were validated against crystals of relevant monosaccharide derivatives obtained from the Cambridge Structural Database (CSD) and larger systems, namely inositol-(tri/tetra/penta) phosphates non-covalently bound to the pleckstrin homology (PH) domain and oligomeric chondroitin sulfate in solution and in complex with cathepsin K protein. PMID:22685386

  3. CHARMM Additive All-Atom Force Field for Aldopentofuranoses, Methyl-Aldopentofuranosides and Fructofuranose

    PubMed Central

    Hatcher, Elizabeth; Guvench, Olgun; MacKerell, Alexander D.

    2009-01-01

    An additive all-atom empirical force field for aldopentofuranoses, methyl-aldopentofuranosides (Me-aldopentofuranosides) and fructofuranose carbohydrates, compatible with existing CHARMM carbohydrate parameters, is presented. Building on existing parameters transferred from cyclic ethers and hexopyranoses, parameters were further developed using target data for complete furanose carbohydrates as well as O-methyl tetrahydrofuran. The bond and angle equilibrium parameters were adjusted to reproduce target geometries from a survey of furanose crystal structures, and dihedral parameters were fit to over 1700 quantum mechanical (QM) MP2/cc-pVTZ//MP2/6-31G(d) conformational energies. The conformational energies were for a variety of complete furanose monosaccharides, and included two-dimensional ring pucker energy surfaces. Bonded parameter optimization led to the correct description of the ring pucker for a large set of furanose compounds, while furanose-water interaction energies and distances reproduced QM HF/6-31G(d) results for a number of furanose monosaccharides, thereby validating the nonbonded parameters. Crystal lattice unit cell parameters and volumes, aqueous-phase densities, and aqueous NMR ring pucker and exocyclic data were used to validate the parameters in condensed-phase environments. Conformational sampling analysis of the ring pucker and exocyclic group showed excellent agreement with experimental NMR data, demonstrating that the conformational energetics in aqueous solution are accurately described by the optimized force field. Overall, the parameters reproduce available experimental data well and are anticipated to be of utility in future computational studies of carbohydrates, including in the context of proteins, nucleic acids and/or lipids when combined with existing CHARMM biomolecular force fields. PMID:19694450

  4. CHARMM General Force Field (CGenFF): A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

    PubMed Central

    Vanommeslaeghe, K.; Hatcher, E.; Acharya, C.; Kundu, S.; Zhong, S.; Shim, J.; Darian, E.; Guvench, O.; Lopes, P.; Vorobyov, I.; MacKerell, A. D.

    2010-01-01

    The widely used CHARMM additive all-atom force field includes parameters for proteins, nucleic acids, lipids and carbohydrates. In the present paper an extension of the CHARMM force field to drug-like molecules is presented. The resulting CHARMM General Force Field (CGenFF) covers a wide range of chemical groups present in biomolecules and drug-like molecules, including a large number of heterocyclic scaffolds. The parametrization philosophy behind the force field focuses on quality at the expense of transferability, with the implementation concentrating on an extensible force field. Statistics related to the quality of the parametrization with a focus on experimental validation are presented. Additionally, the parametrization procedure, described fully in the present paper in the context of the model systems, pyrrolidine, and 3-phenoxymethylpyrrolidine will allow users to readily extend the force field to chemical groups that are not explicitly covered in the force field as well as add functional groups to and link together molecules already available in the force field. CGenFF thus makes it possible to perform “all-CHARMM” simulations on drug-target interactions thereby extending the utility of CHARMM force fields to medicinally relevant systems. PMID:19575467

  5. Improving an all-atom force field.

    PubMed

    Mohanty, Sandipan; Hansmann, U H E

    2007-07-01

    Experimentally well-characterized proteins that are small enough to be computationally tractable provide useful information for refining existing all-atom force fields. This is used by us for reparametrizing a recently developed all-atom force field. Relying on high statistics parallel tempering simulations of a designed 20 residue beta-sheet peptide, we propose incremental changes that improve the force field's range of applicability. PMID:17677516

  6. CHARMM All-Atom Additive Force Field for Sphingomyelin: Elucidation of Hydrogen Bonding and of Positive Curvature

    PubMed Central

    Venable, Richard M.; Sodt, Alexander J.; Rogaski, Brent; Rui, Huan; Hatcher, Elizabeth; MacKerell, Alexander D.; Pastor, Richard W.; Klauda, Jeffery B.

    2014-01-01

    The C36 CHARMM lipid force field has been extended to include sphingolipids, via a combination of high-level quantum mechanical calculations on small molecule fragments, and validation by extensive molecular dynamics simulations on N-palmitoyl and N-stearoyl sphingomyelin. NMR data on these two molecules from several studies in bilayers and micelles played a strong role in the development and testing of the force field parameters. Most previous force fields for sphingomyelins were developed before the availability of the detailed NMR data and relied on x-ray diffraction of bilayers alone for the validation; these are shown to be too dense in the bilayer plane based on published chain order parameter data from simulations and experiments. The present simulations reveal O-H:::O-P intralipid hydrogen bonding occurs 99% of the time, and interlipid N-H:::O=C (26-29%, depending on the lipid) and N-H:::O-H (17–19%). The interlipid hydrogen bonds are long lived, showing decay times of 50 ns, and forming strings of lipids, and leading to reorientational correlation time of nearly 100 ns. The spontaneous radius of curvature for pure N-palmitoyl sphingomyelin bilayers is estimated to be 43–100 Å, depending on the assumptions made in assigning a bending constant; this unusual positive curvature for a two-tailed neutral lipid is likely associated with hydrogen bond networks involving the NH of the sphingosine group. PMID:24988348

  7. Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA

    PubMed Central

    Denning, Elizabeth J.; Priyakumar, U. Deva; Nilsson, Lennart; MacKerell, Alexander D.

    2011-01-01

    Here, we present an update of the CHARMM27 all-atom additive force field for nucleic acids that improves the treatment of RNA molecules. The original CHARMM27 force field parameters exhibit enhanced Watson-Crick (WC) base pair opening which is not consistent with experiment while analysis of MD simulations show the 2′-hydroxyl moiety to almost exclusively sample the O3′ orientation. Quantum mechanical studies of RNA related model compounds indicate the energy minimum associated with the O3′ orientation to be too favorable, consistent with the MD results. Optimization of the dihedral parameters dictating the energy of the 2′-hydroxyl proton targeting the QM data yielded several parameter sets, which sample both the base and O3′ orientations of the 2′-hydroxyl to varying degrees. Selection of the final dihedral parameters was based on reproduction of hydration behavior as related to a survey of crystallographic data and better agreement with experimental NMR J-coupling values. Application of the model, designated CHARMM36, to a collection of canonical and non-canonical RNA molecules reveals overall improved agreement with a range of experimental observables as compared to CHARMM27. The results also indicate the sensitivity of the conformational heterogeneity of RNA to the orientation of the 2′-hydroxyl moiety and support a model whereby the 2′-hydroxyl can enhance the probability of conformational transitions in RNA. PMID:21469161

  8. Ab initio prediction of protein structure with both all-atom and simplified force fields

    NASA Astrophysics Data System (ADS)

    Scheraga, Harold

    2004-03-01

    Using only a physics-based ab initio method, and both all-atom (ECEPP/3) and simplified united-residue (UNRES) force fields, global optimization of both potential functions with Monte Carlo-plus-Minimization (MCM) and Conformational Space Annealing (CSA), respectively, provides predicted structures of proteins without use of knowledge-based information. The all-atom approach has been applied to the 46-residue protein A, and the UNRES approach has been applied to larger CASP targets. The predicted structures will be described.

  9. An all-atom force field developed for Zn₄O(RCO₂)₆ metal organic frameworks.

    PubMed

    Sun, Yingxin; Sun, Huai

    2014-03-01

    An all-atom force field is developed for metal organic frameworks Zn₄O(RCO₂)₆ by fitting to quantum mechanics data. Molecular simulations are conducted to validate the force field by calculating thermal expansion coefficients, crystal bulk and Young's moduli, power spectra, self-diffusion coefficients, and activation energies of self-diffusions for benzene and n-hexane. The calculated results are in good agreement with available experimental data. The proposed force field is suitable for simulations of adsorption or diffusion of organic molecules with flexible frameworks. PMID:24562858

  10. An All-Atom Force Field for Tertiary Structure Prediction of Helical Proteins

    PubMed Central

    Herges, T.; Wenzel, W.

    2004-01-01

    We have developed an all-atom free-energy force field (PFF01) for protein tertiary structure prediction. PFF01 is based on physical interactions and was parameterized using experimental structures of a family of proteins believed to span a wide variety of possible folds. It contains empirical, although sequence-independent terms for hydrogen bonding. Its solvent-accessible surface area solvent model was first fit to transfer energies of small peptides. The parameters of the solvent model were then further optimized to stabilize the native structure of a single protein, the autonomously folding villin headpiece, against competing low-energy decoys. Here we validate the force field for five nonhomologous helical proteins with 20–60 amino acids. For each protein, decoys with 2–3 Å backbone root mean-square deviation and correct experimental Cβ–Cβ distance constraints emerge as those with the lowest energy. PMID:15507688

  11. All-Atom Internal Coordinate Mechanics (ICM) Force Field for Hexopyranoses and Glycoproteins

    PubMed Central

    2016-01-01

    We present an extension of the all-atom internal-coordinate force field, ICMFF, that allows for simulation of heterogeneous systems including hexopyranose saccharides and glycan chains in addition to proteins. A library of standard glycan geometries containing α- and β-anomers of the most common hexapyranoses, i.e., d-galactose, d-glucose, d-mannose, d-xylose, l-fucose, N-acetylglucosamine, N-acetylgalactosamine, sialic, and glucuronic acids, is created based on the analysis of the saccharide structures reported in the Cambridge Structural Database. The new force field parameters include molecular electrostatic potential-derived partial atomic charges and the torsional parameters derived from quantum mechanical data for a collection of minimal molecular fragments and related molecules. The ϕ/ψ torsional parameters for different types of glycosidic linkages are developed using model compounds containing the key atoms in the full carbohydrates, i.e., glycosidic-linked tetrahydropyran–cyclohexane dimers. Target data for parameter optimization include two-dimensional energy surfaces corresponding to the ϕ/ψ glycosidic dihedral angles in the disaccharide analogues, as determined by quantum mechanical MP2/6-31G** single-point energies on HF/6-31G** optimized structures. To achieve better agreement with the observed geometries of glycosidic linkages, the bond angles at the O-linkage atoms are added to the internal variable set and the corresponding bond bending energy term is parametrized using quantum mechanical data. The resulting force field is validated on glycan chains of 1–12 residues from a set of high-resolution X-ray glycoprotein structures based on heavy atom root-mean-square deviations of the lowest-energy glycan conformations generated by the biased probability Monte Carlo (BPMC) molecular mechanics simulations from the native structures. The appropriate BPMC distributions for monosaccharide–monosaccharide and protein–glycan linkages are derived

  12. Refined OPLS all-atom force field for saturated phosphatidylcholine bilayers at full hydration.

    PubMed

    Maciejewski, Arkadiusz; Pasenkiewicz-Gierula, Marta; Cramariuc, Oana; Vattulainen, Ilpo; Rog, Tomasz

    2014-05-01

    We report parametrization of dipalmitoyl-phosphatidylcholine (DPPC) in the framework of the Optimized Parameters for Liquid Simulations all-atom (OPLS-AA) force field. We chose DPPC as it is one of the most studied phospholipid species and thus has plenty of experimental data necessary for model validation, and it is also one of the highly important and abundant lipid types, e.g., in lung surfactant. Overall, PCs have not been previously parametrized in the OPLS-AA force field; thus, there is a need to derive its bonding and nonbonding parameters for both the polar and nonpolar parts of the molecule. In the present study, we determined the parameters for torsion angles in the phosphatidylcholine and glycerol moieties and in the acyl chains, as well the partial atomic charges. In these calculations, we used three methods: (1) Hartree-Fock (HF), (2) second order Møller-Plesset perturbation theory (MP2), and (3) density functional theory (DFT). We also tested the effect of the polar environment by using the polarizable continuum model (PCM), and for acyl chains the van der Waals parameters were also adjusted. In effect, six parameter sets were generated and tested on a DPPC bilayer. Out of these six sets, only one was found to be able to satisfactorily reproduce experimental data for the lipid bilayer. The successful DPPC model was obtained from MP2 calculations in an implicit polar environment (PCM). PMID:24745688

  13. All-Atom Polarizable Force Field for DNA Based on the Classical Drude Oscillator Model

    PubMed Central

    Savelyev, Alexey; MacKerell, Alexander D.

    2014-01-01

    Presented is a first generation atomistic force field for DNA in which electronic polarization is modeled based on the classical Drude oscillator formalism. The DNA model is based on parameters for small molecules representative of nucleic acids, including alkanes, ethers, dimethylphosphate, and the nucleic acid bases and empirical adjustment of key dihedral parameters associated with the phosphodiester backbone, glycosidic linkages and sugar moiety of DNA. Our optimization strategy is based on achieving a compromise between satisfying the properties of the underlying model compounds in the gas phase targeting QM data and reproducing a number of experimental properties of DNA duplexes in the condensed phase. The resulting Drude force field yields stable DNA duplexes on the 100 ns time scale and satisfactorily reproduces (1) the equilibrium between A and B forms of DNA and (2) transitions between the BI and BII sub-states of B form DNA. Consistency with the gas phase QM data for the model compounds is significantly better for the Drude model as compared to the CHARMM36 additive force field, which is suggested to be due to the improved response of the model to changes in the environment associated with the explicit inclusion of polarizability. Analysis of dipole moments associated with the nucleic acid bases shows the Drude model to have significantly larger values than those present in CHARMM36, with the dipoles of individual bases undergoing significant variations during the MD simulations. Additionally, the dipole moment of water was observed to be perturbed in the grooves of DNA. PMID:24752978

  14. All-atom and coarse-grained simulations of the forced unfolding pathways of the SNARE complex.

    PubMed

    Zheng, Wenjun

    2014-07-01

    The SNARE complex, consisting of three proteins (VAMP2, syntaxin, and SNAP-25), is thought to drive membrane fusion by assembling into a four-helix bundle through a zippering process. In support of the above zippering model, a recent single-molecule optical tweezers experiment by Gao et al. revealed a sequential unzipping of SNARE along VAMP2 in the order of the linker domain → the C-terminal domain → the N-terminal domain. To offer detailed structural insights to this unzipping process, we have performed all-atom and coarse-grained steered molecular dynamics (sMD) simulations of the forced unfolding pathways of SNARE using different models and force fields. Our findings are summarized as follows: First, the sMD simulations based on either an all-atom force field (with an implicit solvent model) or a coarse-grained Go model were unable to capture the forced unfolding pathway of SNARE as observed by Gao et al., which may be attributed to insufficient simulation time and inaccurate force fields. Second, the sMD simulations based on a reparameterized coarse-grained model (i.e., modified elastic network model) were able to predict a sequential unzipping of SNARE in good agreement with the findings by Gao et al. The key to this success is to reparameterize the intrahelix and interhelix nonbonded force constants against the pair-wise residue-residue distance fluctuations collected from all-atom MD simulations of SNARE. Therefore, our finding supports the importance of accurately describing the inherent dynamics/flexibility of SNARE (in the absence of force), in order to correctly simulate its unfolding behaviors under force. This study has established a useful computational framework for future studies of the zippering function of SNARE and its perturbations by point mutations with amino-acid level of details, and more generally the forced unfolding pathways of other helix bundle proteins. PMID:24403006

  15. All-atom polarizable force field for DNA based on the classical Drude oscillator model.

    PubMed

    Savelyev, Alexey; MacKerell, Alexander D

    2014-06-15

    Presented is a first generation atomistic force field (FF) for DNA in which electronic polarization is modeled based on the classical Drude oscillator formalism. The DNA model is based on parameters for small molecules representative of nucleic acids, including alkanes, ethers, dimethylphosphate, and the nucleic acid bases and empirical adjustment of key dihedral parameters associated with the phosphodiester backbone, glycosidic linkages, and sugar moiety of DNA. Our optimization strategy is based on achieving a compromise between satisfying the properties of the underlying model compounds in the gas phase targeting quantum mechanical (QM) data and reproducing a number of experimental properties of DNA duplexes in the condensed phase. The resulting Drude FF yields stable DNA duplexes on the 100-ns time scale and satisfactorily reproduce (1) the equilibrium between A and B forms of DNA and (2) transitions between the BI and BII substates of B form DNA. Consistency with the gas phase QM data for the model compounds is significantly better for the Drude model as compared to the CHARMM36 additive FF, which is suggested to be due to the improved response of the model to changes in the environment associated with the explicit inclusion of polarizability. Analysis of dipole moments associated with the nucleic acid bases shows the Drude model to have significantly larger values than those present in CHARMM36, with the dipoles of individual bases undergoing significant variations during the MD simulations. Additionally, the dipole moment of water was observed to be perturbed in the grooves of DNA. PMID:24752978

  16. All-atom force field for the prediction of vapor-liquid equilibria and interfacial properties of HFA134a.

    PubMed

    Peguin, Robson P S; Kamath, Ganesh; Potoff, Jeffrey J; da Rocha, Sandro R P

    2009-01-01

    A new all-atom force field capable of accurately predicting the bulk and interfacial properties of 1,1,1,2-tetrafluoroethane (HFA134a) is reported. Parameterization of several force fields with different initial charge configurations from ab initio calculations was performed using the histogram reweighting method and Monte Carlo simulations in the grand canonical ensemble. The 12-6 Lennard-Jones well depth and diameter for the different HFA134a models were determined by fitting the simulation results to pure-component vapor-equilibrium data. Initial screening of the force fields was achieved by comparing the calculated and experimental bulk properties. The surface tension of pure HFA134a served as an additional screening property to help discriminate an optimum model. The proposed model reproduces the experimental saturated liquid and vapor densities, and the vapor pressure for HFA134a within average errors of 0.7%, 4.4%, and 3.1%, respectively. Critical density, temperature, vapor pressure, normal boiling point, and heat of vaporization at 298 K are also in good agreement with experimental data with errors of 0.2%, 0.1%, 6.2%, 0%, 2.2%, respectively. The calculated surface tension is found to be within the experimental range of 7.7-8.1 mN.m(-1). The dipole moment of the different models was found to significantly affect the prediction of the vapor pressure and surface tension. The ability of the HFA134a models in predicting the interfacial tension against water is also discussed. The results presented here are relevant in the development of technologies where the more environmentally friendly HFA134a is utilized as a substitute to the ozone depleting chlorofluorocarbon propellants. PMID:19086791

  17. Hierarchical atom type definitions and extensible all-atom force fields.

    PubMed

    Jin, Zhao; Yang, Chunwei; Cao, Fenglei; Li, Feng; Jing, Zhifeng; Chen, Long; Shen, Zhe; Xin, Liang; Tong, Sijia; Sun, Huai

    2016-03-15

    The extensibility of force field is a key to solve the missing parameter problem commonly found in force field applications. The extensibility of conventional force fields is traditionally managed in the parameterization procedure, which becomes impractical as the coverage of the force field increases above a threshold. A hierarchical atom-type definition (HAD) scheme is proposed to make extensible atom type definitions, which ensures that the force field developed based on the definitions are extensible. To demonstrate how HAD works and to prepare a foundation for future developments, two general force fields based on AMBER and DFF functional forms are parameterized for common organic molecules. The force field parameters are derived from the same set of quantum mechanical data and experimental liquid data using an automated parameterization tool, and validated by calculating molecular and liquid properties. The hydration free energies are calculated successfully by introducing a polarization scaling factor to the dispersion term between the solvent and solute molecules. © 2015 Wiley Periodicals, Inc. PMID:26537332

  18. Reconciling Structural and Thermodynamic Predictions Using All-Atom and Coarse-Grain Force Fields: The Case of Charged Oligo-Arginine Translocation into DMPC Bilayers

    PubMed Central

    2015-01-01

    Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide–water and peptide–membrane interactions allow prediction of free energy minima at the bilayer–water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are −2.51, −4.28, and −5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are −0.83, −3.33, and −3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of

  19. COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids

    PubMed Central

    2015-01-01

    We describe the derivation of a set of bonded and nonbonded coarse-grained (CG) potential functions for use in implicit-solvent Brownian dynamics (BD) simulations of proteins derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acids. Bonded potential functions were derived from 1 μs MD simulations of each of the 20 canonical amino acids, with histidine modeled in both its protonated and neutral forms; nonbonded potential functions were derived from 1 μs MD simulations of every possible pairing of the amino acids (231 different systems). The angle and dihedral probability distributions and radial distribution functions sampled during MD were used to optimize a set of CG potential functions through use of the iterative Boltzmann inversion (IBI) method. The optimized set of potential functions—which we term COFFDROP (COarse-grained Force Field for Dynamic Representation Of Proteins)—quantitatively reproduced all of the “target” MD distributions. In a first test of the force field, it was used to predict the clustering behavior of concentrated amino acid solutions; the predictions were directly compared with the results of corresponding all-atom explicit-solvent MD simulations and found to be in excellent agreement. In a second test, BD simulations of the small protein villin headpiece were carried out at concentrations that have recently been studied in all-atom explicit-solvent MD simulations by Petrov and Zagrovic (PLoS Comput. Biol.2014, 5, e1003638). The anomalously strong intermolecular interactions seen in the MD study were reproduced in the COFFDROP simulations; a simple scaling of COFFDROP’s nonbonded parameters, however, produced results in better accordance with experiment. Overall, our results suggest that potential functions derived from simulations of pairwise amino acid interactions might be of quite broad applicability, with COFFDROP likely to be especially useful for modeling unfolded or intrinsically

  20. Molecular dynamics study of human carbonic anhydrase II in complex with Zn(2+) and acetazolamide on the basis of all-atom force field simulations.

    PubMed

    Wambo, Thierry O; Chen, Liao Y; McHardy, Stanton F; Tsin, Andrew T

    2016-01-01

    Human carbonic anhydrase II (hCAII) represents an ultimate example of the perfectly efficient metalloenzymes, which is capable of catalyzing the hydration of carbon dioxide with a rate approaching the diffusion controlled limit. Extensive experimental studies of this physiologically important metalloprotein have been done to elucidate the fundamentals of its enzymatic actions: what residues anchor the Zn(2+) (or another divalent cation) at the bottom of the binding pocket; how the relevant residues work concertedly with the divalent cation in the reversible conversions between CO2 and HCO3(-); what are the protonation states of the relevant residues and acetazolamide, an inhibitor complexed with hCAII, etc. In this article, we present a detailed computational study on the basis of the all-atom CHARMM force field where Zn(2+) is represented with a simple model of divalent cation using the transferrable parameters available from the current literature. We compute the hydration free energy of Zn(2+), the characteristics of hCAII-Zn(2+) complexation, and the absolute free energy of binding acetazolamide to the hCAII-Zn(2+) complex. In each of these three problems, our computed results agree with the experimental data within the known margin of error without making any case-by-case adjustments to the parameters. The quantitatively accurate insights we gain in this all-atom molecular dynamics study should be helpful in the search and design of more specific inhibitors of this and other carbonic anhydrases. PMID:27232456

  1. Insight into the Properties of Cardiolipin Containing Bilayers from Molecular Dynamics Simulations, Using a Hybrid All-Atom/United-Atom Force Field.

    PubMed

    Aguayo, Daniel; González-Nilo, Fernando D; Chipot, Christophe

    2012-05-01

    Simulation of three models of cardiolipin (CL) containing membranes using a new set of parameters for tetramyristoyl and tetraoleoyl CLs has been developed in the framework of the united-atom CHARMM27-UA and the all-atom CHARMM36 force fields with the aim of performing molecular dynamics (MD) simulations of cardiolipin-containing mixed-lipid membranes. The new parameters use a hybrid representation of all-atom head groups in conjunction with implicit-hydrogen united-atom (UA) to describe the oleoyl and myristoyl chains of the CLs, in lieu of the fully atomistic description, thereby allowing longer simulations to be undertaken. The physicochemical properties of the bilayers were determined and compared with previously reported data. Furthermore, using tetramyristoyl CL mixed with POPG and POPE lipids, a mitochondrial membrane was simulated. The results presented here show the different behavior of the bilayers as a result of the lipid composition, where the length of the acyl chain and the conformation of the headgroup can be associated with the mitochondrial membrane properties. The new hybrid CL parameters prove to be well suited for the simulation of the molecular structure of CL-containing bilayers and can be extended to other lipid bilayers composed of CLs with different acyl chains or alternate head groups. PMID:26593668

  2. Toward a Coarse Graining/All Atoms Force Field (CG/AA) from a Multiscale Optimization Method: An Application to the MCM-41 Mesoporous Silicates.

    PubMed

    Ghoufi, A; Morineau, D; Lefort, R; Malfreyt, P

    2010-10-12

    Many interesting physical phenomena occur on length and time scales that are not accessible by atomistic molecular simulations. By introducing a coarse graining of the degrees of freedom, coarse-grained (CG) models allow ther study of larger scale systems for longer times. Coarse-grained force fields have been mostly derived for large molecules, including polymeric materials and proteins. By contrast, there exist no satisfactory CG potentials for mesostructured porous solid materials in the literature. This issue has become critical among a growing number of studies on confinement effects on fluid properties, which require both long time and large scale simulations and the conservation of a sufficient level of atomistic description to account for interfacial phenomena. In this paper, we present a general multiscale procedure to derive a hybrid coarse grained/all atoms force field CG/AA model for mesoporous systems. The method is applied to mesostructured MCM-41 molecular sieves, while the parameters of the mesoscopic interaction potentials are obtained and validated from the computation of the adsorption isotherm of methanol by grand canonical molecular dynamic simulation. PMID:26616783

  3. Additive CHARMM force field for naturally occurring modified ribonucleotides.

    PubMed

    Xu, You; Vanommeslaeghe, Kenno; Aleksandrov, Alexey; MacKerell, Alexander D; Nilsson, Lennart

    2016-04-15

    More than 100 naturally occurring modified nucleotides have been found in RNA molecules, in particular in tRNAs. We have determined molecular mechanics force field parameters compatible with the CHARMM36 all-atom additive force field for all these modifications using the CHARMM force field parametrization strategy. Emphasis was placed on fine tuning of the partial atomic charges and torsion angle parameters. Quantum mechanics calculations on model compounds provided the initial set of target data, and extensive molecular dynamics simulations of nucleotides and oligonucleotides in aqueous solutions were used for further refinement against experimental data. The presented parameters will allow for computational studies of a wide range of RNAs containing modified nucleotides, including the ribosome and transfer RNAs. PMID:26841080

  4. Parameterization of backbone flexibility in a coarse-grained force field for proteins (COFFDROP) derived from all-atom explicit-solvent molecular dynamics simulations of all possible two-residue peptides

    PubMed Central

    Frembgen-Kesner, Tamara; Andrews, Casey T.; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A.; Jain, Aakash; Olayiwola, Oluwatoni; Weishaar, Mitch R.; Elcock, Adrian H.

    2015-01-01

    Recently, we reported the parameterization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs, and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downwards in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multi-domain proteins connected by flexible linkers. PMID:26574429

  5. All-atom force field for molecular dynamics simulations on organotransition metal solids and liquids. Application to M(CO)(n) (M = Cr, Fe, Ni, Mo, Ru, or W) compounds.

    PubMed

    Bernardes, Carlos E S; Canongia Lopes, José N; Minas da Piedade, Manuel E

    2013-10-31

    A previously developed OPLS-based all-atom force field for organometallic compounds was extended to a series of first-, second-, and third-row transition metals based on the study of M(CO)(n) (M = Cr, Fe, Ni, Mo, Ru, or W) complexes. For materials that are solid at ambient temperature and pressure (M = Cr, Mo, W) the validation of the force field was based on reported structural data and on the standard molar enthalpies of sublimation at 298.15 K, experimentally determined by Calvet-drop microcalorimetry using samples corresponding to a specific and well-characterized crystalline phase: Δ(sub)H(m)° = 72.6 ± 0.3 kJ·mol(–1) for Cr(CO)(6), 73.4 ± 0.3 kJ·mol(–1) for Mo(CO)(6), and 77.8 ± 0.3 kJ·mol(–1) for W(CO)(6). For liquids, where problems of polymorphism or phase mixtures are absent, critically analyzed literature data were used. The force field was able to reproduce the volumetric properties of the test set (density and unit cell volume) with an average deviations smaller than 2% and the experimentally determined enthalpies of sublimation and vaporization with an accuracy better than 2.3 kJ·mol(–1). The Lennard-Jones (12-6) potential function parameters used to calculate the repulsive and dispersion contributions of the metals within the framework of the force field were found to be transferable between chromium, iron, and nickel (first row) and between molybdenum and ruthenium (second row). PMID:24079472

  6. All-atom Simulation of Amyloid Aggregates

    NASA Astrophysics Data System (ADS)

    Berhanu, Workalemahu M.; Alred, Erik J.; Bernhardt, Nathan A.; Hansmann, Ulrich H. E.

    Molecular simulations are now commonly used to complement experiments in the investigation of amyloid formation and their role in human diseases. While various simulations based on enhanced sampling techniques are used in amyloid formation simulations, this article will focus on those using standard atomistic simulations to evaluate the stability of fibril models. Such studies explore the limitations that arise from the choice of force field or polymorphism; and explore the stability of in vivo and in vitro forms of Aβ fibril aggregates, and the role of heterologous seeding as a link between different amyloid diseases.

  7. Additive CHARMM force field for naturally occurring modified ribonucleotides

    PubMed Central

    Xu, You; Vanommeslaeghe, Kenno; Aleksandrov, Alexey; MacKerell, Alexander D.

    2016-01-01

    More than 100 naturally occurring modified nucleotides have been found in RNA molecules, in particular in tRNAs. We have determined molecular mechanics force field parameters compatible with the CHARMM36 all‐atom additive force field for all these modifications using the CHARMM force field parametrization strategy. Emphasis was placed on fine tuning of the partial atomic charges and torsion angle parameters. Quantum mechanics calculations on model compounds provided the initial set of target data, and extensive molecular dynamics simulations of nucleotides and oligonucleotides in aqueous solutions were used for further refinement against experimental data. The presented parameters will allow for computational studies of a wide range of RNAs containing modified nucleotides, including the ribosome and transfer RNAs. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:26841080

  8. Nonlinearly Additive Forces in Multivalent Ligand Binding to a Single Protein Revealed with Force Spectroscopy

    SciTech Connect

    Ratto, T V; Rudd, R E; Langry, K C; Balhorn, R L; McElfresh, M W

    2005-07-15

    We present evidence of multivalent interactions between a single protein molecule and multiple carbohydrates at a pH where the protein can bind four ligands. The evidence is based not only on measurements of the force required to rupture the bonds formed between ConcanavalinA (ConA) and {alpha}-D-mannose, but also on an analysis of the polymer-extension force curves to infer the polymer architecture that binds the protein to the cantilever and the ligands to the substrate. We find that although the rupture forces for multiple carbohydrate connections to a single protein are larger than the rupture force for a single connection, they do not scale additively with increasing number. Specifically, the most common rupture forces are approximately 46, 66, and 85 pN, which we argue corresponds to 1, 2, and 3 ligands being pulled simultaneously from a single protein as corroborated by an analysis of the linkage architecture. As in our previous work polymer tethers allow us to discriminate between specific and non-specific binding. We analyze the binding configuration (i.e. serial versus parallel connections) through fitting the polymer stretching data with modified Worm-Like Chain (WLC) models that predict how the effective stiffness of the tethers is affected by multiple connections. This analysis establishes that the forces we measure are due to single proteins interacting with multiple ligands, the first force spectroscopy study that establishes single-molecule multivalent binding unambiguously.

  9. Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge.

    PubMed

    Genheden, Samuel; Cabedo Martinez, Ana I; Criddle, Michael P; Essex, Jonathan W

    2014-03-01

    We present our predictions for the SAMPL4 hydration free energy challenge. Extensive all-atom Monte Carlo simulations were employed to sample the compounds in explicit solvent. While the focus of our study was to demonstrate well-converged and reproducible free energies, we attempted to address the deficiencies in the general Amber force field force field with a simple QM/MM correction. We show that by using multiple independent simulations, including different starting configurations, and enhanced sampling with parallel tempering, we can obtain well converged hydration free energies. Additional analysis using dihedral angle distributions, torsion-root mean square deviation plots and thermodynamic cycles support this assertion. We obtain a mean absolute deviation of 1.7 kcal mol(-1) and a Kendall's τ of 0.65 compared with experiment. PMID:24488307

  10. An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields.

    PubMed

    Whitford, Paul C; Noel, Jeffrey K; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y; Onuchic, José N

    2009-05-01

    Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Go) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase, and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a C(alpha) structure-based model and an all-atom empirical forcefield. Key findings include: (1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature, (2) folding mechanisms are robust to variations of the energetic parameters, (3) protein folding free-energy barriers can be manipulated through parametric modifications, (4) the global folding mechanisms in a C(alpha) model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model, and (5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Because this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function. PMID:18837035

  11. An effective all-atom potential for proteins

    PubMed Central

    Irbäck, Anders; Mitternacht, Simon; Mohanty, Sandipan

    2009-01-01

    We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary structure. Results obtained using the final form of the potential are presented for all these peptides. The same model, with unchanged parameters, is furthermore applied to a heterodimeric coiled-coil system, a mixed α/β protein and a three-helix-bundle protein, with very good results. The computational efficiency of the potential makes it possible to investigate the free-energy landscape of these 49–67-residue systems with high statistical accuracy, using only modest computational resources by today's standards. PACS Codes: 87.14.E-, 87.15.A-, 87.15.Cc PMID:19356242

  12. Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models

    SciTech Connect

    Kouza, Maksim Kolinski, Andrzej; Co, Nguyen Truong; Nguyen, Phuong H.; Li, Mai Suan

    2015-04-14

    Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer’s and Parkinson’s diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in

  13. Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models

    NASA Astrophysics Data System (ADS)

    Kouza, Maksim; Co, Nguyen Truong; Nguyen, Phuong H.; Kolinski, Andrzej; Li, Mai Suan

    2015-04-01

    Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in

  14. Preformed template fluctuations promote fibril formation: insights from lattice and all-atom models.

    PubMed

    Kouza, Maksim; Co, Nguyen Truong; Nguyen, Phuong H; Kolinski, Andrzej; Li, Mai Suan

    2015-04-14

    Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in

  15. CHARMM additive and polarizable force fields for biophysics and computer-aided drug design

    PubMed Central

    Vanommeslaeghe, K.

    2014-01-01

    Background Molecular Mechanics (MM) is the method of choice for computational studies of biomolecular systems owing to its modest computational cost, which makes it possible to routinely perform molecular dynamics (MD) simulations on chemical systems of biophysical and biomedical relevance. Scope of Review As one of the main factors limiting the accuracy of MD results is the empirical force field used, the present paper offers a review of recent developments in the CHARMM additive force field, one of the most popular bimolecular force fields. Additionally, we present a detailed discussion of the CHARMM Drude polarizable force field, anticipating a growth in the importance and utilization of polarizable force fields in the near future. Throughout the discussion emphasis is placed on the force fields’ parametrization philosophy and methodology. Major Conclusions Recent improvements in the CHARMM additive force field are mostly related to newly found weaknesses in the previous generation of additive force fields. Beyond the additive approximation is the newly available CHARMM Drude polarizable force field, which allows for MD simulations of up to 1 microsecond on proteins, DNA, lipids and carbohydrates. General Significance Addressing the limitations ensures the reliability of the new CHARMM36 additive force field for the types of calculations that are presently coming into routine computational reach while the availability of the Drude polarizable force fields offers a model that is an inherently more accurate model of the underlying physical forces driving macromolecular structures and dynamics. PMID:25149274

  16. All-atom simulations of crowding effects on ubiquitin dynamics

    NASA Astrophysics Data System (ADS)

    Abriata, Luciano A.; Spiga, Enrico; Dal Peraro, Matteo

    2013-08-01

    It is well-known that crowded environments affect the stability of proteins, with strong biological and biotechnological implications; however, beyond this, crowding is also expected to affect the dynamic properties of proteins, an idea that is hard to probe experimentally. Here we report on a simulation study aimed at evaluating the effects of crowding on internal protein dynamics, based on fully all-atom descriptions of the protein, the solvent and the crowder. Our model system consists of ubiquitin, a protein whose dynamic features are closely related to its ability to bind to multiple partners, in a 325 g L-1 solution of glucose in water, a condition widely employed in in vitro studies of crowding effects. We observe a slight reduction in loop flexibility accompanied by a dramatic restriction of the conformational space explored in the timescale of the simulations (˜0.5 µs), indicating that crowding slows down collective motions and the rate of exploration of the conformational space. This effect is attributed to the extensive and long-lasting interactions observed between protein residues and glucose molecules throughout the entire protein surface. Potential implications of the observed effects are discussed.

  17. Analysis of Ligand-Receptor Association and Intermediate Transfer Rates in Multienzyme Nanostructures with All-Atom Brownian Dynamics Simulations.

    PubMed

    Roberts, Christopher C; Chang, Chia-En A

    2016-08-25

    We present the second-generation GeomBD Brownian dynamics software for determining interenzyme intermediate transfer rates and substrate association rates in biomolecular complexes. Substrate and intermediate association rates for a series of enzymes or biomolecules can be compared between the freely diffusing disorganized configuration and various colocalized or complexed arrangements for kinetic investigation of enhanced intermediate transfer. In addition, enzyme engineering techniques, such as synthetic protein conjugation, can be computationally modeled and analyzed to better understand changes in substrate association relative to native enzymes. Tools are provided to determine nonspecific ligand-receptor association residence times, and to visualize common sites of nonspecific association of substrates on receptor surfaces. To demonstrate features of the software, interenzyme intermediate substrate transfer rate constants are calculated and compared for all-atom models of DNA origami scaffold-bound bienzyme systems of glucose oxidase and horseradish peroxidase. Also, a DNA conjugated horseradish peroxidase enzyme was analyzed for its propensity to increase substrate association rates and substrate local residence times relative to the unmodified enzyme. We also demonstrate the rapid determination and visualization of common sites of nonspecific ligand-receptor association by using HIV-1 protease and an inhibitor, XK263. GeomBD2 accelerates simulations by precomputing van der Waals potential energy grids and electrostatic potential grid maps, and has a flexible and extensible support for all-atom and coarse-grained force fields. Simulation software is written in C++ and utilizes modern parallelization techniques for potential grid preparation and Brownian dynamics simulation processes. Analysis scripts, written in the Python scripting language, are provided for quantitative simulation analysis. GeomBD2 is applicable to the fields of biophysics, bioengineering

  18. Pairwise-additive force fields for selected aqueous monovalent ions from adaptive force matching

    NASA Astrophysics Data System (ADS)

    Li, Jicun; Wang, Feng

    2015-11-01

    Simple non-polarizable potentials were developed for Na+, K+, Cl-, and Br- using the adaptive force matching (AFM) method with ab initio MP2 method as reference. Our MP2-AFM force field predicts the solvation free energies of the four salts formed by the ions with an error of no more than 5%. Other properties such as the ion-water radial distribution functions, first solvation shell water tilt angle distributions, ion diffusion constants, concentration dependent diffusion constant of water, and concentration dependent surface tension of the solutions were calculated with this potential. Very good agreement was achieved for these properties. In particular, the diffusion constants of the ions are within 6% of experimental measurements. The model predicts bromide to be enriched at the interface in the 1.6M KBr solution but predicts the ion to be repelled for the surface at lower concentration.

  19. A simple and transferable all-atom/coarse-grained hybrid model to study membrane processes.

    PubMed

    Genheden, Samuel; Essex, Jonathan W

    2015-10-13

    We present an efficient all-atom/coarse-grained hybrid model and apply it to membrane processes. This model is an extension of the all-atom/ELBA model applied previously to processes in water. Here, we improve the efficiency of the model by implementing a multiple-time step integrator that allows the atoms and the coarse-grained beads to be propagated at different timesteps. Furthermore, we fine-tune the interaction between the atoms and the coarse-grained beads by computing the potential of mean force of amino acid side chain analogs along the membrane normal and comparing to atomistic simulations. The model was independently validated on the calculation of small-molecule partition coefficients. Finally, we apply the model to membrane peptides. We studied the tilt angle of the Walp23 and Kalp23 helices in two different model membranes and the stability of the glycophorin A dimer. The model is efficient, accurate, and straightforward to use, as it does not require any extra interaction particles, layers of atomistic solvent molecules or tabulated potentials, thus offering a novel, simple approach to study membrane processes. PMID:26574264

  20. Benchmarking all-atom simulations using hydrogen exchange

    PubMed Central

    Skinner, John J.; Yu, Wookyung; Gichana, Elizabeth K.; Baxa, Michael C.; Hinshaw, James R.; Freed, Karl F.; Sosnick, Tobin R.

    2014-01-01

    Long-time molecular dynamics (MD) simulations are now able to fold small proteins reversibly to their native structures [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517–520]. These results indicate that modern force fields can reproduce the energy surface near the native structure. To test how well the force fields recapitulate the other regions of the energy surface, MD trajectories for a variant of protein G are compared with data from site-resolved hydrogen exchange (HX) and other biophysical measurements. Because HX monitors the breaking of individual H-bonds, this experimental technique identifies the stability and H-bond content of excited states, thus enabling quantitative comparison with the simulations. Contrary to experimental findings of a cooperative, all-or-none unfolding process, the simulated denatured state ensemble, on average, is highly collapsed with some transient or persistent native 2° structure. The MD trajectories of this protein G variant and other small proteins exhibit excessive intramolecular H-bonding even for the most expanded conformations, suggesting that the force fields require improvements in describing H-bonding and backbone hydration. Moreover, these comparisons provide a general protocol for validating the ability of simulations to accurately capture rare structural fluctuations. PMID:25349413

  1. Molecular jamming—The cystine slipknot mechanical clamp in all-atom simulations

    NASA Astrophysics Data System (ADS)

    Pepłowski, Łukasz; Sikora, Mateusz; Nowak, Wiesław; Cieplak, Marek

    2011-02-01

    A recent survey of 17 134 proteins has identified a new class of proteins which are expected to yield stretching induced force peaks in the range of 1 nN. Such high force peaks should be due to forcing of a slip-loop through a cystine ring, i.e., by generating a cystine slipknot. The survey has been performed in a simple coarse grained model. Here, we perform all-atom steered molecular dynamics simulations on 15 cystine knot proteins and determine their resistance to stretching. In agreement with previous studies within a coarse grained structure based model, the level of resistance is found to be substantially higher than in proteins in which the mechanical clamp operates through shear. The large stretching forces arise through formation of the cystine slipknot mechanical clamp and the resulting steric jamming. We elucidate the workings of such a clamp in an atomic detail. We also study the behavior of five top strength proteins with the shear-based mechanostability in which no jamming is involved. We show that in the atomic model, the jamming state is relieved by moving one amino acid at a time and there is a choice in the selection of the amino acid that advances the first. In contrast, the coarse grained model also allows for a simultaneous passage of two amino acids.

  2. Molecular jamming--the cystine slipknot mechanical clamp in all-atom simulations.

    PubMed

    Pepłowski, Lukasz; Sikora, Mateusz; Nowak, Wiesław; Cieplak, Marek

    2011-02-28

    A recent survey of 17 134 proteins has identified a new class of proteins which are expected to yield stretching induced force peaks in the range of 1 nN. Such high force peaks should be due to forcing of a slip-loop through a cystine ring, i.e., by generating a cystine slipknot. The survey has been performed in a simple coarse grained model. Here, we perform all-atom steered molecular dynamics simulations on 15 cystine knot proteins and determine their resistance to stretching. In agreement with previous studies within a coarse grained structure based model, the level of resistance is found to be substantially higher than in proteins in which the mechanical clamp operates through shear. The large stretching forces arise through formation of the cystine slipknot mechanical clamp and the resulting steric jamming. We elucidate the workings of such a clamp in an atomic detail. We also study the behavior of five top strength proteins with the shear-based mechanostability in which no jamming is involved. We show that in the atomic model, the jamming state is relieved by moving one amino acid at a time and there is a choice in the selection of the amino acid that advances the first. In contrast, the coarse grained model also allows for a simultaneous passage of two amino acids. PMID:21361557

  3. All-atom crystal simulations of DNA and RNA duplexes

    PubMed Central

    Liu, Chunmei; Janowski, Pawel A.; Case, David A.

    2014-01-01

    Background Molecular dynamics simulations can complement experimental measures of structure and dynamics of biomolecules. The quality of such simulations can be tested by comparisons to models refined against experimental crystallographic data. Methods We report simulations of a DNA and RNA duplex in their crystalline environment. The calculations mimic the conditions for PDB entries 1D23 [d(CGATCGATCG)2] and 1RNA [(UUAUAUAUAUAUAA)2], and contain 8 unit cells, each with 4 copies of the Watson-Crick duplex; this yields in aggregate 64 µs of duplex sampling for DNA and 16 µs for RNA. Results The duplex structures conform much more closely to the average structure seen in the crystal than do structures extracted from a solution simulation with the same force field. Sequence-dependent variations in helical parameters, and in groove widths, are largely maintained in the crystal structure, but are smoothed out in solution. However, the integrity of the crystal lattice is slowly degraded in both simulations, with the result that the interfaces between chains become heterogeneous. This problem is more severe for the DNA crystal, which has fewer inter-chain hydrogen bond contacts than does the RNA crystal. Conclusions Crystal simulations using current force fields reproduce many features of observed crystal structures, but suffer from a gradual degradation of the integrity of the crystal lattice. General significance The results offer insights into force-field simulations that tests their ability to preserve weak interactions between chains, which will be of importance also in non-crystalline applications that involve binding and recognition. PMID:25255706

  4. An All-Atom Model of the Structure of Human Copper Transporter 1

    PubMed Central

    Sharikov, Yuriy; Greenberg, Jerry P.; Miller, Mark A.; Kouznetsova, Valentina L.; Larson, Christopher A.; Howell, Stephen B.

    2013-01-01

    Human copper transporter 1 (hCTR1) is the major high affinity copper influx transporter in mammalian cells that also mediates uptake of the cancer chemotherapeutic agent cisplatin. A low resolution structure of hCTR1 determined by cryoelectron microscopy was recently published. Several protein structure simulation techniques were used to create an all-atom model of this important transporter using the low resolution structure as a starting point. The all-atom model provides new insights into the roles of specific residues of the N-terminal extracellular domain, the intracellular loop, and C-terminal region in metal ion transport. In particular, the model demonstrates that the central region of the pore contains four sets of methionine triads in the intramembranous region. The structure confirms that two triads of methionine residues delineate the intramembranous region of the transporter, and further identifies two additional methionine triads that are located in the extracellular N-terminal part of the transporter. Together, the four triads create a structure that promotes stepwise transport of metal ions into and then through the intramembranous channel of the transporter via transient thioether bonds to methionine residues. Putative copper-binding sites in the hCTR1 trimer were identified by a program developed by us for prediction of metal-binding sites. These sites correspond well with the known effects of mutations on the ability of the protein to transport copper and cisplatin. PMID:22569840

  5. All-atom simulation study of protein PTH(1-34) by using the Wang-Landau sampling method

    NASA Astrophysics Data System (ADS)

    Kim, Seung-Yeon; Kwak, Wooseop

    2014-12-01

    We perform simulations of the N-terminal 34-residue protein fragment PTH(1-34), consisting of 581 atoms, of the 84-residue human parathyroid hormone by using the all-atom ECEPP/3 force field and the Wang-Landau sampling method. Through a massive high-performance computation, the density of states and the partition function Z( T), as a continuous function of T, are obtained for PTH(1-34). From the continuous partition function Z( T), the partition function zeros of PTH(1-34) are evaluated for the first time. From both the specific heat and the partition function zeros, two characteristic transition temperatures are obtained for the all-atom protein PTH(1-34). The higher transition temperature T 1 and the lower transition temperature T 2 of PTH(1-34) can be interpreted as the collapse temperature T θ and the folding temperature T f , respectively.

  6. Local order parameters for use in driving homogeneous ice nucleation with all-atom models of water.

    PubMed

    Reinhardt, Aleks; Doye, Jonathan P K; Noya, Eva G; Vega, Carlos

    2012-11-21

    We present a local order parameter based on the standard Steinhardt-Ten Wolde approach that is capable both of tracking and of driving homogeneous ice nucleation in simulations of all-atom models of water. We demonstrate that it is capable of forcing the growth of ice nuclei in supercooled liquid water simulated using the TIP4P/2005 model using over-biassed umbrella sampling Monte Carlo simulations. However, even with such an order parameter, the dynamics of ice growth in deeply supercooled liquid water in all-atom models of water are shown to be very slow, and so the computation of free energy landscapes and nucleation rates remains extremely challenging. PMID:23181323

  7. Additional interfacial force in lattice Boltzmann models for incompressible multiphase flows.

    PubMed

    Li, Q; Luo, K H; Gao, Y J; He, Y L

    2012-02-01

    The existing lattice Boltzmann models for incompressible multiphase flows are mostly constructed with two distribution functions: one is the order parameter distribution function, which is used to track the interface between different phases, and the other is the pressure distribution function for solving the velocity field. In this paper, it is shown that in these models the recovered momentum equation is inconsistent with the target one: an additional force is included in the recovered momentum equation. The additional force has the following features. First, it is proportional to the macroscopic velocity. Second, it is zero in every single-phase region but is nonzero in the interface. Therefore it can be interpreted as an interfacial force. To investigate the effects of the additional interfacial force, numerical simulations are carried out for the problem of Rayleigh-Taylor instability, droplet splashing on a thin liquid film, and the evolution of a falling droplet under gravity. Numerical results demonstrate that, with the increase of the velocity or the Reynolds number, the additional interfacial force will gradually have an important influence on the interface and affect the numerical accuracy. PMID:22463354

  8. Multiscale approach for the construction of equilibrated all-atom models of a poly(ethylene glycol)-based hydrogel.

    PubMed

    Li, Xianfeng; Murthy, N Sanjeeva; Becker, Matthew L; Latour, Robert A

    2016-06-01

    A multiscale modeling approach is presented for the efficient construction of an equilibrated all-atom model of a cross-linked poly(ethylene glycol) (PEG)-based hydrogel using the all-atom polymer consistent force field (PCFF). The final equilibrated all-atom model was built with a systematic simulation toolset consisting of three consecutive parts: (1) building a global cross-linked PEG-chain network at experimentally determined cross-link density using an on-lattice Monte Carlo method based on the bond fluctuation model, (2) recovering the local molecular structure of the network by transitioning from the lattice model to an off-lattice coarse-grained (CG) model parameterized from PCFF, followed by equilibration using high performance molecular dynamics methods, and (3) recovering the atomistic structure of the network by reverse mapping from the equilibrated CG structure, hydrating the structure with explicitly represented water, followed by final equilibration using PCFF parameterization. The developed three-stage modeling approach has application to a wide range of other complex macromolecular hydrogel systems, including the integration of peptide, protein, and/or drug molecules as side-chains within the hydrogel network for the incorporation of bioactivity for tissue engineering, regenerative medicine, and drug delivery applications. PMID:27013229

  9. Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields.

    PubMed

    Lin, Bin; Lopes, Pedro E M; Roux, Benoît; MacKerell, Alexander D

    2013-08-28

    Kirkwood-Buff analysis was performed on aqueous solutions of N-methylacetamide and acetamide using the Chemistry at HARvard Molecular Mechanics additive and Drude polarizable all-atom force fields. Comparison of a range of properties with experimental results, including Kirkwood-Buff integrals, excess coordination numbers, solution densities, partial molar values, molar enthalpy of mixing, showed both models to be well behaved at higher solute concentrations with the Drude model showing systematic improvement at lower solution concentrations. However, both models showed difficulties reproducing experimental activity derivatives and the excess Gibbs energy, with the Drude model performing slightly better. At the molecular level, the improved agreement of the Drude model at low solute concentrations is due to increased structure in the solute-solute and solute-solvent interactions. The present results indicate that the explicit inclusion of electronic polarization leads to improved modeling of dilute solutions even when those properties are not included as target data during force field optimization. PMID:24007020

  10. Local elasticity of strained DNA studied by all-atom simulations

    NASA Astrophysics Data System (ADS)

    Mazur, Alexey K.

    2011-08-01

    Genomic DNA is constantly subjected to various mechanical stresses arising from its biological functions and cell packaging. If the local mechanical properties of DNA change under torsional and tensional stress, the activity of DNA-modifying proteins and transcription factors can be affected and regulated allosterically. To check this possibility, appropriate steady forces and torques were applied in the course of all-atom molecular dynamics simulations of DNA with AT- and GC-alternating sequences. It is found that the stretching rigidity grows with tension as well as twisting. The torsional rigidity is not affected by stretching, but it varies with twisting very strongly, and differently for the two sequences. Surprisingly, for AT-alternating DNA it passes through a minimum with the average twist close to the experimental value in solution. For this fragment, but not for the GC-alternating sequence, the bending rigidity noticeably changes with both twisting and stretching. The results have important biological implications and shed light on earlier experimental observations.

  11. Non-additivity of molecule-surface van der Waals potentials from force measurements

    NASA Astrophysics Data System (ADS)

    Tautz, Stefan

    2014-03-01

    Van der Waals (vdW) forces act ubiquitously in condensed matter. Their description as an inherently quantum mechanical phenomenon was developed for single atoms and homogeneous macroscopic bodies by London, Casimir, and Lifshitz. For intermediate-sized objects like organic molecules an atomistic description is required, but explicit first principles calculations are very difficult since correlations between many interacting electrons have to be considered. Hence, semi-empirical correction schemes are often used that simplify the vdW interaction to a sum over atom-pair potentials. A similar gap exists between successful measurements of vdW and Casimir forces for single atoms on the one hand and macroscopic bodies on the other, as comparable experiments for molecules are absent. I will present experiments in which long-range vdW potentials between a series of related molecules and a metal surface have been determined experimentally. The experiments rely on the extremely sensitive force detection of an atomic force microscope in combination with its molecular manipulation capabilities. The results allow us to confirm the asymptotic force law and to quantify the non-additive part of the vdW interaction which is particularly challenging for theory. In the present case, cooperative effects account for 10% of the total interaction. This effect is of general validity in molecules and thus relevant at the intersection of chemistry, physics, biology, and materials science.

  12. Matching of additive and polarizable force fields for multiscale condensed phase simulations

    PubMed Central

    Baker, Christopher M.; Best, Robert B.

    2013-01-01

    Inclusion of electronic polarization effects is one of the key aspects in which the accuracy of current biomolecular force fields may be improved. The principal drawback of such approaches is the computational cost, which typically ranges from 3 – 10 times that of the equivalent additive model, and may be greater for more sophisticated treatments of polarization or other many-body effects. Here, we present a multiscale approach which may be used to enhance the sampling in simulations with polarizable models, by using the additive model as a tool to explore configuration space. We use a method based on information theory to determine the charges for an additive model that has optimal overlap with the polarizable one, and we demonstrate the feasibility of enhancing sampling via a hybrid replica exchange scheme for several model systems. An additional advantage is that, in the process, we obtain a systematic method for deriving charges for an additive model that will be the natural complement to its polarizable parent. The additive charges are found by an effective coarse-graining of the polarizable force field, rather than by ad hoc procedures. PMID:23997691

  13. Non-additivity of molecule-surface van der Waals potentials from force measurements

    NASA Astrophysics Data System (ADS)

    Wagner, Christian; Fournier, Norman; Ruiz, Victor G.; Li, Chen; Müllen, Klaus; Rohlfing, Michael; Tkatchenko, Alexandre; Temirov, Ruslan; Tautz, F. Stefan

    2014-11-01

    Van der Waals (vdW) forces act ubiquitously in condensed matter. Despite being weak on an atomic level, they substantially influence molecular and biological systems due to their long range and system-size scaling. The difficulty to isolate and measure vdW forces on a single-molecule level causes our present understanding to be strongly theory based. Here we show measurements of the attractive potential between differently sized organic molecules and a metal surface using an atomic force microscope. Our choice of molecules and the large molecule-surface separation cause this attraction to be purely of vdW type. The experiment allows testing the asymptotic vdW force law and its validity range. We find a superlinear growth of the vdW attraction with molecular size, originating from the increased deconfinement of electrons in the molecules. Because such non-additive vdW contributions are not accounted for in most first-principles or empirical calculations, we suggest further development in that direction.

  14. Non-additivity of molecule-surface van der Waals potentials from force measurements

    PubMed Central

    Wagner, Christian; Fournier, Norman; Ruiz, Victor G.; Li, Chen; Müllen, Klaus; Rohlfing, Michael; Tkatchenko, Alexandre; Temirov, Ruslan; Tautz, F. Stefan

    2014-01-01

    Van der Waals (vdW) forces act ubiquitously in condensed matter. Despite being weak on an atomic level, they substantially influence molecular and biological systems due to their long range and system-size scaling. The difficulty to isolate and measure vdW forces on a single-molecule level causes our present understanding to be strongly theory based. Here we show measurements of the attractive potential between differently sized organic molecules and a metal surface using an atomic force microscope. Our choice of molecules and the large molecule-surface separation cause this attraction to be purely of vdW type. The experiment allows testing the asymptotic vdW force law and its validity range. We find a superlinear growth of the vdW attraction with molecular size, originating from the increased deconfinement of electrons in the molecules. Because such non-additive vdW contributions are not accounted for in most first-principles or empirical calculations, we suggest further development in that direction. PMID:25424490

  15. A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

    SciTech Connect

    Markutsya, Sergiy; Lamm, Monica H

    2014-11-07

    We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems.

  16. Computing the acoustic radiation force exerted on a sphere using the translational addition theorem.

    PubMed

    Silva, Glauber T; Baggio, André L; Lopes, J Henrique; Mitri, Farid G

    2015-03-01

    In this paper, the translational addition theorem for spherical functions is employed to calculate the acoustic radiation force produced by an arbitrary shaped beam on a sphere arbitrarily suspended in an inviscid fluid. The procedure is also based on the partial-wave expansion method, which depends on the beam-shape and scattering coefficients. Given a set of beam-shape coefficients (BSCs) for an acoustic beam relative to a reference frame, the translational addition theorem can be used to obtain the BSCs relative to the sphere positioned anywhere in the medium. The scattering coefficients are obtained from the acoustic boundary conditions across the sphere's surface. The method based on the addition theorem is particularly useful to avoid quadrature schemes to obtain the BSCs. We use it to compute the acoustic radiation force exerted by a spherically focused beam (in the paraxial approximation) on a silicone-oil droplet (compressible fluid sphere). The analysis is carried out in the Rayleigh (i.e., the particle diameter is much smaller than the wavelength) and Mie (i.e., the particle diameter is of the order of the wavelength or larger) scattering regimes. The obtained results show that the paraxial focused beam can only trap particles in the Rayleigh scattering regime. PMID:25768823

  17. Influence of Polarization on Carbohydrate Hydration: A Comparative Study Using Additive and Polarizable Force Fields.

    PubMed

    Pandey, Poonam; Mallajosyula, Sairam S

    2016-07-14

    Carbohydrates are known to closely modulate their surrounding solvent structures and influence solvation dynamics. Spectroscopic investigations studying far-IR regions (below 1000 cm(-1)) have observed spectral shifts in the libration band (around 600 cm(-1)) of water in the presence of monosaccharides and polysaccharides. In this paper, we use molecular dynamics simulations to gain atomistic insight into carbohydrate-water interactions and to specifically highlight the differences between additive (nonpolarizable) and polarizable simulations. A total of six monosaccharide systems, α and β anomers of glucose, galactose, and mannose, were studied using additive and polarizable Chemistry at HARvard Macromolecular Mechanics (CHARMM) carbohydrate force fields. Solvents were modeled using three additive water models TIP3P, TIP4P, and TIP5P in additive simulations and polarizable water model SWM4 in polarizable simulations. The presence of carbohydrate has a significant effect on the microscopic water structure, with the effects being pronounced for proximal water molecules. Notably, disruption of the tetrahedral arrangement of proximal water molecules was observed due to the formation of strong carbohydrate-water hydrogen bonds in both additive and polarizable simulations. However, the inclusion of polarization resulted in significant water-bridge occupancies, improved ordered water structures (tetrahedral order parameter), and longer carbohydrate-water H-bond correlations as compared to those for additive simulations. Additionally, polarizable simulations also allowed the calculation of power spectra from the dipole-dipole autocorrelation function, which corresponds to the IR spectra. From the power spectra, we could identify spectral signatures differentiating the proximal and bulk water structures, which could not be captured from additive simulations. PMID:27266974

  18. Influence of Additional Tensile Force on Springback of Tube Under Rotary Draw Bending

    NASA Astrophysics Data System (ADS)

    E, Daxin; Guan, Zhiping; Chen, Jisheng

    2012-11-01

    According to the characteristics of tube under rotary draw bending, the formulae were derived to calculate the springback angles of tubes subjected to combined bending and additional tension. Especially, as the neutral layer (NL) moves to the inner concave surface of the bend, the analytical values agree very well with the experimental results. The analysis shows that the additional tensile force causes the movement of the NL toward the bending center and makes the deformation behavior under rotary draw bending or numerically controlled (NC) bending different with that under pure bending, and also it could enlarge the springback angle if taking the movement of the NL into consideration. In some range, the springback angle would increase slightly with larger wall thickness/diameter ratio and decrease with wall thinning. The investigation could provide reference for the analysis of rotary draw bending, the design of NC tube bender and the related techniques.

  19. Transferability and additivity of dihedral parameters in polarizable and nonpolarizable empirical force fields.

    PubMed

    Zgarbová, Marie; Rosnik, Andreana M; Luque, F Javier; Curutchet, Carles; Jurečka, Petr

    2015-09-30

    Recent advances in polarizable force fields have revealed that major reparameterization is necessary when the polarization energy is treated explicitly. This study is focused on the torsional parameters, which are crucial for the accurate description of conformational equilibria in biomolecules. In particular, attention is paid to the influence of polarization on the (i) transferability of dihedral terms between molecules, (ii) transferability between different environments, and (iii) additivity of dihedral energies. To this end, three polarizable force fields based on the induced point dipole model designed for use in AMBER are tested, including two recent ff02 reparameterizations. Attention is paid to the contributions due to short range interactions (1-2, 1-3, and 1-4) within the four atoms defining the dihedral angle. The results show that when short range 1-2 and 1-3 polarization interactions are omitted, as for instance in ff02, the 1-4 polarization contribution is rather small and unlikely to improve the description of the torsional energy. Conversely, when screened 1-2 and 1-3 interactions are included, the polarization contribution is sizeable and shows potential to improve the transferability of parameters between different molecules and environments as well as the additivity of dihedral terms. However, to reproduce intramolecular polarization effects accurately, further fine-tuning of the short range damping of polarization is necessary. PMID:26224547

  20. All-atom normal-mode analysis reveals an RNA-induced allostery in a bacteriophage coat protein

    NASA Astrophysics Data System (ADS)

    Dykeman, Eric C.; Twarock, Reidun

    2010-03-01

    Assembly of the T=3 bacteriophage MS2 is initiated by the binding of a 19 nucleotide RNA stem loop from within the phage genome to a symmetric coat protein dimer. This binding event effects a folding of the FG loop in one of the protein subunits of the dimer and results in the formation of an asymmetric dimer. Since both the symmetric and asymmetric forms of the dimer are needed for the assembly of the protein container, this allosteric switch plays an important role in the life cycle of the phage. We provide here details of an all-atom normal-mode analysis of this allosteric effect. The results suggest that asymmetric contacts between the A -duplex RNA phosphodiester backbone of the stem loop with the EF loop in one coat protein subunit results in an increased dynamic behavior of its FG loop. The four lowest-frequency modes, which encompass motions predominantly on the FG loops, account for over 90% of the increased dynamic behavior due to a localization of the vibrational pattern on a single FG loop. Finally, we show that an analysis of the allosteric effect using an elastic network model fails to predict this localization effect, highlighting the importance of using an all-atom full force field method for this problem.

  1. Simulation of uphill/downhill running on a level treadmill using additional horizontal force.

    PubMed

    Gimenez, Philippe; Arnal, Pierrick J; Samozino, Pierre; Millet, Guillaume Y; Morin, Jean-Benoit

    2014-07-18

    Tilting treadmills allow a convenient study of biomechanics during uphill/downhill running, but they are not commonly available and there is even fewer tilting force-measuring treadmill. The aim of the present study was to compare uphill/downhill running on a treadmill (inclination of ± 8%) with running on a level treadmill using additional backward or forward pulling forces to simulate the effect of gravity. This comparison specifically focused on the energy cost of running, stride frequency (SF), electromyographic activity (EMG), leg and foot angles at foot strike, and ground impact shock. The main results are that SF, impact shock, and leg and foot angle parameters determined were very similar and significantly correlated between the two methods, the intercept and slope of the linear regression not differing significantly from zero and unity, respectively. The correlation of oxygen uptake (V̇O2) data between both methods was not significant during uphill running (r=0.42; P>0.05). V̇O2 data were correlated during downhill running (r=0.74; P<0.01) but there was a significant difference between the methods (bias=-2.51 ± 1.94 ml min(-1) kg(-1)). Linear regressions for EMG of vastus lateralis, biceps femoris, gastrocnemius lateralis, soleus and tibialis anterior were not different from the identity line but the systematic bias was elevated for this parameter. In conclusion, this method seems appropriate for the study of SF, leg and foot angle, impact shock parameters but is less applicable for physiological variables (EMG and energy cost) during uphill/downhill running when using a tilting force-measuring treadmill is not possible. PMID:24811045

  2. Additives

    NASA Technical Reports Server (NTRS)

    Smalheer, C. V.

    1973-01-01

    The chemistry of lubricant additives is discussed to show what the additives are chemically and what functions they perform in the lubrication of various kinds of equipment. Current theories regarding the mode of action of lubricant additives are presented. The additive groups discussed include the following: (1) detergents and dispersants, (2) corrosion inhibitors, (3) antioxidants, (4) viscosity index improvers, (5) pour point depressants, and (6) antifouling agents.

  3. Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics

    PubMed Central

    2016-01-01

    Molecular dynamics (MD) simulations of ions (K+, Na+, Ca2+ and Cl−) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parametrized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain. PMID:27118886

  4. Folding peptides and proteins with all-atom physics: methods and applications

    NASA Astrophysics Data System (ADS)

    Shell, M. Scott

    2008-03-01

    Computational methods offer powerful tools for investigating proteins and peptides at the molecular-level; however, it has proven challenging to reproduce the long time scale folding processes of these molecules at a level that is both faithful to the atomic driving forces and attainable with modern commodity cluster computing. Alternatively, the past decade has seen significant progress in using bioinformatics-based approaches to infer the three dimensional native structures of proteins, drawing upon extensive knowledge databases of known protein structures [1]. These methods work remarkably well when a homologous protein can be found to provide a structural template for a candidate sequence. However, in cases where homology to database proteins is low, where the folding pathway is of interest, or where conformational flexibility is substantial---as in many emerging protein and peptide technologies---bioinformatics methods perform poorly. There is therefore great interest in seeing purely physics-based approaches succeed. We discuss a purely physics-based, database-free folding method, relying on proper thermal sampling (replica exchange molecular dynamics) and molecular potential energy functions. In order to surmount the tremendous computational demands of all-atom folding simulations, our approach implements a conformational search strategy based on a putative protein folding mechanism called zipping and assembly [2-4]. That is, we explicitly seek out potential folding pathways inferred from short simulations, and iteratively pursue all such routes by coaxing a polypeptide chain along them. The method is called the Zipping and Assembly Method (ZAM) and it works in two parts: (1) the full polypeptide chain is broken into small fragments that are first simulated independently and then successively re-assembled into larger segments with further sampling, and (2) consistently stable structure in fragments is detected and locked into place, in order to avoid re

  5. Demonstration of non-additivity and asymmetry in the lateral Casimir force

    NASA Astrophysics Data System (ADS)

    Chiu, Hsiang-Chih

    2009-10-01

    The Casimir effect is a purely quantum mechanical phenomenon which has drawn extensive attention in the last decade. With the rapid development of modern scientific instruments, it has been demonstrated and measured with unprecedented precision. Because of its unique dependence on the separation and geometry, the Casimir force is expected to play an important role in modern nano-electro-mechanical systems. An understanding of the shape dependence of the Casimir force and its control has become a very important research topic for the future nano-technology. Since the demonstration of the lateral Casimir force in 2002 at UC Riverside, this special effect has inspired a lot of theoretical research. The asymmetry of the lateral Casimir has been predicted and exact theories which take into account diffraction-like correlation effect between the scattered zero point photons from the boundaries have been proposed. We improved the experimental setup and experimental conditions (grating period of order of the separation distance) to study these new phenomenon. In this research, we demonstrate the asymmetrical lateral Casimir force for the first time. The experimental results show very good agreement with a recently developed exact theory based on the scattering approach with no tting parameters. The measured force also show the expected deviation from the commonly used proximity force approximation. The results provide a further understanding of the shape dependence of the Casimir force and will enhance the capabilities for its application in nano technology, especially for the frictionless transmission of lateral motion.

  6. Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX

    SciTech Connect

    Bell, Jeffrey A.; Ho, Kenneth L.; Farid, Ramy

    2012-08-01

    All-atom models derived from moderate-resolution protein crystal structures contain a high frequency of close nonbonded contacts, independent of the major refinement program used for structure determination. All-atom refinement with PrimeX corrects many of these problematic interactions, producing models that are better suited for use in computational chemistry and related applications. All-atom models are essential for many applications in molecular modeling and computational chemistry. Nonbonded atomic contacts much closer than the sum of the van der Waals radii of the two atoms (clashes) are commonly observed in such models derived from protein crystal structures. A set of 94 recently deposited protein structures in the resolution range 1.5–2.8 Å were analyzed for clashes by the addition of all H atoms to the models followed by optimization and energy minimization of the positions of just these H atoms. The results were compared with the same set of structures after automated all-atom refinement with PrimeX and with nonbonded contacts in protein crystal structures at a resolution equal to or better than 0.9 Å. The additional PrimeX refinement produced structures with reasonable summary geometric statistics and similar R{sub free} values to the original structures. The frequency of clashes at less than 0.8 times the sum of van der Waals radii was reduced over fourfold compared with that found in the original structures, to a level approaching that found in the ultrahigh-resolution structures. Moreover, severe clashes at less than or equal to 0.7 times the sum of atomic radii were reduced 15-fold. All-atom refinement with PrimeX produced improved crystal structure models with respect to nonbonded contacts and yielded changes in structural details that dramatically impacted on the interpretation of some protein–ligand interactions.

  7. Force.

    ERIC Educational Resources Information Center

    Gamble, Reed

    1989-01-01

    Discusses pupil misconceptions concerning forces. Summarizes some of Assessment of Performance Unit's findings on meaning of (1) force, (2) force and motion in one dimension and two dimensions, and (3) Newton's second law. (YP)

  8. Hydration Properties and Solvent Effects for All-Atom Solutes in Polarizable Coarse-Grained Water.

    PubMed

    Yan, Xin Cindy; Tirado-Rives, Julian; Jorgensen, William L

    2016-08-25

    Due to the importance of water in chemical and biological systems, a coarse-grained representation of the solvent can greatly simplify the description of the system while retaining key thermodynamic properties of the medium. A multiscale solvation model that couples all-atom solutes and polarizable Martini coarse-grained water (AAX/CGS) is developed to reproduce free energies of hydration of organic solutes. Using Monte Carlo/free energy perturbation (MC/FEP) calculations, results from multiscale and all-atom simulations are compared. Improved accuracy is obtained with the AAX/CGS approach for hydrophobic and sulfur- or halogen-containing solutes, but larger deviations are found for polar solute molecules where hydrogen bonding is featured. Furthermore, solvent effects on conformational and tautomeric equilibria of AA solutes were investigated using AA, CG, and GB/SA solvent models. It is found that the CG solvent model can reproduce well the medium effects from experiment and AA simulations; however, the GB/SA solvent model fails in some cases. A 7-30-fold reduction in computational cost is found for the present AAX/CGS multiscale simulations compared to the AA alternative. PMID:26901452

  9. All-atom molecular dynamics analysis of multi-peptide systems reproduces peptide solubility in line with experimental observations

    PubMed Central

    Kuroda, Yutaka; Suenaga, Atsushi; Sato, Yuji; Kosuda, Satoshi; Taiji, Makoto

    2016-01-01

    In order to investigate the contribution of individual amino acids to protein and peptide solubility, we carried out 100 ns molecular dynamics (MD) simulations of 106 Å3 cubic boxes containing ~3 × 104 water molecules and 27 tetra-peptides regularly positioned at 23 Å from each other and composed of a single amino acid type for all natural amino acids but cysteine and glycine. The calculations were performed using Amber with a standard force field on a special purpose MDGRAPE-3 computer, without introducing any “artificial” hydrophobic interactions. Tetra-peptides composed of I, V, L, M, N, Q, F, W, Y, and H formed large amorphous clusters, and those containing A, P, S, and T formed smaller ones. Tetra-peptides made of D, E, K, and R did not cluster at all. These observations correlated well with experimental solubility tendencies as well as hydrophobicity scales with correlation coefficients of 0.5 to > 0.9. Repulsive Coulomb interactions were dominant in ensuring high solubility, whereas both Coulomb and van der Waals (vdW) energies contributed to the aggregations of low solubility amino acids. Overall, this very first all-atom molecular dynamics simulation of a multi-peptide system appears to reproduce the basic properties of peptide solubility, essentially in line with experimental observations. PMID:26817663

  10. Addition of Electrostatic Forces to EDEM with Applications to Triboelectrically Charged Particles

    NASA Technical Reports Server (NTRS)

    Hogue, Michael D.; Calle, Carlos; Curry, David

    2008-01-01

    Tribocharging of particles is common in many processes including fine powder handling and mixing, printer toner transport and dust extraction. In a lunar environment with its high vacuum and lack of water, electrostatic forces are an important factor to consider when designing and operating equipment. Dust mitigation and management is critical to safe and predictable performance of people and equipment. The extreme nature of lunar conditions makes it difficult and costly to carryout experiments on earth which are necessary to better understand how particles gather and transfer charge between each other and with equipment surfaces. DEM (Discrete Element Modeling) provides an excellent virtual laboratory for studying tribocharging of particles as well as for design of devices for dust mitigation and for other purposes related to handling and processing of lunar regolith. Theoretical and experimental work has been performed pursuant to incorporating screened Coulombic electrostatic forces into EDEM Tm, a commercial DEM software package. The DEM software is used to model the trajectories of large numbers of particles for industrial particulate handling and processing applications and can be coupled with other solvers and numerical models to calculate particle interaction with surrounding media and force fields. In this paper we will present overview of the theoretical calculations and experimental data and their comparison to the results of the DEM simulations. We will also discuss current plans to revise the DEM software with advanced electrodynamic and mechanical algorithms.

  11. All-Atom Molecular Dynamics of Virus Capsids as Drug Targets.

    PubMed

    Perilla, Juan R; Hadden, Jodi A; Goh, Boon Chong; Mayne, Christopher G; Schulten, Klaus

    2016-05-19

    Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid-protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways. When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Here, the current challenges of performing all-atom capsid-drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets. PMID:27128262

  12. All-atom homology model of the Escherichia coli 30S ribosomal subunit.

    PubMed

    Tung, Chang-Shung; Joseph, Simpson; Sanbonmatsu, Kevin Y

    2002-10-01

    Understanding the structural basis of ribosomal function requires close comparison between biochemical and structural data. Although a large amount of biochemical data are available for the Escherichia coli ribosome, the structure has not been solved to atomic resolution. Using a new RNA homology procedure, we have modeled the all-atom structure of the E. coli 30S ribosomal subunit. We find that the tertiary structure of the ribosome core, including the A-, P- and E-sites, is highly conserved. The hypervariable regions in our structure, which differ from the structure of the 30S ribosomal subunit from Thermus thermophilus, are consistent with the cryo-EM map of the E. coli ribosome. PMID:12244297

  13. All-atomic generation and noise-quadrature filtering of squeezed vacuum in hot Rb vapor

    NASA Astrophysics Data System (ADS)

    Horrom, Travis; Romanov, Gleb; Novikova, Irina; Mikhailov, Eugeniy E.

    2013-01-01

    With our all-atomic squeezing and filtering setup, we demonstrate control over the noise amplitudes and manipulation of the frequency-dependent squeezing angle of a squeezed vacuum quantum state by passing it through an atomic medium with electromagnetically induced transparency (EIT). We generate low sideband frequency squeezed vacuum using the polarization self-rotation effect in a hot Rb vapor cell, and direct it through a second atomic vapor subject to EIT conditions. We use the frequency-dependent absorption of the EIT window to demonstrate an example of squeeze amplitude attenuation and squeeze angle rotation of the quantum noise quadratures of the squeezed probe. These studies have implications for quantum memory and storage as well as gravitational wave interferometric detectors.

  14. All-Atom Molecular Dynamics of Virus Capsids as Drug Targets

    PubMed Central

    2016-01-01

    Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid–protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways. When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Here, the current challenges of performing all-atom capsid–drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets. PMID:27128262

  15. Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling

    PubMed Central

    Moritsugu, Kei; Terada, Tohru; Kidera, Akinori

    2014-01-01

    Protein-protein interactions are regulated by a subtle balance of complicated atomic interactions and solvation at the interface. To understand such an elusive phenomenon, it is necessary to thoroughly survey the large configurational space from the stable complex structure to the dissociated states using the all-atom model in explicit solvent and to delineate the energy landscape of protein-protein interactions. In this study, we carried out a multiscale enhanced sampling (MSES) simulation of the formation of a barnase-barstar complex, which is a protein complex characterized by an extraordinary tight and fast binding, to determine the energy landscape of atomistic protein-protein interactions. The MSES adopts a multicopy and multiscale scheme to enable for the enhanced sampling of the all-atom model of large proteins including explicit solvent. During the 100-ns MSES simulation of the barnase-barstar system, we observed the association-dissociation processes of the atomistic protein complex in solution several times, which contained not only the native complex structure but also fully non-native configurations. The sampled distributions suggest that a large variety of non-native states went downhill to the stable complex structure, like a fast folding on a funnel-like potential. This funnel landscape is attributed to dominant configurations in the early stage of the association process characterized by near-native orientations, which will accelerate the native inter-molecular interactions. These configurations are guided mostly by the shape complementarity between barnase and barstar, and lead to the fast formation of the final complex structure along the downhill energy landscape. PMID:25340714

  16. Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of viruses.

    PubMed

    Hoang Man, Viet; Van-Oanh, Nguyen-Thi; Derreumaux, Philippe; Li, Mai Suan; Roland, Christopher; Sagui, Celeste; Nguyen, Phuong H

    2016-04-28

    Since the discovery of the plant pathogen tobacco mosaic virus as the first viral entity in the late 1800s, viruses traditionally have been mainly thought of as pathogens for disease-resistances. However, viruses have recently been exploited as nanoplatforms with applications in biomedicine and materials science. To this aim, a large majority of current methods and tools have been developed to improve the physical stability of viral particles, which may be critical to the extreme physical or chemical conditions that viruses may encounter during purification, fabrication processes, storage and use. However, considerably fewer studies are devoted to developing efficient methods to degrade or recycle such enhanced stability biomaterials. With this in mind, we carry out all-atom nonequilibrium molecular dynamics simulation, inspired by the recently developed mid-infrared free-electron laser pulse technology, to dissociate viruses. Adopting the poliovirus as a representative example, we find that the primary step in the dissociation process is due to the strong resonance between the amide I vibrational modes of the virus and the tuned laser frequencies. This process is determined by a balance between the formation and dissociation of the protein shell, reflecting the highly plasticity of the virus. Furthermore, our method should provide a feasible approach to simulate viruses, which is otherwise too expensive for conventional equilibrium all-atom simulations of such very large systems. Our work shows a proof of concept which may open a new, efficient way to cleave or to recycle virus-based materials, provide an extremely valuable tool for elucidating mechanical aspects of viruses, and may well play an important role in future fighting against virus-related diseases. PMID:27071540

  17. Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX.

    PubMed

    Bell, Jeffrey A; Ho, Kenneth L; Farid, Ramy

    2012-08-01

    All-atom models are essential for many applications in molecular modeling and computational chemistry. Nonbonded atomic contacts much closer than the sum of the van der Waals radii of the two atoms (clashes) are commonly observed in such models derived from protein crystal structures. A set of 94 recently deposited protein structures in the resolution range 1.5-2.8 Å were analyzed for clashes by the addition of all H atoms to the models followed by optimization and energy minimization of the positions of just these H atoms. The results were compared with the same set of structures after automated all-atom refinement with PrimeX and with nonbonded contacts in protein crystal structures at a resolution equal to or better than 0.9 Å. The additional PrimeX refinement produced structures with reasonable summary geometric statistics and similar R(free) values to the original structures. The frequency of clashes at less than 0.8 times the sum of van der Waals radii was reduced over fourfold compared with that found in the original structures, to a level approaching that found in the ultrahigh-resolution structures. Moreover, severe clashes at less than or equal to 0.7 times the sum of atomic radii were reduced 15-fold. All-atom refinement with PrimeX produced improved crystal structure models with respect to nonbonded contacts and yielded changes in structural details that dramatically impacted on the interpretation of some protein-ligand interactions. PMID:22868759

  18. Variational Optimization of an All-Atom Implicit Solvent Force Field to Match Explicit Solvent Simulation Data.

    PubMed

    Bottaro, Sandro; Lindorff-Larsen, Kresten; Best, Robert B

    2013-12-10

    The development of accurate implicit solvation models with low computational cost is essential for addressing many large-scale biophysical problems. Here, we present an efficient solvation term based on a Gaussian solvent-exclusion model (EEF1) for simulations of proteins in aqueous environment, with the primary aim of having a good overlap with explicit solvent simulations, particularly for unfolded and disordered states - as would be needed for multiscale applications. In order to achieve this, we have used a recently proposed coarse-graining procedure based on minimization of an entropy-related objective function to train the model to reproduce the equilibrium distribution obtained from explicit water simulations. Via this methodology, we have optimized both a charge screening parameter and a backbone torsion term against explicit solvent simulations of an α-helical and a β-stranded peptide. The performance of the resulting effective energy function, termed EEF1-SB, is tested with respect to the properties of folded proteins, the folding of small peptides or fast-folding proteins, and NMR data for intrinsically disordered proteins. The results show that EEF1-SB provides a reasonable description of a wide range of systems, but its key advantage over other methods tested is that it captures very well the structure and dimension of disordered or weakly structured peptides. EEF1-SB is thus a computationally inexpensive (~ 10 times faster than Generalized-Born methods) and transferable approximation for treating solvent effects. PMID:24748852

  19. Magnetic Force Microscopy Study of Zr2Co11 -Based Nanocrystalline Materials: Effect of Mo Addition

    DOE PAGESBeta

    Yue, Lanping; Jin, Yunlong; Zhang, Wenyong; Sellmyer, David J.

    2015-01-01

    Tmore » he addition of Molybdenum was used to modify the nanostructure and enhance coercivity of rare-earth-free Zr2Co11-based nanocrystalline permanent magnets. he effect of Mo addition on magnetic domain structures of melt spun nanocrystalline Zr16Co84-xMox(x=0, 0.5, 1, 1.5, and 2.0) ribbons has been investigated. It was found that magnetic properties and local domain structures are strongly influenced by Mo doping. he coercivity of the samples increases with the increase in Mo content (x≤1.5). he maximum energy product(BH)maxincreases with increasingxfrom 0.5 MGOe forx=0to a maximum value of 4.2 MGOe forx=1.5. he smallest domain size with a relatively short magnetic correlation length of 128 nm and largest root-mean-square phase shiftΦrmsvalue of 0.66° are observed for thex=1.5. he optimal Mo addition promotes magnetic domain structure refinement and thus leads to a significant increase in coercivity and energy product in this sample.« less

  20. A Real-Time All-Atom Structural Search Engine for Proteins

    PubMed Central

    Gonzalez, Gabriel; Hannigan, Brett; DeGrado, William F.

    2014-01-01

    Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new “designability”-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license), https://github.com/Gabriel439/suns-cmd (command line client, BSD license), and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license). PMID:25079944

  1. All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

    SciTech Connect

    Andoh, Y.; Yoshii, N.; Yamada, A.; Kojima, H.; Mizutani, K.; Okazaki, S.; Fujimoto, K.; Nakagawa, A.; Nomoto, A.

    2014-10-28

    Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 10{sup 6} all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.

  2. ALMOST: an all atom molecular simulation toolkit for protein structure determination.

    PubMed

    Fu, Biao; Sahakyan, Aleksandr B; Camilloni, Carlo; Tartaglia, Gian Gaetano; Paci, Emanuele; Caflisch, Amedeo; Vendruscolo, Michele; Cavalli, Andrea

    2014-05-30

    Almost (all atom molecular simulation toolkit) is an open source computational package for structure determination and analysis of complex molecular systems including proteins, and nucleic acids. Almost has been designed with two primary goals: to provide tools for molecular structure determination using various types of experimental measurements as conformational restraints, and to provide methods for the analysis and assessment of structural and dynamical properties of complex molecular systems. The methods incorporated in Almost include the determination of structural and dynamical features of proteins using distance restraints derived from nuclear Overhauser effect measurements, orientational restraints obtained from residual dipolar couplings and the structural restraints from chemical shifts. Here, we present the first public release of Almost, highlight the key aspects of its computational design and discuss the main features currently implemented. Almost is available for the most common Unix-based operating systems, including Linux and Mac OS X. Almost is distributed free of charge under the GNU Public License, and is available both as a source code and as a binary executable from the project web site at http://www.open-almost.org. Interested users can follow and contribute to the further development of Almost on http://sourceforge.net/projects/almost. PMID:24676684

  3. All-atom molecular dynamics simulation studies of fully hydrated gel phase DPPG and DPPE bilayers

    NASA Astrophysics Data System (ADS)

    Pimthon, Jutarat; Willumeit, Regine; Lendlein, Andreas; Hofmann, Dieter

    2009-03-01

    Here in silico lipid membranes are described providing a structural background of the organization of the lipid components of membranes and aiding further biological or biophysical studies. An all-atom molecular dynamics simulations has been performed to investigate structural and dynamical properties of two fully hydrated gel-phase bilayers of 1,2-dipalmitoyl- sn-glycero-3-phosphoglycerol (DPPG) and 1,2-dipalmitoyl- sn-glycero-3-phospho-ethanolamine (DPPE) bilayers at 303 K. The respective starting configuration of lipids in the simulation bilayer unit cells were taken on the basis of scattering data. In both simulations, we found overall reasonably good agreement with the available experimental data (area per lipid, phosphorus-phosphorus distance). The distribution of the water/counterions at the membrane interface, interactions/orientations of lipid headgroups, and hydrocarbon chain organization were extensively studied in terms of pair distribution functions between main structural components of the system. Intra/intermolecular hydrogen bond formation was discussed in detail. The water orientation at the lipid membrane interface was explored thoroughly in terms of dipole moment as a function of the water molecule positions along the membrane, where we found that the counterions changed the orientation of the water at the interface. Special attention has been devoted to the distribution of the sodium counterions around the DPPG headgroup. We found preferential binding of Na + ions to the phosphate oxygen species.

  4. All-atom Multiscale Simulation of Cowpea Chlorotic Mottle Virus Capsid Swelling

    PubMed Central

    Miao, Yinglong; Johnson, John E.; Ortoleva, Peter J.

    2010-01-01

    An all-atom multiscale computational modeling approach, Molecular Dynamics/Order Parameter eXtrapolation (MD/OPX), has recently been developed for simulating large bionanosystems. It accelerates MD simulations and addresses rapid atomistic fluctuations and slowly-varying nanoscale dynamics of bionanosystems simultaneously. With modules added to account for water molecules and ions, MD/OPX is applied to simulate the swelling of cowpea chlorotic mottle virus (CCMV) capsid solvated in a host medium in this study. Simulation results show that the N-terminal arms of capsid proteins undergo large deviations from the initial configurations with their length extended quickly during the early stage of capsid swelling. The capsid swelling is a symmetry-breaking process involving local initiation and front propagation. The capsid swelling rate is ~0.25 nm/ns (npn) during early stage of the simulation and propagation of the structural transition across the capsid is roughly 0.6npn. The system conditions that affect swelling of the capsid are analyzed. Prospects for creating a phase diagram for CCMV capsid swelling and using predictions to guide experiments are discussed. PMID:20695471

  5. All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

    NASA Astrophysics Data System (ADS)

    Andoh, Y.; Yoshii, N.; Yamada, A.; Fujimoto, K.; Kojima, H.; Mizutani, K.; Nakagawa, A.; Nomoto, A.; Okazaki, S.

    2014-10-01

    Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 106 all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.

  6. Non-equilibrium all-atom molecular dynamics simulations of free and tethered DNA molecules in nanochannel shear flows

    NASA Astrophysics Data System (ADS)

    Wang, Guan M.; Sandberg, William C.

    2007-04-01

    In order to gain insight into the mechanical and dynamical behaviour of free and tethered short chains of ss/ds DNA molecules in flow, and in parallel to investigate the properties of long chain molecules in flow fields, we have developed a series of quantum and molecular methods to extend the well developed equilibrium software CHARMM to handle non-equilibrium dynamics. These methods have been applied to cases of DNA molecules in shear flows in nanochannels. Biomolecules, both free and wall-tethered, have been simulated in the all-atom style in solvent-filled nanochannels. The new methods were demonstrated by carrying out NEMD simulations of free single-stranded DNA (ssDNA) molecules of 21 bases as well as double-stranded DNA (dsDNA) molecules of 21 base pairs tethered on gold surfaces in an ionic water shear flow. The tethering of the linker molecule (6-mercapto-1-hexanol) to perfect Au(111) surfaces was parametrized based on density functional theory (DFT) calculations. Force field parameters were incorporated into the CHARMM database. Gold surfaces are simulated in a Lennard-Jones style model that was fitted to the Morse potential model of bulk gold. The bonding force of attachment of the DNA molecules to the gold substrate linker molecule was computed to be up to a few nN when the DNA molecules are fully stretched at high shear rates. For the first time, we calculated the relaxation time of DNA molecules in picoseconds (ps) and the hydrodynamic force up to a few nanoNewtons (nN) per base pair in a nanochannel flow. The velocity profiles in the solvent due to the presence of the tethered DNA molecules were found to be nonlinear only at high shear flow rates. Free ssDNA molecules in a shear flow were observed to behave differently from each other depending upon their initial orientation in the flow field. Both free and tethered DNA molecules are clearly observed to be stretching, rotating and relaxing. Methods developed in this initial work can be incorporated

  7. On Using Atomistic Solvent Layers in Hybrid All-Atom/Coarse-Grained Molecular Dynamics Simulations.

    PubMed

    Kuhn, Alexander B; Gopal, Srinivasa M; Schäfer, Lars V

    2015-09-01

    Hybrid all-atom/coarse-grained (AA-CG) simulations in which AA solutes are embedded in a CG environment can provide a significant computational speed-up over conventional fully atomistic simulations and thus alleviate the current length and time scale limitations of molecular dynamics (MD) simulations of large biomolecular systems. On one hand, coarse graining the solvent is particularly appealing, since it typically constitutes the largest part of the simulation system and thus dominates computational cost. On the other hand, retaining atomic-level solvent layers around the solute is desirable for a realistic description of hydrogen bonds and other local solvation effects. Here, we devise and systematically validate fixed resolution AA-CG schemes, both with and without atomistic water layers. To quantify the accuracy and diagnose possible pitfalls, Gibbs free energies of solvation of amino acid side chain analogues were calculated, and the influence of the nature of the CG solvent surrounding (polarizable vs nonpolarizable CG water) and the size of the AA solvent region was investigated. We show that distance restraints to keep the AA solvent around the solute lead to too high of a density in the inner shell. Together with a long-ranged effect due to orientational ordering of water molecules at the AA-CG boundary, this affects solvation free energies. Shifting the onset of the distance restraints slightly away from the central solute significantly improves solvation free energies, down to mean unsigned errors with respect to experiment of 2.3 and 2.6 kJ/mol for the polarizable and nonpolarizable CG water surrounding, respectively. The speed-up of the nonpolarizable model renders it computationally more attractive. The present work thus highlights challenges, and outlines possible solutions, involved with modeling the boundary between different levels of resolution in hybrid AA-CG simulations. PMID:26575936

  8. Human Inducible Hsp70: Structures, Dynamics, and Interdomain Communication from All-Atom Molecular Dynamics Simulations.

    PubMed

    Nicolaï, Adrien; Senet, Patrick; Delarue, Patrice; Ripoll, Daniel R

    2010-08-10

    The 70 kDa human heat shock protein is a major molecular chaperone involved in de novo folding of proteins in vivo and refolding of proteins under stress conditions. Hsp70 is related to several "misfolding diseases" and other major pathologies, such as cancer, and is a target for new therapies. Hsp70 is comprised of two main domains: an N-terminal nucleotide binding domain (NBD) and a C-terminal substrate protein binding domain (SBD). The chaperone function of Hsp70 is based on an allosteric mechanism. Binding of ATP in NBD decreases the affinity of the substrate for SBD, and hydrolysis of ATP is promoted by binding of polypeptide segments in the SBD. No complete structure of human Hsp70 is known. Here, we report two models of human Hsp70, constructed by homology with Saccharomyces cerevisiae cochaperone protein Hsp110 (open model) and with Escherichia coli 70 kDa DnaK (closed model) and relaxed for several tens to hundreds of nanoseconds by using all-atom molecular dynamics simulations in explicit solvent. We obtain two stable states, Hsp70 with SBD open and SBD closed, which agree with experimental and structural information for ATP-Hsp70 and ADP-Hsp70, respectively. The dynamics of the transition from the open to closed states is investigated with a coarse-grained model and normal-mode analysis. The results show that the conformational change between the two states can be represented by a relatively small number of collective modes which involved major conformational changes in the two domains. These modes provide a mechanistic representation of the communication between NBD and SBD and allow us to identify subdomains and residues that appear to have a critical role in the conformational change mechanism that guides the chaperoning cycle of Hsp70. PMID:26613502

  9. Lipid receptor S1P₁ activation scheme concluded from microsecond all-atom molecular dynamics simulations.

    PubMed

    Yuan, Shuguang; Wu, Rongliang; Latek, Dorota; Trzaskowski, Bartosz; Filipek, Slawomir

    2013-01-01

    Sphingosine 1-phosphate (S1P) is a lysophospholipid mediator which activates G protein-coupled sphingosine 1-phosphate receptors and thus evokes a variety of cell and tissue responses including lymphocyte trafficking, endothelial development, integrity, and maturation. We performed five all-atom 700 ns molecular dynamics simulations of the sphingosine 1-phosphate receptor 1 (S1P₁) based on recently released crystal structure of that receptor with an antagonist. We found that the initial movements of amino acid residues occurred in the area of highly conserved W269⁶·⁴⁸ in TM6 which is close to the ligand binding location. Those residues located in the central part of the receptor and adjacent to kinks of TM helices comprise of a transmission switch. Side chains movements of those residues were coupled to the movements of water molecules inside the receptor which helped in the gradual opening of intracellular part of the receptor. The most stable parts of the protein were helices TM1 and TM2, while the largest movement was observed for TM7, possibly due to the short intracellular part starting with a helix kink at P⁷·⁵⁰, which might be the first helix to move at the intracellular side. We show for the first time the detailed view of the concerted action of the transmission switch and Trp (W⁶·⁴⁸) rotamer toggle switch leading to redirection of water molecules flow in the central part of the receptor. That event is a prerequisite for subsequent changes in intracellular part of the receptor involving water influx and opening of the receptor structure. PMID:24098103

  10. All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences

    PubMed Central

    Hayat, Sikander; Sander, Chris; Marks, Debora S.

    2015-01-01

    Transmembrane β-barrels (TMBs) carry out major functions in substrate transport and protein biogenesis but experimental determination of their 3D structure is challenging. Encouraged by successful de novo 3D structure prediction of globular and α-helical membrane proteins from sequence alignments alone, we developed an approach to predict the 3D structure of TMBs. The approach combines the maximum-entropy evolutionary coupling method for predicting residue contacts (EVfold) with a machine-learning approach (boctopus2) for predicting β-strands in the barrel. In a blinded test for 19 TMB proteins of known structure that have a sufficient number of diverse homologous sequences available, this combined method (EVfold_bb) predicts hydrogen-bonded residue pairs between adjacent β-strands at an accuracy of ∼70%. This accuracy is sufficient for the generation of all-atom 3D models. In the transmembrane barrel region, the average 3D structure accuracy [template-modeling (TM) score] of top-ranked models is 0.54 (ranging from 0.36 to 0.85), with a higher (44%) number of residue pairs in correct strand–strand registration than in earlier methods (18%). Although the nonbarrel regions are predicted less accurately overall, the evolutionary couplings identify some highly constrained loop residues and, for FecA protein, the barrel including the structure of a plug domain can be accurately modeled (TM score = 0.68). Lower prediction accuracy tends to be associated with insufficient sequence information and we therefore expect increasing numbers of β-barrel families to become accessible to accurate 3D structure prediction as the number of available sequences increases. PMID:25858953

  11. Coriolis Force Mass-Flow Meter Composed of a Straight Pipe and an Additional Resonance-Vibrator

    NASA Astrophysics Data System (ADS)

    Tsutsui, Hirohide; Tomikawa, Yoshiro

    1993-05-01

    This paper deals with a new construction for a mass-flow meter using Coriolis force, and its basic experimental results. Some Coriolis force mass-flow meters, proposed up to now, are of a twin construction of, for example, a U-type pipe or a straight-type pipe, where the mass-flow is determined by measuring the relative displacement between the pipes. Therefore, their structure is too complex. To improve this situation, the authors propose a new mass-flow meter using one straight pipe, together with an additional flexural resonance-vibrator. The experimental results prove that a mass-flow meter can be realized by such a simple construction as dealt with here.

  12. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    NASA Astrophysics Data System (ADS)

    Zheng, Wenjun; Glenn, Paul

    2015-01-01

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  13. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    SciTech Connect

    Zheng, Wenjun Glenn, Paul

    2015-01-21

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  14. Dissociation of a Dynamic Protein Complex Studied by All-Atom Molecular Simulations.

    PubMed

    Zhang, Liqun; Borthakur, Susmita; Buck, Matthias

    2016-02-23

    The process of protein complex dissociation remains to be understood at the atomic level of detail. Computers now allow microsecond timescale molecular-dynamics simulations, which make the visualization of such processes possible. Here, we investigated the dissociation process of the EphA2-SHIP2 SAM-SAM domain heterodimer complex using unrestrained all-atom molecular-dynamics simulations. Previous studies on this system have shown that alternate configurations are sampled, that their interconversion can be fast, and that the complex is dynamic by nature. Starting from different NMR-derived structures, mutants were designed to stabilize a subset of configurations by swapping ion pairs across the protein-protein interface. We focused on two mutants, K956D/D1235K and R957D/D1223R, with attenuated binding affinity compared with the wild-type proteins. In contrast to calculations on the wild-type complexes, the majority of simulations of these mutants showed protein dissociation within 2.4 μs. During the separation process, we observed domain rotation and pivoting as well as a translation and simultaneous rolling, typically to alternate and weaker binding interfaces. Several unsuccessful recapturing attempts occurred once the domains were moderately separated. An analysis of protein solvation suggests that the dissociation process correlates with a progressive loss of protein-protein contacts. Furthermore, an evaluation of internal protein dynamics using quasi-harmonic and order parameter analyses indicates that changes in protein internal motions are expected to contribute significantly to the thermodynamics of protein dissociation. Considering protein association as the reverse of the separation process, the initial role of charged/polar interactions is emphasized, followed by changes in protein and solvent dynamics. The trajectories show that protein separation does not follow a single distinct pathway, but suggest that the mechanism of dissociation is common in

  15. Lessons Learned at the Idaho National Laboratory for the Entry into Force of the U.S. Additional Protocol

    SciTech Connect

    Jeffrey C. Joe; Shauna A. Hoiland

    2009-07-01

    For a number of years, the Idaho National Laboratory (INL) has been preparing for the entry into force of the U.S. Additional Protocol (AP). These preparations included attending training, participating in tabletop exercises, preparing draft declarations, developing INL-specific guidance documents, preparing for and hosting a mock complementary access visit, and preparing declarations for official submittal. All of these activities, the training materials, and software developed by other U.S. DOE national laboratories (PNNL, ORNL, LANL, and BNL) were very helpful in preparing for the entry into force of the AP. As with any endeavor of this size and complexity, however, there are always instances where even the best preparations and advanced planning do not anticipate every challenge. As the DOE's lead nuclear energy research and development facility, the INL faced many unique challenges. The majority of research conducted at the INL is nuclear fuel cycle related, most of which is not protected by the National Security Exclusion. This paper describes the lessons learned from the INL’s experience of preparing for the entry into force of the AP, specifically how translating and implementing general principles into actual activities proved to be one of many challenges, and provides general suggestions on how to respond effectively and efficiently to routine annual data calls and other AP requests.

  16. Peptides (P1, P2 and its mutations) binding with a graphene sheet: an all-atom to all-residue hierarchical coarse-grained approach

    NASA Astrophysics Data System (ADS)

    Kuang, Zhifeng; Farmer, Barry; Pandey, Ras

    2013-03-01

    Binding of peptide P2 (EPLQLKM) [1] and its mutations (P2G, P2Q) to a graphene sheet are studied by a coarse-grained computer simulation. Our hierarchical coarse-grained approach involves all-atom MD simulation to assess the binding interaction of each residue with the graphene sheet. Data from all-atom simulations are then used as input to phenomenological interaction in a coarse-grained MC simulation [2]. Binding of each peptide and its residue in corresponding sequence (P2, P2G, P2Q) are evaluated by analyzing the adsorption of each residue, its mobility, and structural profiles. Although it is difficult to identify overall morphological differences in adsorbed peptides by visual inspections, quantitative analysis of the conformational changes of adsorbed peptides shows variations in size among P2E and its mutations. Results on binding of peptide P1 (HSSYWYAFNNKT) may also be presented if data become available. This work is supported by the Air Force Research Laboratory.

  17. Resonance scattering and radiation force calculations for an elastic cylinder using the translational addition theorem for cylindrical wave functions

    SciTech Connect

    Mitri, F. G.

    2015-09-15

    The standard Resonance Scattering Theory (RST) of plane waves is extended for the case of any two-dimensional (2D) arbitrarily-shaped monochromatic beam incident upon an elastic cylinder with arbitrary location using an exact methodology based on Graf’s translational addition theorem for the cylindrical wave functions. The analysis is exact as it does not require numerical integration procedures. The formulation is valid for any cylinder of finite size and material that is immersed in a nonviscous fluid. Partial-wave series expansions (PWSEs) for the incident, internal and scattered linear pressure fields are derived, and the analysis is further extended to obtain generalized expressions for the on-axis and off-axis acoustic radiation force components. The wave-fields are expressed using generalized PWSEs involving the beam-shape coefficients (BSCs) and the scattering coefficients of the cylinder. The off-axial BSCs are expressed analytically in terms of an infinite PWSE with emphasis on the translational offset distance d. Numerical computations are considered for a zeroth-order quasi-Gaussian beam chosen as an example to illustrate the analysis. Acoustic resonance scattering directivity diagrams are calculated by subtracting an appropriate background from the expression of the scattered pressure field. In addition, computations for the radiation force exerted on an elastic cylinder centered on the axis of wave propagation of the beam, and shifted off-axially are analyzed and discussed.

  18. Repeated forced swim stress has additive effects in anxiety behavior and in cathecolamine levels of adult rats exposed to deltamethrin.

    PubMed

    Habr, Soraya F; Macrini, Daclé J; Florio, Jorge C; Bernardi, Maria M

    2014-01-01

    Deltamethrin (DTM) is a type II pyrethroid insecticide that elicits autonomic and neuroendocrine responses that indicate high levels of stress, presumably caused by the neurotoxic effect of the insecticide. This study investigated the effect of DTM exposure (10 mg/kg, p.o.) and an additional stress induced in the forced swim test (FST) in behavioral tasks related to anxiety, serum corticosterone levels, and striatal neurotransmitter levels. Open field behavior and social interaction were evaluated after DTM administration (10 mg kg(-1), p.o). DTM per se reduced rearing frequency in the open field, but no alterations in locomotion frequency or immobility duration were detected. Stress increased immobility duration compared with non-stressed animals. DTM reduced social interaction and increased corticosterone levels, and these effects were enhanced in stressed animals. Mainly stress affected dopaminergic and serotoninergic activity. In anxiety behavior and in both neurotransmitters and metabolites levels it was observed an additive effect of stress in DTM treated rat data. These results indicate that DTM enhanced the anxiogenic responses and stress had an additive effect over the DTM stress. The neurochemical data did not indicate an interaction between stress and DTM exposure. The present results maybe important for implementing pyrethroid insecticide safety standards. PMID:25444720

  19. Effects of Water Models on Binding Affinity: Evidence from All-Atom Simulation of Binding of Tamiflu to A/H5N1 Neuraminidase

    PubMed Central

    Nguyen, Trang Truc; Viet, Man Hoang

    2014-01-01

    The influence of water models SPC, SPC/E, TIP3P, and TIP4P on ligand binding affinity is examined by calculating the binding free energy ΔGbind of oseltamivir carboxylate (Tamiflu) to the wild type of glycoprotein neuraminidase from the pandemic A/H5N1 virus. ΔGbind is estimated by the Molecular Mechanic-Poisson Boltzmann Surface Area method and all-atom simulations with different combinations of these aqueous models and four force fields AMBER99SB, CHARMM27, GROMOS96 43a1, and OPLS-AA/L. It is shown that there is no correlation between the binding free energy and the water density in the binding pocket in CHARMM. However, for three remaining force fields ΔGbind decays with increase of water density. SPC/E provides the lowest binding free energy for any force field, while the water effect is the most pronounced in CHARMM. In agreement with the popular GROMACS recommendation, the binding score obtained by combinations of AMBER-TIP3P, OPLS-TIP4P, and GROMOS-SPC is the most relevant to the experiments. For wild-type neuraminidase we have found that SPC is more suitable for CHARMM than TIP3P recommended by GROMACS for studying ligand binding. However, our study for three of its mutants reveals that TIP3P is presumably the best choice for CHARMM. PMID:24672329

  20. Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models

    PubMed Central

    Na, Hyuntae; Jernigan, Robert L.; Song, Guang

    2015-01-01

    Dynamics can provide deep insights into the functional mechanisms of proteins and protein complexes. For large protein complexes such as GroEL/GroES with more than 8,000 residues, obtaining a fine-grained all-atom description of its normal mode motions can be computationally prohibitive and is often unnecessary. For this reason, coarse-grained models have been used successfully. However, most existing coarse-grained models use extremely simple potentials to represent the interactions within the coarse-grained structures and as a result, the dynamics obtained for the coarse-grained structures may not always be fully realistic. There is a gap between the quality of the dynamics of the coarse-grained structures given by all-atom models and that by coarse-grained models. In this work, we resolve an important question in protein dynamics computations—how can we efficiently construct coarse-grained models whose description of the dynamics of the coarse-grained structures remains as accurate as that given by all-atom models? Our method takes advantage of the sparseness of the Hessian matrix and achieves a high efficiency with a novel iterative matrix projection approach. The result is highly significant since it can provide descriptions of normal mode motions at an all-atom level of accuracy even for the largest biomolecular complexes. The application of our method to GroEL/GroES offers new insights into the mechanism of this biologically important chaperonin, such as that the conformational transitions of this protein complex in its functional cycle are even more strongly connected to the first few lowest frequency modes than with other coarse-grained models. PMID:26473491

  1. Molecular insights into diphenylalanine nanotube assembly: all-atom simulations of oligomerization.

    PubMed

    Jeon, Joohyun; Mills, Carolyn E; Shell, M Scott

    2013-04-18

    Self-assembling peptides represent a growing class of inexpensive, environmentally benign, nanostructured materials. In particular, diphenylalanine (FF) self-assembles into nanotubes with remarkable strength and thermal stability that have found use in a wide variety of applications, including as sacrificial templates and scaffolds for structuring inorganic materials and as interfacial "nanoforests" for superhydrophobic surfaces and high-performance supercapacitors and biosensors. However, little is known about the assembly mechanisms of FF nanotubes or the forces underlying their stability. Here, we perform a variety of molecular dynamics simulations on both zwitterionic and capped (uncharged) versions of the FF peptide to understand the early stages of self-assembly. We compare these results to simulations of the proposed nanotube X-ray crystal structure. When comparing the zwitterionic and uncharged FF peptides, we find that, while electrostatic interactions steer the former into more ordered dimers and trimers, the hydrophobic side chain interactions play a strong role in determining the structures of larger oligomers. Simulations of the crystal structure fragment also suggest that the strongest interactions occur between side chains, not between the charged termini that form salt bridges. We conclude that the amphiphilic nature of FF is key to understanding its self-assembly, and that the early precursors to nanotube structures are likely to involve substantial hydrophobic clustering, rather than hexamer ring motifs as has been previously suggested. PMID:23521630

  2. Forced and natural carbonation of lime-based mortars with and without additives: Mineralogical and textural changes

    SciTech Connect

    Cultrone, G.

    2005-12-15

    We have studied the carbonation process in different types of mortars, with and without pozzolana or air-entraining additives, subject to a CO{sub 2}-rich atmosphere and compared the results with those of similar naturally carbonated mortars. We used X-ray diffraction technique to demonstrate that high CO{sub 2} concentrations favour a faster, more complete carbonation process with 8 days being sufficient to convert portlandite into 90 wt.% calcite. Full carbonation, however, is not reached during the life-span of the tests, not even in forced carbonation experiments. This could be due to at least one of the following phenomena: a premature drying of samples during carbonation reaction, the temperature at which the carbonation process was carried out or the reduction of pore volume occupied by newly formed calcite crystals. This last option seems to be the least probable. We observed a more prolific development of calcite crystals in the pores and fissures through which the carbonic anhydride flows. Under natural conditions, carbonation is much slower and similar levels are not reached for 6 months. These differences suggest that the carbonation process is influenced by the amount of CO{sub 2} used. Both the mineralogy and texture of mortars vary depending on the type of additive used but the speed of the portlandite-calcite transformation does not change significantly. Pozzolana produces hydraulic mortars although the quantity of calcium aluminosilicate crystals is low. The air-entraining agent significantly alters the texture of the mortars creating rounded pores and eliminating or reducing the drying cracks.

  3. Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): time-resolved fluorescence measurements and all-atom molecular dynamics simulations.

    PubMed

    Das, Anuradha; Das, Suman; Biswas, Ranjit

    2015-01-21

    Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH3CONH2) and urea (NH2CONH2) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH3CONH2 + (1 - f)NH2CONH2] have been studied in a temperature range of 328-353 K which is ∼120-145 K above the measured glass transition temperatures (∼207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (∼70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α2) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems. PMID:25612718

  4. Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): Time-resolved fluorescence measurements and all-atom molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Das, Anuradha; Das, Suman; Biswas, Ranjit

    2015-01-01

    Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH3CONH2) and urea (NH2CONH2) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH3CONH2 + (1 - f)NH2CONH2] have been studied in a temperature range of 328-353 K which is ˜120-145 K above the measured glass transition temperatures (˜207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (˜70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α2) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.

  5. Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): Time-resolved fluorescence measurements and all-atom molecular dynamics simulations

    SciTech Connect

    Das, Anuradha; Das, Suman; Biswas, Ranjit

    2015-01-21

    Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH{sub 3}CONH{sub 2}) and urea (NH{sub 2}CONH{sub 2}) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH{sub 3}CONH{sub 2} + (1 − f)NH{sub 2}CONH{sub 2}] have been studied in a temperature range of 328-353 K which is ∼120-145 K above the measured glass transition temperatures (∼207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (∼70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α{sub 2}) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.

  6. All-Atom Structural Models of the Transmembrane Domains of Insulin and Type 1 Insulin-Like Growth Factor Receptors

    PubMed Central

    Mohammadiarani, Hossein; Vashisth, Harish

    2016-01-01

    The receptor tyrosine kinase superfamily comprises many cell-surface receptors including the insulin receptor (IR) and type 1 insulin-like growth factor receptor (IGF1R) that are constitutively homodimeric transmembrane glycoproteins. Therefore, these receptors require ligand-triggered domain rearrangements rather than receptor dimerization for activation. Specifically, binding of peptide ligands to receptor ectodomains transduces signals across the transmembrane domains for trans-autophosphorylation in cytoplasmic kinase domains. The molecular details of these processes are poorly understood in part due to the absence of structures of full-length receptors. Using MD simulations and enhanced conformational sampling algorithms, we present all-atom structural models of peptides containing 51 residues from the transmembrane and juxtamembrane regions of IR and IGF1R. In our models, the transmembrane regions of both receptors adopt helical conformations with kinks at Pro961 (IR) and Pro941 (IGF1R), but the C-terminal residues corresponding to the juxtamembrane region of each receptor adopt unfolded and flexible conformations in IR as opposed to a helix in IGF1R. We also observe that the N-terminal residues in IR form a kinked-helix sitting at the membrane–solvent interface, while homologous residues in IGF1R are unfolded and flexible. These conformational differences result in a larger tilt-angle of the membrane-embedded helix in IGF1R in comparison to IR to compensate for interactions with water molecules at the membrane–solvent interfaces. Our metastable/stable states for the transmembrane domain of IR, observed in a lipid bilayer, are consistent with a known NMR structure of this domain determined in detergent micelles, and similar states in IGF1R are consistent with a previously reported model of the dimerized transmembrane domains of IGF1R. Our all-atom structural models suggest potentially unique structural organization of kinase domains in each receptor. PMID

  7. Effects of Bi-2212 addition on the levitation force properties of bulk MgB2 superconductors

    NASA Astrophysics Data System (ADS)

    Taylan Koparan, E.; Savaskan, B.; Guner, S. B.; Celik, S.

    2016-02-01

    We present a detailed investigation of the effects of Bi2Sr2Ca1Cu2O8+κ (Bi-2212) adding on the levitation force and magnetic properties of bulk MgB2 obtained by hot press method. The amount of Bi-2212 was varied between 0 and 10 wt% (0, 2, 4, 6, 10 wt%) of the total MgB2. Moreover, we present MgB2 bulk samples fabricated by using different production methods including hot pressing method to our knowledge. All samples were prepared by using elemental magnesium (Mg) powder, amorphous nano-boron (B) powder and Bi-2212 powder which are produced by hot press method. As a result of hot press process, compact pellet samples were manufactured. The vertical and lateral levitation force measurements were executed at the temperatures of 20, 24 and 28 K under zero-field-cooled (ZFC) and field-cooled (FC) regimes for samples with various adding levels. At 24 K and 28 K under ZFC regime, the 2 wt% Bi-2212 added sample exhibits a higher vertical levitation force than the pure sample. Bi-2212 added MgB2 samples compared to the pure sample have lower attractive force values in FC regime. The magnetic field dependence of the critical current density J c was calculated from the M-H loops for Bi-2212 added MgB2 samples. The 2 wt% Bi-2212 added sample has the best levitation and critical current density performance compared to other samples. The critical temperature ( T c ) has slightly dropped from 37.8 K for the pure MgB2 sample to 36.7 K for the 10 wt% of Bi-2212 added sample. The transition temperature slightly decreases when Bi-2212 adding level is increased.

  8. Theoretical study of the molecular force field and vibration analysis of the hydrogen cyanide addition compound with boron tribromide.

    PubMed

    Hase, Y

    2010-01-01

    An extensive HF, MP2, B3LYP and CCSD study of the molecular structure, force field and normal vibrations has been carried out for the hydrogen cyanide compound with boron tribromide. Most of the calculations agree that the HCN-BBr(3) molecule belongs to C(3v) point group and has a N-B length of 1.55-1.70 A and a N-B-Br angle of 103-105 degrees. These calculations also have estimated the missing low-wavenumber fundamentals in the 190 (nu(5)), 150 (nu(9)) and 105 cm(-1) (nu(10)) regions, instead of the supposed fundamentals at 207, 188 and 150 cm(-1), respectively, based on the combination bands. The quantum chemical force constants, by the B3LYP/6-31G and CCSD/3-21G calculations, have been adjusted by the scaling factors to reproduce the fundamentals in the literature [3] to include the bands below 200 cm(-1) proposed in this study. Normal coordinate analysis using the scaled force constants has been performed to interpret the molecular vibrations of four isotopic molecules, HCN-(10)BBr(3), HCN-(11)BBr(3), DCN-(10)BBr(3) and DCN-(11)BBr(3). PMID:19955013

  9. Theoretical study of the molecular force field and vibration analysis of the hydrogen cyanide addition compound with boron tribromide

    NASA Astrophysics Data System (ADS)

    Hase, Y.

    2010-01-01

    An extensive HF, MP2, B3LYP and CCSD study of the molecular structure, force field and normal vibrations has been carried out for the hydrogen cyanide compound with boron tribromide. Most of the calculations agree that the HCN-BBr 3 molecule belongs to C3v point group and has a N-B length of 1.55-1.70 Å and a N-B-Br angle of 103-105°. These calculations also have estimated the missing low-wavenumber fundamentals in the 190 ( ν5), 150 ( ν9) and 105 cm -1 ( ν10) regions, instead of the supposed fundamentals at 207, 188 and 150 cm -1, respectively, based on the combination bands. The quantum chemical force constants, by the B3LYP/6-31G and CCSD/3-21G calculations, have been adjusted by the scaling factors to reproduce the fundamentals in the literature [3] to include the bands below 200 cm -1 proposed in this study. Normal coordinate analysis using the scaled force constants has been performed to interpret the molecular vibrations of four isotopic molecules, HCN- 10BBr 3, HCN- 11BBr 3, DCN- 10BBr 3 and DCN- 11BBr 3.

  10. Effect of water on structure and dynamics of [BMIM][PF6] ionic liquid: An all-atom molecular dynamics simulation investigation

    NASA Astrophysics Data System (ADS)

    Sharma, Anirban; Ghorai, Pradip Kr.

    2016-03-01

    Composition dependent structural and dynamical properties of aqueous hydrophobic 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) ionic liquid (IL) have been investigated by using all-atom molecular dynamics simulation. We observe that addition of water does not increase significant number of dissociated ions in the solution over the pure state. As a consequence, self-diffusion coefficient of the cation and anion is comparable to each other at all water concentration similar to that is observed for the pure state. Voronoi polyhedra analysis exhibits strong dependence on the local environment of IL concentration. Void and neck distributions in Voronoi tessellation are approximately Gaussian for pure IL but upon subsequent addition of water, we observe deviation from the Gaussian behaviour with an asymmetric broadening with long tail of exponential decay at large void radius, particularly at higher water concentrations. The increase in void space and neck size at higher water concentration facilitates ionic motion, thus, decreasing dynamical heterogeneity and IL reorientation time and increases self-diffusion coefficient significantly.

  11. Comparison of operation efficiency for the insert task when using stereoscopic images with additional lines, stereoscopic images, and a manipulator with force feedback

    NASA Astrophysics Data System (ADS)

    Matsunaga, Katsuya; Shidoji, Kazunori; Matsubara, Kenjiro

    1999-05-01

    It has been reported that operation efficiency for the teleoperations using stereoscopic video images is lower than when using the naked eye in real environments. Here, the authors tried to improve the human-machine interface of this particular system to achieve higher operation efficiency for stereoscopic video imags by adding other information. An experiment was carried out under the four following conditions: when the insert task was performed by subjects using conventional stereoscopic video imags, when the centering lines of the cylindrical objects and holes were added to the conventional stereoscopic video images, when the force feedback was provided to the system manipulator as one object touched another object, and when both of the additional centering lines and force feedback were provided. The subject's task was to inset a cylindrical object into a round hole. The completion time was measured from the time of the starting signal to the time when the object was inserted into the hole. Completion time, when additional lines were given, was shorter than when the force feedback was provided, and when no additional information was provided. It was concluded that additional visual information contributed more to the recognition of the space rather than providing additional information about surface phenomena.

  12. Temperature-Dependent Conformational Properties of Human Neuronal Calcium Sensor-1 Protein Revealed by All-Atom Simulations.

    PubMed

    Zhu, Yuzhen; Ma, Buyong; Qi, Ruxi; Nussinov, Ruth; Zhang, Qingwen

    2016-04-14

    Neuronal calcium sensor-1 (NCS-1) protein has orthologues from Saccharomyces cerevisiae to human with highly conserved amino acid sequences. NCS-1 is an important factor controlling the animal's response to temperature change. This leads us to investigate the temperature effects on the conformational dynamics of human NCS-1 at 310 and 316 K by all-atom molecular dynamics (MD) simulations and dynamic community network analysis. Four independent 500 ns MD simulations show that secondary structure content at 316 K is similar to that at 310 K, whereas the global protein structure is expanded. Loop 3 (L3) adopts an extended state occuping the hydrophobic crevice, and the number of suboptimal communication paths between residue D176 and V190 is reduced at 316 K. The dynamic community network analysis suggests that the interdomain correlation is weakened, and the intradomain coupling is strengthened at 316 K. The elevated temperature reduces the number of the salt bridges, especially in C-domain. This study suggests that the elevated temperature affects the conformational dynamics of human NCS-1 protein. Comparison of the structural dynamics of R102Q mutant and Δ176-190 truncated NCS-1 suggests that the structural and dynamical response of NCS-1 protein to elevated temperature may be one of its intrinsic functional properties. PMID:27007011

  13. Insights into the Tunnel Mechanism of Cholesteryl Ester Transfer Protein through All-atom Molecular Dynamics Simulations.

    PubMed

    Lei, Dongsheng; Rames, Matthew; Zhang, Xing; Zhang, Lei; Zhang, Shengli; Ren, Gang

    2016-07-01

    Cholesteryl ester transfer protein (CETP) mediates cholesteryl ester (CE) transfer from the atheroprotective high density lipoprotein (HDL) cholesterol to the atherogenic low density lipoprotein cholesterol. In the past decade, this property has driven the development of CETP inhibitors, which have been evaluated in large scale clinical trials for treating cardiovascular diseases. Despite the pharmacological interest, little is known about the fundamental mechanism of CETP in CE transfer. Recent electron microscopy (EM) experiments have suggested a tunnel mechanism, and molecular dynamics simulations have shown that the flexible N-terminal distal end of CETP penetrates into the HDL surface and takes up a CE molecule through an open pore. However, it is not known whether a CE molecule can completely transfer through an entire CETP molecule. Here, we used all-atom molecular dynamics simulations to evaluate this possibility. The results showed that a hydrophobic tunnel inside CETP is sufficient to allow a CE molecule to completely transfer through the entire CETP within a predicted transfer time and at a rate comparable with those obtained through physiological measurements. Analyses of the detailed interactions revealed several residues that might be critical for CETP function, which may provide important clues for the effective development of CETP inhibitors and treatment of cardiovascular diseases. PMID:27143480

  14. Insights into the Tunnel Mechanism of Cholesteryl Ester Transfer Protein through All-atom Molecular Dynamics Simulations*

    PubMed Central

    Lei, Dongsheng; Rames, Matthew; Zhang, Xing; Zhang, Lei; Zhang, Shengli; Ren, Gang

    2016-01-01

    Cholesteryl ester transfer protein (CETP) mediates cholesteryl ester (CE) transfer from the atheroprotective high density lipoprotein (HDL) cholesterol to the atherogenic low density lipoprotein cholesterol. In the past decade, this property has driven the development of CETP inhibitors, which have been evaluated in large scale clinical trials for treating cardiovascular diseases. Despite the pharmacological interest, little is known about the fundamental mechanism of CETP in CE transfer. Recent electron microscopy (EM) experiments have suggested a tunnel mechanism, and molecular dynamics simulations have shown that the flexible N-terminal distal end of CETP penetrates into the HDL surface and takes up a CE molecule through an open pore. However, it is not known whether a CE molecule can completely transfer through an entire CETP molecule. Here, we used all-atom molecular dynamics simulations to evaluate this possibility. The results showed that a hydrophobic tunnel inside CETP is sufficient to allow a CE molecule to completely transfer through the entire CETP within a predicted transfer time and at a rate comparable with those obtained through physiological measurements. Analyses of the detailed interactions revealed several residues that might be critical for CETP function, which may provide important clues for the effective development of CETP inhibitors and treatment of cardiovascular diseases. PMID:27143480

  15. Reorientation and Dimerization of the Membrane-Bound Antimicrobial Peptide PGLa from Microsecond All-Atom MD Simulations

    PubMed Central

    Ulmschneider, Jakob P.; Smith, Jeremy C.; Ulmschneider, Martin B.; Ulrich, Anne S.; Strandberg, Erik

    2012-01-01

    The membrane-active antimicrobial peptide PGLa from Xenopus laevis is known from solid-state 2H-, 15N-, and 19F-NMR spectroscopy to occupy two distinct α-helical surface adsorbed states in membranes: a surface-bound S-state with a tilt angle of ∼95° at low peptide/lipid molar ratio (P/L = 1:200), and an obliquely tilted T-state with a tilt angle of 127° at higher peptide concentration (P/L = 1:50). Using a rapid molecular-dynamics insertion protocol in combination with microsecond-scale simulation, we have characterized the structure of both states in detail. As expected, the amphiphilic peptide resides horizontally on the membrane surface in a monomeric form at a low P/L, whereas the T-state is seen in the simulations to be a symmetric antiparallel dimer, with close contacts between small glycine and alanine residues at the interface. The computed tilt angles and azimuthal rotations, as well as the quadrupolar splittings predicted from the simulations agree with the experimental NMR data. The simulations reveal many structural details previously inaccessible, such as the immersion depth of the peptide in the membrane and the packing of the dimerization interface. The study highlights the ability and limitations of current state-of-the-art multimicrosecond all-atom simulations of membrane-active peptides to complement experimental data from solid-state NMR. PMID:22947863

  16. Development of the CHARMM Force Field for Lipids

    PubMed Central

    Pastor, R.W.; MacKerell, A.D.

    2011-01-01

    The development of the CHARMM additive all-atom lipid force field (FF) is traced from the early 1990’s to the most recent version (C36) published in 2010. Though simulations with early versions yielded useful results, they failed to reproduce two important quantities: a zero surface tension at the experimental bilayer surface area, and the signature splitting of the deuterium order parameters in the glycerol and upper chain carbons. Systematic optimization of parameters based on high level quantum mechanical data and free energy simulations have resolved these issues, and bilayers with a wide range of lipids can be simulated in tensionless ensembles using C36. Issues associated with other all-atom lipid FFs, success and limitations in the C36 FF and ongoing developments are also discussed. PMID:21760975

  17. Lessons learned during the training exercise for the entry into force of the U.S. additional protocol in the DOE complex

    SciTech Connect

    Boyer, Brian D

    2009-01-01

    In 2008 in anticipation of the United States bringing into force the Additional Protocol in early 2009 DOE/NNSA planned and executed training exercises in the conduct of Additional Protocol complementary access activities. Brookhaven National Laboratory and Los Alamos National Laboratory together produced the exercises designed to prepare the following types of DOE laboratories for complementary access - weapons laboratories, nuclear engineering laboratories, and science laboratories. This panel provides a forum to discuss and summarize the results and lessons learned from the 2008 exercise.

  18. Insights into activation and RNA binding of trp RNA-binding attenuation protein (TRAP) through all-atom simulations.

    PubMed

    Murtola, Teemu; Vattulainen, Ilpo; Falck, Emma

    2008-06-01

    Tryptophan biosynthesis in Bacillus stearothermophilus is regulated by a trp RNA binding attenuation protein (TRAP). It is a ring-shaped 11-mer of identical 74 residue subunits. Tryptophan binding pockets are located between adjacent subunits, and tryptophan binding activates TRAP to bind RNA. Here, we report results from all-atom molecular dynamics simulations of the system, complementing existing extensive experimental studies. We focus on two questions. First, we look at the activation mechanism, of which relatively little is known experimentally. We find that the absence of tryptophan allows larger motions close to the tryptophan binding site, and we see indication of a conformational change in the BC loop. However, complete deactivation seems to occur on much longer time scales than the 40 ns studied here. Second, we study the TRAP-RNA interactions. We look at the relative flexibilities of the different bases in the complex and analyze the hydrogen bonds between the protein and RNA. We also study the role of Lys37, Lys56, and Arg58, which have been experimentally identified as essential for RNA binding. Hydrophobic stacking of Lys37 with the nearby RNA base is confirmed, but we do not see direct hydrogen bonding between RNA and the other two residues, in contrast to the crystal structure. Rather, these residues seem to stabilize the RNA-binding surface, and their positive charge may also play a role in RNA binding. Simulations also indicate that TRAP is able to attract RNA nonspecifically, and the interactions are quantified in more detail using binding energy calculations. The formation of the final binding complex is a very slow process: within the simulation time scale of 40 ns, only two guanine bases become bound (and no others), indicating that the binding initiates at these positions. In general, our results are in good agreement with experimental studies, and provide atomic-scale insights into the processes. PMID:18186477

  19. A combined coarse-grained and all-atom simulation of TRPV1 channel gating and heat activation

    PubMed Central

    Qin, Feng

    2015-01-01

    The transient receptor potential (TRP) channels act as key sensors of various chemical and physical stimuli in eukaryotic cells. Despite years of study, the molecular mechanisms of TRP channel activation remain unclear. To elucidate the structural, dynamic, and energetic basis of gating in TRPV1 (a founding member of the TRPV subfamily), we performed coarse-grained modeling and all-atom molecular dynamics (MD) simulation based on the recently solved high resolution structures of the open and closed form of TRPV1. Our coarse-grained normal mode analysis captures two key modes of collective motions involved in the TRPV1 gating transition, featuring a quaternary twist motion of the transmembrane domains (TMDs) relative to the intracellular domains (ICDs). Our transition pathway modeling predicts a sequence of structural movements that propagate from the ICDs to the TMDs via key interface domains (including the membrane proximal domain and the C-terminal domain), leading to sequential opening of the selectivity filter followed by the lower gate in the channel pore (confirmed by modeling conformational changes induced by the activation of ICDs). The above findings of coarse-grained modeling are robust to perturbation by lipids. Finally, our MD simulation of the ICD identifies key residues that contribute differently to the nonpolar energy of the open and closed state, and these residues are predicted to control the temperature sensitivity of TRPV1 gating. These computational predictions offer new insights to the mechanism for heat activation of TRPV1 gating, and will guide our future electrophysiology and mutagenesis studies. PMID:25918362

  20. Probing the Huntingtin 1-17 Membrane Anchor on a Phospholipid Bilayer by Using All-Atom Simulations

    PubMed Central

    Côté, Sébastien; Binette, Vincent; Salnikov, Evgeniy S.; Bechinger, Burkhard; Mousseau, Normand

    2015-01-01

    Mislocalization and aggregation of the huntingtin protein are related to Huntington’s disease. Its first exon—more specifically the first 17 amino acids (Htt17)—is crucial for the physiological and pathological functions of huntingtin. It regulates huntingtin’s activity through posttranslational modifications and serves as an anchor to membrane-containing organelles of the cell. Recently, structure and orientation of the Htt17 membrane anchor were determined using a combined solution and solid-state NMR approach. This prompted us to refine this model by investigating the dynamics and thermodynamics of this membrane anchor on a POPC bilayer using all-atom, explicit solvent molecular dynamics and Hamiltonian replica exchange. Our simulations are combined with various experimental measurements to generate a high-resolution atomistic model for the huntingtin Htt17 membrane anchor on a POPC bilayer. More precisely, we observe that the single α-helix structure is more stable in the phospholipid membrane than the NMR model obtained in the presence of dodecylphosphocholine detergent micelles. The resulting Htt17 monomer has its hydrophobic plane oriented parallel to the bilayer surface. Our results further unveil the key residues interacting with the membrane in terms of hydrogen bonds, salt-bridges, and nonpolar contributions. We also observe that Htt17 equilibrates at a well-defined insertion depth and that it perturbs the physical properties—order parameter, thickness, and area per lipid—of the bilayer in a manner that could favor its dimerization. Overall, our observations reinforce and refine the NMR measurements on the Htt17 membrane anchor segment of huntingtin that is of fundamental importance to its biological functions. PMID:25762330

  1. Exploring the retention properties of CaF2 nanoparticles as possible additives for dental care application with tapping-mode atomic force microscope in liquid.

    PubMed

    Wasem, Matthias; Köser, Joachim; Hess, Sylvia; Gnecco, Enrico; Meyer, Ernst

    2014-01-13

    Amplitude-modulation atomic force microscopy (AM-AFM) is used to determine the retention properties of CaF2 nanoparticles adsorbed on mica and on tooth enamel in liquid. From the phase-lag of the forced cantilever oscillation the local energy dissipation at the detachment point of the nanoparticle was determined. This enabled us to compare different as-synthesized CaF2 nanoparticles that vary in shape, size and surface structure. CaF2 nanoparticles are candidates for additives in dental care products as they could serve as fluorine-releasing containers preventing caries during a cariogenic acid attack on the teeth. We show that the adherence of the nanoparticles is increased on the enamel substrate compared to mica, independently of the substrate roughness, morphology and size of the particles. PMID:24455460

  2. Exploring the retention properties of CaF2 nanoparticles as possible additives for dental care application with tapping-mode atomic force microscope in liquid

    PubMed Central

    Köser, Joachim; Hess, Sylvia; Gnecco, Enrico; Meyer, Ernst

    2014-01-01

    Summary Amplitude-modulation atomic force microscopy (AM-AFM) is used to determine the retention properties of CaF2 nanoparticles adsorbed on mica and on tooth enamel in liquid. From the phase-lag of the forced cantilever oscillation the local energy dissipation at the detachment point of the nanoparticle was determined. This enabled us to compare different as-synthesized CaF2 nanoparticles that vary in shape, size and surface structure. CaF2 nanoparticles are candidates for additives in dental care products as they could serve as fluorine-releasing containers preventing caries during a cariogenic acid attack on the teeth. We show that the adherence of the nanoparticles is increased on the enamel substrate compared to mica, independently of the substrate roughness, morphology and size of the particles. PMID:24455460

  3. Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

    PubMed

    Shen, Lin; Yang, Weitao

    2016-04-12

    We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer. PMID:26930454

  4. An FFT-based method for modeling protein folding and binding under crowding: benchmarking on ellipsoidal and all-atom crowders.

    PubMed

    Qin, Sanbo; Zhou, Huan-Xiang

    2013-10-01

    It is now well recognized that macromolecular crowding can exert significant effects on protein folding and binding stability. In order to calculate such effects in direct simulations of proteins mixed with bystander macromolecules, the latter (referred to as crowders) are usually modeled as spheres and the proteins represented at a coarse-grained level. Our recently developed postprocessing approach allows the proteins to be represented at the all-atom level but, for computational efficiency, has only been implemented for spherical crowders. Modeling crowder molecules in cellular environments and in vitro experiments as spheres may distort their effects on protein stability. Here we present a new method that is capable for treating aspherical crowders. The idea, borrowed from protein-protein docking, is to calculate the excess chemical potential of the proteins in crowded solution by fast Fourier transform (FFT). As the first application, we studied the effects of ellipsoidal crowders on the folding and binding free energies of all-atom proteins, and found, in agreement with previous direct simulations with coarse-grained protein models, that the aspherical crowders exert greater stabilization effects than spherical crowders of the same volume. Moreover, as demonstrated here, the FFT-based method has the important property that its computational cost does not increase strongly even when the level of details in representing the crowders is increased all the way to all-atom, thus significantly accelerating realistic modeling of protein folding and binding in cell-like environments. PMID:24187527

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

    PubMed Central

    Savelyev, Alexey; MacKerell, Alexander D.

    2015-01-01

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

  6. Collision-Induced Dissociation of Electrosprayed Protein Complexes: An All-Atom Molecular Dynamics Model with Mobile Protons.

    PubMed

    Popa, Vlad; Trecroce, Danielle A; McAllister, Robert G; Konermann, Lars

    2016-06-16

    Electrospray ionization mass spectrometry (ESI-MS) has become an indispensable technique for examining noncovalent protein complexes. Collision-induced dissociation (CID) of these multiply protonated gaseous ions usually culminates in ejection of a single subunit with a disproportionately large amount of charge. Experiments suggest that this process involves subunit unfolding prior to separation from the residual complex, as well as H(+) migration onto the unravelling chain. Molecular dynamics (MD) simulations are a promising avenue for gaining detailed insights into these CID events. Unfortunately, typical MD algorithms do not allow for mobile protons. Here we address this limitation by implementing a strategy that combines atomistic force fields (such as OPLS/AA and CHARMM36) with a proton hopping algorithm, focusing on the tetrameric complexes transthyretin and streptavidin. Protons are redistributed over all acidic and basic sites in 20 ps intervals, subject to an energy function that reflects electrostatic interactions and proton affinities. Our simulations predict that nativelike conformers at the onset of collisional heating contain multiple salt bridges. Collisional heating initially causes subtle structural changes that lead to a gradual decline of these zwitterionic patterns. Many of the MD runs show gradual unfolding of a single subunit in conjunction with H(+) migration, culminating in subunit separation from the complex. However, there are also instances where two or more chains start to unfold simultaneously, giving rise to charge competition. The scission point where the "winning" subunit separates from the complex can be attained for different degrees of unfolding, giving rise to product ions in various charge states. The simulated product ion distributions are in close agreement with experimental CID data. Proton enrichment in the departing subunit is driven by charge-charge repulsion, but the combination of salt bridge depletion, charge migration

  7. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

    SciTech Connect

    Lee, Jumin; Cheng, Xi; Swails, Jason M.; Yeom, Min Sun; Eastman, Peter K.; Lemkul, Justin A.; Wei, Shuai; Buckner, Joshua; Jeong, Jong Cheol; Qi, Yifei; Jo, Sunhwan; Pande, Vijay S.; Case, David A.; Brooks, Charles L.; MacKerell, Alexander D.; Klauda, Jeffery B.; Im, Wonpil

    2015-11-12

    Here we report that proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find the optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as well as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.

  8. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

    PubMed Central

    2015-01-01

    Proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find the optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as well as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules. PMID:26631602

  9. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

    DOE PAGESBeta

    Lee, Jumin; Cheng, Xi; Swails, Jason M.; Yeom, Min Sun; Eastman, Peter K.; Lemkul, Justin A.; Wei, Shuai; Buckner, Joshua; Jeong, Jong Cheol; Qi, Yifei; et al

    2015-11-12

    Here we report that proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find themore » optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as well as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.« less

  10. The relaxation of intrinsic compressive stress in complementary metal-oxide-semiconductor transistors by additional N ion implantation treatment with atomic force microscope-Raman stress extraction

    NASA Astrophysics Data System (ADS)

    Liao, M.-H.; Chen, C.-H.; Chang, L.-C.; Yang, C.; Kao, S.-C.

    2012-05-01

    Based on the stress extraction and measurement by atomic force microscope-Raman technique with the nanometer level space resolution, the high compressive stress about 550 MPa on the Si active region (OD) is observed for the current complementary metal-oxide-semiconductor (CMOS) transistor. During the thermal budget for the standard manufacture process of the current CMOS transistor, the difference of thermal expansion coefficients between Si and Shallow Trench Isolation (STI) oxide results in this high compressive stress in Si OD and further degrades the electron carrier mobility seriously. In order to relax this intrinsic processed compressive stress in Si OD and try to recover this performance loss, the novel process is proposed in this work in addition to the usage of one-side pad SiN layer. With this novel process of additional N-ion implantation (IMP) treatment in STI oxide, it can be found that the less compressive stress about 438 MPa in Si OD can be achieved by the smaller difference of thermal expansion coefficients between Si and N-doped SiO2 STI oxide. The formation of Si-N bonding in N-doped SiO2 STI region can be monitored by Fourier transform infrared spectroscopy spectra and thermal expansion coefficients for Si, SiO2, and SiN are 2.6 ppm/K, 0.4 ppm/K, and 2.87 ppm/K, respectively. The effective relaxation of intrinsic processed compressive stress in Si OD about 112 MPa (from 550 MPa to 438 MPa) by this proposed additional N IMP treatment contributes ˜14% electron carrier mobility enhancement/recovery. The experimental electrical data agree well with the theoretical piezoelectricity calculation for the strained-Si theory.

  11. Reduced Cardiac Contractile Force Due to Sympathovagal Dysfunction Mediates the Additive Hypotensive Effects of Limited-Access Regimens of Ethanol and Clonidine in Spontaneously Hypertensive Rats

    PubMed Central

    El-Mas, Mahmoud M.

    2010-01-01

    Our previous attempts to investigate the long-term hemodynamic interaction between ethanol and clonidine in telemetered spontaneously hypertensive rats (SHRs) were hampered by the lack of a sustained hypotensive response to continuous clonidine exposure. This limitation was circumvented when we adopted a limited-access clonidine (8:30 AM–4:30 PM) paradigm in a recent study. The latter paradigm was employed here to evaluate the ethanol-clonidine interaction and possible roles of myocardial function and autonomic control in this interaction. Changes in blood pressure (BP), heart rate, maximum rate of rise in BP wave (+dP/dtmax), and spectral cardiovascular autonomic profiles were measured by radiotelemetry in pair-fed SHRs receiving clonidine (150 μg/kg/day), ethanol [2.5% (w/v)], or their combination during the day for 12 weeks. Ethanol or clonidine elicited long-term decreases in BP, and their combination caused additive hypotensive response. Significant reductions in +dP/dtmax were observed upon concurrent treatment with ethanol and clonidine, in contrast to no effect for individual treatment. In addition, the combined treatment increased the high-frequency (HF) spectral band of interbeat interval (IBI-HFnu, 0.75–3 Hz) and decreased low-frequency (IBI-LFnu, 0.2–0.75 Hz) bands and IBILF/HF ratios. Clonidine-evoked reductions in plasma and urine norepinephrine and BP-LF spectral power (measure of vasomotor sympathetic tone) were not affected by ethanol. In conclusion, concurrent treatment with ethanol and clonidine shifts the sympathovagal balance toward parasympathetic dominance and elicits exaggerated hypotension as a result of a reduction in cardiac contractile force. PMID:20864507

  12. Analysis of solvation structure and thermodynamics of methane in water by reference interaction site model theory using an all-atom model

    NASA Astrophysics Data System (ADS)

    Cui, Qizhi; Smith, Vedene H.

    2000-12-01

    An all-atom molecular model and optimized site-site pair potential parameters are employed for methane solute. By use of the reference interaction site model theory, the methane hydration structure is analyzed at the atomic level and its hydration free energies, energies, enthalpies, and entropies for four different thermodynamic states: temperature T=283.15, 298.15, 313.15, 328.15 K and the corresponding bulk water density ρ=0.9997, 0.9970, 0.9922, 0.9875 g cm-3 are calculated. Our calculated thermodynamic properties are in rather good agreement with experiments.

  13. Free-energy analysis of lysozyme-triNAG binding modes with all-atom molecular dynamics simulation combined with the solution theory in the energy representation

    NASA Astrophysics Data System (ADS)

    Takemura, Kazuhiro; Burri, Raghunadha Reddy; Ishikawa, Takeshi; Ishikura, Takakazu; Sakuraba, Shun; Matubayasi, Nobuyuki; Kuwata, Kazuo; Kitao, Akio

    2013-02-01

    We propose a method for calculating the binding free energy of protein-ligand complexes using all-atom molecular dynamics simulation combined with the solution theory in the energy representation. Four distinct modes for the binding of tri-N-acetyl-D-glucosamine (triNAG) to hen egg-white lysozyme were investigated, one from the crystal structure and three generated by docking predictions. The proposed method was demonstrated to be used to distinguish the most plausible binding mode (crystal model) as the lowest binding energy mode.

  14. Analysis of solvation structure and thermodynamics of ethane and propane in water by reference interaction site model theory using all-atom models

    NASA Astrophysics Data System (ADS)

    Cui, Qizhi; Smith, Vedene H.

    2001-08-01

    Following our previous paper on methane [Cui and Smith, J. Chem. Phys. 113, 10240 (2000)], we study the solvation structures and thermodynamics of ethane and propane in water at the infinite dilution limit by using the hypernetted chain closure reference interaction site model (HNC-RISM) theory with all-atom representations for solute molecules. At four thermodynamic states: temperature T=283.15, 298.15, 313.15, 328.15 K and the corresponding bulk water density ρ=0.9997, 0.9970, 0.9922, 0.9875 g cm-3, all the atomic solute-solvent radial distribution functions are obtained, and the corresponding running coordination numbers and the hydration free energies, energies, enthalpies, and entropies are calculated with the radial distribution functions as input. The hydration structures of ethane and propane are presented and analyzed at the atomic level in terms of the atomic solute-solvent radial distribution functions. With the optimized nonbonded potential parameters based on the CHARMM96 all-atom model for alkanes [Yin and Mackerell, J. Comput. Chem. 19, 334 (1998)], the ethane and propane hydration thermodynamic properties predicted by the HNC-RISM theory are improved in the specified temperature range (10-55 °C).

  15. Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation

    NASA Astrophysics Data System (ADS)

    Takemura, Kazuhiro; Guo, Hao; Sakuraba, Shun; Matubayasi, Nobuyuki; Kitao, Akio

    2012-12-01

    We propose a method to evaluate binding free energy differences among distinct protein-protein complex model structures through all-atom molecular dynamics simulations in explicit water using the solution theory in the energy representation. Complex model structures are generated from a pair of monomeric structures using the rigid-body docking program ZDOCK. After structure refinement by side chain optimization and all-atom molecular dynamics simulations in explicit water, complex models are evaluated based on the sum of their conformational and solvation free energies, the latter calculated from the energy distribution functions obtained from relatively short molecular dynamics simulations of the complex in water and of pure water based on the solution theory in the energy representation. We examined protein-protein complex model structures of two protein-protein complex systems, bovine trypsin/CMTI-1 squash inhibitor (PDB ID: 1PPE) and RNase SA/barstar (PDB ID: 1AY7), for which both complex and monomer structures were determined experimentally. For each system, we calculated the energies for the crystal complex structure and twelve generated model structures including the model most similar to the crystal structure and very different from it. In both systems, the sum of the conformational and solvation free energies tended to be lower for the structure similar to the crystal. We concluded that our energy calculation method is useful for selecting low energy complex models similar to the crystal structure from among a set of generated models.

  16. Poly(Ethylene Glycol) in Drug Delivery, Why Does it Work, and Can We do Better? All Atom Molecular Dynamics Simulation Provides Some Answers

    NASA Astrophysics Data System (ADS)

    Bunker, Alex

    We summarize our recent work, using all atom molecular dynamics simulation to study the role of poly(ethylene glycol) (PEG) in drug delivery. We have simulated the drug delivery liposome membrane, in both the Gel and Liquid crystalline states. The simulations of the PEGylated membrane have been carried out in the presence of a physiological concentration of NaCl, and two other salts encountered in physiological conditions, KCL and CaCl2. We also simulated targeting moieties on the PEGylated membrane, comparing the behavior of two targeting moieties. We also simulated PEG with three drug molecules for which it is used as a delivery aid: paclitaxel, piroxicam, and hematoporphyrin. We found that the specific properties of PEG, its solubility in both polar and non-polar solvents, and its acting as a polymer electrolyte, have a significant e_ect on its behavior when used in drug delivery.

  17. Non-additive Empirical Force Fields for Short-Chain Linear Alcohols: Methanol to Butanol. Hydration Free Energetics and Kirkwood-Buff Analysis Using Charge Equilibration Models

    PubMed Central

    Zhong, Yang; Patel, Sandeep

    2010-01-01

    Building upon the nonadditive electrostatic force field for alcohols based on the CHARMM charge equilibration (CHEQ) formalism, we introduce atom-pair specific solute-solvent Lennard-Jones (LJ) parameters for alcohol-water interaction force fields targeting improved agreement with experimental hydration free energies of a series of small molecule linear alcohols as well as ab initio water-alcohol geometries and energetics. We consider short-chain, linear alcohols from methanol to butanol as they are canonical small-molecule organic model compounds to represent the hydroxyl chemical functionality for parameterizing biomolecular force fields for proteins. We discuss molecular dynamics simulations of dilute aqueous solutions of methanol and ethanol in TIP4P-FQ water, with particular discussion of solution densities, structure defined in radial distribution functions, electrostatic properties (dipole moment distributions), hydrogen bonding patterns of water, as well as a Kirkwood-Buff (KB) integral analysis. Calculation of the latter provides an assessment of how well classical force fields parameterized to at least semi-quantitatively match experimental hydration free energies capture the microscopic structures of dilute alcohol solutions; the latter translate into macroscopic thermodynamic properties through the application of KB analysis. We find that the CHEQ alcohol force fields of this work semi-quantitatively match experimental KB integrals for methanol and ethanol mole fractions of 0.1 and 0.2. The force field combination qualitatively captures the concentration dependence of the alcohol-alcohol and water-water KB integrals, but due to inadequacies in the representation of the microscopic structures in such systems (which cannot be parameterized in any systematic fashion), a priori quantitative description of alcohol-water KB integrals remains elusive. PMID:20687517

  18. 77 FR 9251 - Designation of a Class of Employees for Addition to the Special Exposure Cohort

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-16

    ... designate a class of employees from the Linde Ceramics Plant in Tonawanda, New York, as an addition to the... addition to the SEC: All Atomic Weapons Employees who worked in any area at the Linde Ceramics Plant...

  19. All-atom simulations and free-energy calculations of coiled-coil peptides with lipid bilayers: binding strength, structural transition, and effect on lipid dynamics.

    PubMed

    Woo, Sun Young; Lee, Hwankyu

    2016-01-01

    Peptides E and K, which are synthetic coiled-coil peptides for membrane fusion, were simulated with lipid bilayers composed of lipids and cholesterols at different ratios using all-atom models. We first calculated free energies of binding from umbrella sampling simulations, showing that both E and K peptides tend to adsorb onto the bilayer surface, which occurs more strongly in the bilayer composed of smaller lipid headgroups. Then, unrestrained simulations show that K peptides more deeply insert into the bilayer with partially retaining the helical structure, while E peptides less insert and predominantly become random coils, indicating the structural transition from helices to random coils, in quantitative agreement with experiments. This is because K peptides electrostatically interact with lipid phosphates, as well as because hydrocarbons of lysines of K peptide are longer than those of glutamic acids of E peptide and thus form stronger hydrophobic interactions with lipid tails. This deeper insertion of K peptide increases the bilayer dynamics and a vacancy below the peptide, leading to the rearrangement of smaller lipids. These findings help explain the experimentally observed or proposed differences in the insertion depth, binding strength, and structural transition of E and K peptides, and support the snorkeling effect. PMID:26926570

  20. All-atom simulations and free-energy calculations of coiled-coil peptides with lipid bilayers: binding strength, structural transition, and effect on lipid dynamics

    PubMed Central

    Woo, Sun Young; Lee, Hwankyu

    2016-01-01

    Peptides E and K, which are synthetic coiled-coil peptides for membrane fusion, were simulated with lipid bilayers composed of lipids and cholesterols at different ratios using all-atom models. We first calculated free energies of binding from umbrella sampling simulations, showing that both E and K peptides tend to adsorb onto the bilayer surface, which occurs more strongly in the bilayer composed of smaller lipid headgroups. Then, unrestrained simulations show that K peptides more deeply insert into the bilayer with partially retaining the helical structure, while E peptides less insert and predominantly become random coils, indicating the structural transition from helices to random coils, in quantitative agreement with experiments. This is because K peptides electrostatically interact with lipid phosphates, as well as because hydrocarbons of lysines of K peptide are longer than those of glutamic acids of E peptide and thus form stronger hydrophobic interactions with lipid tails. This deeper insertion of K peptide increases the bilayer dynamics and a vacancy below the peptide, leading to the rearrangement of smaller lipids. These findings help explain the experimentally observed or proposed differences in the insertion depth, binding strength, and structural transition of E and K peptides, and support the snorkeling effect. PMID:26926570

  1. Energetics of nonpolar and polar compounds in cationic, anionic, and nonionic micelles studied by all-atom molecular dynamics simulation combined with a theory of solutions.

    PubMed

    Date, Atsushi; Ishizuka, Ryosuke; Matubayasi, Nobuyuki

    2016-05-21

    Energetic analysis was conducted for nonpolar and polar solutes bound in a cationic micelle of dodecyl trimethyl ammonium bromide (DTAB), an anionic micelle of sodium dodecyl sulfate (SDS), and a nonionic micelle of tetraethylene glycol monododecyl ether (Brij30). All-atom molecular dynamics simulation was performed, and the free energies of binding the solutes in the hydrophobic-core and headgroup regions of the micelles were computed using the energy-representation method. It was found in all the micelles examined that aromatic naphthalene is preferably located more outward than aliphatic propane and that the polar solutes are localized at the interface of the hydrophobic and hydrophilic regions. The roles of the surfactant and water were then elucidated by decomposing the free energy into the contributions from the respective species. Water was observed to play a decisive role in determining the binding location of the solute, while the surfactant was found to be more important for the overall stabilization of the solute within the micelle. The effects of attractive and repulsive interactions of the solute with the surfactant and water were further examined, and their competition was analyzed in connection with the preferable location of the solute in the micellar system. PMID:27117093

  2. The Ensemble Folding Kinetics of the FBP28 WW Domain Revealed by an All-atom Monte Carlo Simulation in a Knowledge-based Potential

    PubMed Central

    Xu, Jiabin; Huang, Lei; Shakhnovich, Eugene I.

    2011-01-01

    In this work, we apply a detailed all-atom model with a transferable knowledge-based potential to study the folding kinetics of Formin-Binding protein, FBP28, which is a canonical three-stranded β-sheet WW domain. Replica exchange Monte Carlo (REMC) simulations starting from random coils find native-like (C α RMSD of 2.68Å) lowest energy structure. We also study the folding kinetics of FBP28 WW domain by performing a large number of ab initio Monte Carlo folding simulations. Using these trajectories, we examine the order of formation of two β –hairpins, the folding mechanism of each individual β– hairpin, and transition state ensemble (TSE) of FBP28 WW domain and compare our results with experimental data and previous computational studies. To obtain detailed structural information on the folding dynamics viewed as an ensemble process, we perform a clustering analysis procedure based on graph theory. Further, a rigorous Pfold analysis is used to obtain representative samples of the TSEs showing good quantitative agreement between experimental and simulated Φ values. Our analysis shows that the turn structure between first and second β strands is a partially stable structural motif that gets formed before entering the TSE in FBP28 WW domain and there exist two major pathways for the folding of FBP28 WW domain, which differ in the order and mechanism of hairpin formation. PMID:21365688

  3. C6 Coefficients and Dipole Polarizabilities for All Atoms and Many Ions in Rows 1-6 of the Periodic Table.

    PubMed

    Gould, Tim; Bučko, Tomáš

    2016-08-01

    Using time-dependent density functional theory (TDDFT) with exchange kernels, we calculate and test imaginary frequency-dependent dipole polarizabilities for all atoms and many ions in rows 1-6 of the periodic table. These are then integrated over frequency to produce C6 coefficients. Results are presented under different models: straight TDDFT calculations using two different kernels; "benchmark" TDDFT calculations corrected by more accurate quantum chemical and experimental data; and "benchmark" TDDFT with frozen orbital anions. Parametrizations are presented for 411+ atoms and ions, allowing results to be easily used by other researchers. A curious relationship, C6,XY ∝ [αX(0)αY(0)](0.73), is found between C6 coefficients and static polarizabilities α(0). The relationship C6,XY = 2C6,XC6,Y/[(αX/αY)C6,Y + (αY/αX)C6,X] is tested and found to work well (<5% errors) in ∼80% of the cases, but can break down badly (>30% errors) in a small fraction of cases. PMID:27304856

  4. All-atom simulations and free-energy calculations of coiled-coil peptides with lipid bilayers: binding strength, structural transition, and effect on lipid dynamics

    NASA Astrophysics Data System (ADS)

    Woo, Sun Young; Lee, Hwankyu

    2016-03-01

    Peptides E and K, which are synthetic coiled-coil peptides for membrane fusion, were simulated with lipid bilayers composed of lipids and cholesterols at different ratios using all-atom models. We first calculated free energies of binding from umbrella sampling simulations, showing that both E and K peptides tend to adsorb onto the bilayer surface, which occurs more strongly in the bilayer composed of smaller lipid headgroups. Then, unrestrained simulations show that K peptides more deeply insert into the bilayer with partially retaining the helical structure, while E peptides less insert and predominantly become random coils, indicating the structural transition from helices to random coils, in quantitative agreement with experiments. This is because K peptides electrostatically interact with lipid phosphates, as well as because hydrocarbons of lysines of K peptide are longer than those of glutamic acids of E peptide and thus form stronger hydrophobic interactions with lipid tails. This deeper insertion of K peptide increases the bilayer dynamics and a vacancy below the peptide, leading to the rearrangement of smaller lipids. These findings help explain the experimentally observed or proposed differences in the insertion depth, binding strength, and structural transition of E and K peptides, and support the snorkeling effect.

  5. Free energetics of carbon nanotube association in aqueous inorganic NaI salt solutions: Temperature effects using all-atom molecular dynamics simulations.

    PubMed

    Ou, Shu-Ching; Cui, Di; Wezowicz, Matthew; Taufer, Michela; Patel, Sandeep

    2015-06-15

    In this study, we examine the temperature dependence of free energetics of nanotube association using graphical processing unit-enabled all-atom molecular dynamics simulations (FEN ZI) with two (10,10) single-walled carbon nanotubes in 3 m NaI aqueous salt solution. Results suggest that the free energy, enthalpy and entropy changes for the association process are all reduced at the high temperature, in agreement with previous investigations using other hydrophobes. Via the decomposition of free energy into individual components, we found that solvent contribution (including water, anion, and cation contributions) is correlated with the spatial distribution of the corresponding species and is influenced distinctly by the temperature. We studied the spatial distribution and the structure of the solvent in different regions: intertube, intratube and the bulk solvent. By calculating the fluctuation of coarse-grained tube-solvent surfaces, we found that tube-water interfacial fluctuation exhibits the strongest temperature dependence. By taking ions to be a solvent-like medium in the absence of water, tube-anion interfacial fluctuation shows similar but weaker dependence on temperature, while tube-cation interfacial fluctuation shows no dependence in general. These characteristics are discussed via the malleability of their corresponding solvation shells relative to the nanotube surface. Hydrogen bonding profiles and tetrahedrality of water arrangement are also computed to compare the structure of solvent in the solvent bulk and intertube region. The hydrophobic confinement induces a relatively lower concentration environment in the intertube region, therefore causing different intertube solvent structures which depend on the tube separation. This study is relevant in the continuing discourse on hydrophobic interactions (as they impact generally a broad class of phenomena in biology, biochemistry, and materials science and soft condensed matter research), and

  6. Free Energetics of Carbon Nanotube Association in Aqueous Inorganic NaI Salt Solutions: Temperature Effects using All-Atom Molecular Dynamics Simulations

    PubMed Central

    Ou, Shu-Ching; Cui, Di; Wezowicz, Matthew; Taufer, Michela; Patel, Sandeep

    2015-01-01

    In this study we examine the temperature dependence of free energetics of nanotube association by using GPU-enabled all-atom molecular dynamics simulations (FEN ZI) with two (10,10) single-walled carbon nanotubes in 3 m NaI aqueous salt solution. Results suggest that the free energy, enthalpy and entropy changes for the association process are all reduced at the high temperature, in agreement with previous investigations using other hydrophobes. Via the decomposition of free energy into individual components, we found that solvent contribution (including water, anion and cation contributions) is correlated with the spatial distribution of the corresponding species and is influenced distinctly by the temperature. We studied the spatial distribution and the structure of the solvent in different regions: intertube, intra-tube and the bulk solvent. By calculating the fluctuation of coarse-grained tube-solvent surfaces, we found that tube-water interfacial fluctuation exhibits the strongest temperature dependence. By taking ions to be a solvent-like medium in the absence of water, tube-anion interfacial fluctuation also shows similar but weaker dependence on temperature, while tube-cation interfacial fluctuation shows no dependence in general. These characteristics are discussed via the malleability of their corresponding solvation shells relative to the nanotube surface. Hydrogen bonding profiles and tetrahedrality of water arrangement are also computed to compare the structure of solvent in the solvent bulk and intertube region. The hydrophobic confinement induces a relatively lower concentration environment in the intertube region, therefore causing different intertube solvent structures which depend on the tube separation. This study is relevant in the continuing discourse on hydrophobic interactions (as they impact generally a broad class of phenomena in biology, biochemistry, and materials science and soft condensed matter research), and interpretations of

  7. Balancing the interactions of ions, water, and DNA in the Drude polarizable force field.

    PubMed

    Savelyev, Alexey; MacKerell, Alexander D

    2014-06-19

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

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

    PubMed Central

    2015-01-01

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

  9. Surface Tension of Organic Liquids Using the OPLS/AA Force Field.

    PubMed

    Zubillaga, Rafael A; Labastida, Ariana; Cruz, Bibiana; Martínez, Juan Carlos; Sánchez, Enrique; Alejandre, José

    2013-03-12

    Molecular dynamics simulations are performed to obtain the surface tension of 61 organic liquids using the OPLS/AA (all-atom optimized potential for liquid simulations). The force field parameters are the same as those recently used (Caleman et al. J. Chem. Theory Comput.2012, 8, 61) to determine several thermodynamic properties of 146 organic liquids. The correct evaluation of surface tension using slab simulations of liquids requires one to properly take into account the long-range interactions (Trukhymchuk and Alejandre J. Chem. Phys.1999, 111, 8510). In addition, the liquid density from slab simulations has to be the same as that obtained in liquid simulations at constant temperature and pressure. The new results of surface tensions from this work improve those reported by Caleman et al. The OPLS/AA force field gives good surface tensions compared with experimental data for most of the systems studied in this work, although it was developed to simulate liquids. PMID:26587622

  10. Hydration force fluctuations in hydrophilic planar systems.

    PubMed

    Kanduč, Matej; Netz, Roland R

    2016-03-01

    Utilizing all-atom simulations with explicit solvent, the authors model hydrophilic surfaces interacting across water at a fixed chemical potential. They extract the hydration forces acting between the surfaces and assess force fluctuations as well as interlamellar water number fluctuations. The trends obtained from the simulations are captured by a continuum-based description with effective model parameters. The significance of fluctuations depends on surface hydrophilicity and rigidity. The authors show that the force fluctuations play an important role in kinetic processes in systems with lateral sizes smaller than several tens of nanometers. PMID:26746163

  11. NGSI student activities in open source information analysis in support of the training program of the U.S. DOE laboratories for the entry into force of the additional protocol

    SciTech Connect

    Sandoval, M Analisa; Uribe, Eva C; Sandoval, Marisa N; Boyer, Brian D; Stevens, Rebecca S

    2009-01-01

    In 2008 a joint team from Los Alamos National Laboratory (LANL) and Brookhaven National Laboratory (BNL) consisting of specialists in training of IAEA inspectors in the use of complementary access activities formulated a training program to prepare the U.S. Doe laboratories for the entry into force of the Additional Protocol. As a major part of the support of the activity, LANL summer interns provided open source information analysis to the LANL-BNL mock inspection team. They were a part of the Next Generation Safeguards Initiative's (NGSI) summer intern program aimed at producing the next generation of safeguards specialists. This paper describes how they used open source information to 'backstop' the LANL-BNL team's effort to construct meaningful Additional Protocol Complementary Access training scenarios for each of the three DOE laboratories, Lawrence Livermore National Laboratory, Idaho National Laboratory, and Oak Ridge National Laboratory.

  12. Crossflow force transducer. [LMFBR

    SciTech Connect

    Mulcahy, T M

    1982-05-01

    A force transducer for measuring lift and drag coefficients for a circular cylinder in turbulent water flow is presented. In addition to describing the actual design and construction of the strain-gauged force- ring based transducer, requirements for obtained valid fluid force test data are discussed, and pertinent flow test experience is related.

  13. 77 FR 15759 - Final Effect of Designation of a Class of Employees for Addition to the Special Exposure Cohort

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-16

    ... Ceramics Plant in Tonawanda, New York, as an addition to the Special Exposure Cohort (SEC) under the Energy... to the SEC: All Atomic Weapons Employees who worked in any area at the Linde Ceramics Plant...

  14. Food additives

    MedlinePlus

    Food additives are substances that become part of a food product when they are added during the processing or making of that food. "Direct" food additives are often added during processing to: Add nutrients ...

  15. Food additives

    PubMed Central

    Spencer, Michael

    1974-01-01

    Food additives are discussed from the food technology point of view. The reasons for their use are summarized: (1) to protect food from chemical and microbiological attack; (2) to even out seasonal supplies; (3) to improve their eating quality; (4) to improve their nutritional value. The various types of food additives are considered, e.g. colours, flavours, emulsifiers, bread and flour additives, preservatives, and nutritional additives. The paper concludes with consideration of those circumstances in which the use of additives is (a) justified and (b) unjustified. PMID:4467857

  16. Nanonet Force Microscopy for Measuring Cell Forces.

    PubMed

    Sheets, Kevin; Wang, Ji; Zhao, Wei; Kapania, Rakesh; Nain, Amrinder S

    2016-07-12

    The influence of physical forces exerted by or felt by cells on cell shape, migration, and cytoskeleton arrangement is now widely acknowledged and hypothesized to occur due to modulation of cellular inside-out forces in response to changes in the external fibrous environment (outside-in). Our previous work using the non-electrospinning Spinneret-based Tunable Engineered Parameters' suspended fibers has revealed that cells are able to sense and respond to changes in fiber curvature and structural stiffness as evidenced by alterations to focal adhesion cluster lengths. Here, we present the development and application of a suspended nanonet platform for measuring C2C12 mouse myoblast forces attached to fibers of three diameters (250, 400, and 800 nm) representing a wide range of structural stiffness (3-50 nN/μm). The nanonet force microscopy platform measures cell adhesion forces in response to symmetric and asymmetric external perturbation in single and cyclic modes. We find that contractility-based, inside-out forces are evenly distributed at the edges of the cell, and that forces are dependent on fiber structural stiffness. Additionally, external perturbation in symmetric and asymmetric modes biases cell-fiber failure location without affecting the outside-in forces of cell-fiber adhesion. We then extend the platform to measure forces of (1) cell-cell junctions, (2) single cells undergoing cyclic perturbation in the presence of drugs, and (3) cancerous single-cells transitioning from a blebbing to a pseudopodial morphology. PMID:27410747

  17. Relativistic Linear Restoring Force

    ERIC Educational Resources Information Center

    Clark, D.; Franklin, J.; Mann, N.

    2012-01-01

    We consider two different forms for a relativistic version of a linear restoring force. The pair comes from taking Hooke's law to be the force appearing on the right-hand side of the relativistic expressions: d"p"/d"t" or d"p"/d["tau"]. Either formulation recovers Hooke's law in the non-relativistic limit. In addition to these two forces, we…

  18. Nuclear forces

    SciTech Connect

    Machleidt, R.

    2013-06-10

    These lectures present an introduction into the theory of nuclear forces. We focus mainly on the modern approach, in which the forces between nucleons emerge from low-energy QCD via chiral effective field theory.

  19. Food additives.

    PubMed

    Berglund, F

    1978-01-01

    The use of additives to food fulfils many purposes, as shown by the index issued by the Codex Committee on Food Additives: Acids, bases and salts; Preservatives, Antioxidants and antioxidant synergists; Anticaking agents; Colours; Emulfifiers; Thickening agents; Flour-treatment agents; Extraction solvents; Carrier solvents; Flavours (synthetic); Flavour enhancers; Non-nutritive sweeteners; Processing aids; Enzyme preparations. Many additives occur naturally in foods, but this does not exclude toxicity at higher levels. Some food additives are nutrients, or even essential nutritents, e.g. NaCl. Examples are known of food additives causing toxicity in man even when used according to regulations, e.g. cobalt in beer. In other instances, poisoning has been due to carry-over, e.g. by nitrate in cheese whey - when used for artificial feed for infants. Poisonings also occur as the result of the permitted substance being added at too high levels, by accident or carelessness, e.g. nitrite in fish. Finally, there are examples of hypersensitivity to food additives, e.g. to tartrazine and other food colours. The toxicological evaluation, based on animal feeding studies, may be complicated by impurities, e.g. orthotoluene-sulfonamide in saccharin; by transformation or disappearance of the additive in food processing in storage, e.g. bisulfite in raisins; by reaction products with food constituents, e.g. formation of ethylurethane from diethyl pyrocarbonate; by metabolic transformation products, e.g. formation in the gut of cyclohexylamine from cyclamate. Metabolic end products may differ in experimental animals and in man: guanylic acid and inosinic acid are metabolized to allantoin in the rat but to uric acid in man. The magnitude of the safety margin in man of the Acceptable Daily Intake (ADI) is not identical to the "safety factor" used when calculating the ADI. The symptoms of Chinese Restaurant Syndrome, although not hazardous, furthermore illustrate that the whole ADI

  20. Labor Force

    ERIC Educational Resources Information Center

    Occupational Outlook Quarterly, 2012

    2012-01-01

    The labor force is the number of people ages 16 or older who are either working or looking for work. It does not include active-duty military personnel or the institutionalized population, such as prison inmates. Determining the size of the labor force is a way of determining how big the economy can get. The size of the labor force depends on two…

  1. A Generic Force Field for Protein Coarse-Grained Molecular Dynamics Simulation

    PubMed Central

    Gu, Junfeng; Bai, Fang; Li, Honglin; Wang, Xicheng

    2012-01-01

    Coarse-grained (CG) force fields have become promising tools for studies of protein behavior, but the balance of speed and accuracy is still a challenge in the research of protein coarse graining methodology. In this work, 20 CG beads have been designed based on the structures of amino acid residues, with which an amino acid can be represented by one or two beads, and a CG solvent model with five water molecules was adopted to ensure the consistence with the protein CG beads. The internal interactions in protein were classified according to the types of the interacting CG beads, and adequate potential functions were chosen and systematically parameterized to fit the energy distributions. The proposed CG force field has been tested on eight proteins, and each protein was simulated for 1000 ns. Even without any extra structure knowledge of the simulated proteins, the Cα root mean square deviations (RMSDs) with respect to their experimental structures are close to those of relatively short time all atom molecular dynamics simulations. However, our coarse grained force field will require further refinement to improve agreement with and persistence of native-like structures. In addition, the root mean square fluctuations (RMSFs) relative to the average structures derived from the simulations show that the conformational fluctuations of the proteins can be sampled. PMID:23203075

  2. Potlining Additives

    SciTech Connect

    Rudolf Keller

    2004-08-10

    In this project, a concept to improve the performance of aluminum production cells by introducing potlining additives was examined and tested. Boron oxide was added to cathode blocks, and titanium was dissolved in the metal pool; this resulted in the formation of titanium diboride and caused the molten aluminum to wet the carbonaceous cathode surface. Such wetting reportedly leads to operational improvements and extended cell life. In addition, boron oxide suppresses cyanide formation. This final report presents and discusses the results of this project. Substantial economic benefits for the practical implementation of the technology are projected, especially for modern cells with graphitized blocks. For example, with an energy savings of about 5% and an increase in pot life from 1500 to 2500 days, a cost savings of $ 0.023 per pound of aluminum produced is projected for a 200 kA pot.

  3. Phosphazene additives

    SciTech Connect

    Harrup, Mason K; Rollins, Harry W

    2013-11-26

    An additive comprising a phosphazene compound that has at least two reactive functional groups and at least one capping functional group bonded to phosphorus atoms of the phosphazene compound. One of the at least two reactive functional groups is configured to react with cellulose and the other of the at least two reactive functional groups is configured to react with a resin, such as an amine resin of a polycarboxylic acid resin. The at least one capping functional group is selected from the group consisting of a short chain ether group, an alkoxy group, or an aryloxy group. Also disclosed are an additive-resin admixture, a method of treating a wood product, and a wood product.

  4. Analytical catch-slip bond model for arbitrary forces and loading rates.

    PubMed

    Bullerjahn, J T; Kroy, K

    2016-01-01

    Some biological bonds exhibit a so-called catch regime, where the bond strengthens with increasing load. We build upon recent advances in slip-bond kinetics to develop an analytically tractable, microscopic catch-slip bond model. To facilitate the analysis of force-spectroscopy data, we calculate the bond's mean lifetime and the rupture-force distribution for static loading and linear force ramps. Our results are applicable for arbitrary forces and loading rates, covering the whole range of conditions found in experiments and all-atom simulations. A generalization to account for force transducers of finite stiffness is also provided. PMID:26871098

  5. Analytical catch-slip bond model for arbitrary forces and loading rates

    NASA Astrophysics Data System (ADS)

    Bullerjahn, J. T.; Kroy, K.

    2016-01-01

    Some biological bonds exhibit a so-called catch regime, where the bond strengthens with increasing load. We build upon recent advances in slip-bond kinetics to develop an analytically tractable, microscopic catch-slip bond model. To facilitate the analysis of force-spectroscopy data, we calculate the bond's mean lifetime and the rupture-force distribution for static loading and linear force ramps. Our results are applicable for arbitrary forces and loading rates, covering the whole range of conditions found in experiments and all-atom simulations. A generalization to account for force transducers of finite stiffness is also provided.

  6. Labor Force

    ERIC Educational Resources Information Center

    Occupational Outlook Quarterly, 2010

    2010-01-01

    The labor force is the number of people aged 16 or older who are either working or looking for work. It does not include active-duty military personnel or institutionalized people, such as prison inmates. Quantifying this total supply of labor is a way of determining how big the economy can get. Labor force participation rates vary significantly…

  7. One Force

    NASA Astrophysics Data System (ADS)

    Kotas, Ronald R.

    2002-04-01

    There is only one entity that can extend force and couple through space; and it should be apparent that Electromagnetism is that entity. In the cases of the nuclear strong force and the nuclear weak force, this is the same fundamental Electromagnetism manifesting itself in two different ways in the nucleus. It remains the same basic Electromagnetism. On the other hand, General Relativity fails to produce force at a distance, fails the Cavendish experiment, and does not allow an apple to fall to the ground. The result shows there is only Electromagnetism that functions through physical nature providing gravity, actions in the nucleus, as well as all other physical actions universally, including Gravity and Gravitation. There are many direct proofs of this, the same proofs as in NUCLEAR QUANTUM GRAVITATION. In contrast, General Relativity plainly relies on fallacy abstract and incoherent proofs; proofs which have now been mostly disproved. In the past it was deemed necessary by some to have an "ether" to propagate Electromagnetic waves. The fallacy concept of time space needs "space distortions" in order to cause gravity. However, Electromagnetic gravity does not have this problem. Clearly there is only ONE FORCE that causes Gravity, Electromagnetism, the Nuclear Strong Force, and the Nuclear Weak Force, and that ONE FORCE is Electromagnetism.

  8. Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field

    PubMed Central

    Maisuradze, Gia G.; Senet, Patrick; Czaplewski, Cezary; Liwo, Adam; Scheraga, Harold A.

    2010-01-01

    Coarse-grained molecular-dynamics simulations offer a dramatic extension of the time-scale of simulations compared to all-atom approaches. In this article, we describe the use of the physics-based united-residue (UNRES) force field, developed in our laboratory, in protein-structure simulations. We demonstrate that this force field offers about a 4000-times extension of the simulation time scale; this feature arises both from averaging out the fast-moving degrees of freedom and reduction of the cost of energy and force calculations compared to all-atom approaches with explicit solvent. With massively parallel computers, microsecond folding simulation times of proteins containing about 1000 residues can be obtained in days. A straightforward application of canonical UNRES/MD simulations, demonstrated with the example of the N-terminal part of the B-domain of staphylococcal protein A (PDB code: 1BDD, a three-α-helix bundle), discerns the folding mechanism and determines kinetic parameters by parallel simulations of several hundred or more trajectories. Use of generalized-ensemble techniques, of which the multiplexed replica exchange method proved to be the most effective, enables us to compute thermodynamics of folding and carry out fully physics-based prediction of protein structure, in which the predicted structure is determined as a mean over the most populated ensemble below the folding-transition temperature. By using principal component analysis of the UNRES folding trajectories of the formin-binding protein WW domain (PDB code: 1E0L; a three-stranded antiparallel β-sheet) and 1BDD, we identified representative structures along the folding pathways and demonstrated that only a few (low-indexed) principal components can capture the main structural features of a protein-folding trajectory; the potentials of mean force calculated along these essential modes exhibit multiple minima, as opposed to those along the remaining modes which are unimodal. In addition, a

  9. Force sensor

    DOEpatents

    Grahn, Allen R.

    1993-01-01

    A force sensor and related method for determining force components. The force sensor includes a deformable medium having a contact surface against which a force can be applied, a signal generator for generating signals that travel through the deformable medium to the contact surface, a signal receptor for receiving the signal reflected from the contact surface, a generation controller, a reception controller, and a force determination apparatus. The signal generator has one or more signal generation regions for generating the signals. The generation controller selects and activates the signal generation regions. The signal receptor has one or more signal reception regions for receiving signals and for generating detections signals in response thereto. The reception controller selects signal reception regions and detects the detection signals. The force determination apparatus measures signal transit time by timing activation and detection and, optionally, determines force components for selected cross-field intersections. The timer which times by activation and detection can be any means for measuring signal transit time. A cross-field intersection is defined by the overlap of a signal generation region and a signal reception region.

  10. Force sensor

    DOEpatents

    Grahn, A.R.

    1993-05-11

    A force sensor and related method for determining force components is described. The force sensor includes a deformable medium having a contact surface against which a force can be applied, a signal generator for generating signals that travel through the deformable medium to the contact surface, a signal receptor for receiving the signal reflected from the contact surface, a generation controller, a reception controller, and a force determination apparatus. The signal generator has one or more signal generation regions for generating the signals. The generation controller selects and activates the signal generation regions. The signal receptor has one or more signal reception regions for receiving signals and for generating detections signals in response thereto. The reception controller selects signal reception regions and detects the detection signals. The force determination apparatus measures signal transit time by timing activation and detection and, optionally, determines force components for selected cross-field intersections. The timer which times by activation and detection can be any means for measuring signal transit time. A cross-field intersection is defined by the overlap of a signal generation region and a signal reception region.

  11. Vacuum force

    NASA Astrophysics Data System (ADS)

    Han, Yongquan

    2015-03-01

    To study on vacuum force, we must clear what is vacuum, vacuum is a space do not have any air and also ray. There is not exist an absolute the vacuum of space. The vacuum of space is relative, so that the vacuum force is relative. There is a certain that vacuum vacuum space exists. In fact, the vacuum space is relative, if the two spaces compared to the existence of relative vacuum, there must exist a vacuum force, and the direction of the vacuum force point to the vacuum region. Any object rotates and radiates. Rotate bend radiate- centripetal, gravity produced, relative gravity; non gravity is the vacuum force. Gravity is centripetal, is a trend that the objects who attracted wants to Centripetal, or have been do Centripetal movement. Any object moves, so gravity makes the object curve movement, that is to say, the radiation range curve movement must be in the gravitational objects, gravity must be existed in non vacuum region, and make the object who is in the region of do curve movement (for example: The earth moves around the sun), or final attracted in the form gravitational objects, and keep relatively static with attract object. (for example: objects on the earth moves but can't reach the first cosmic speed).

  12. Causal reasoning with forces

    PubMed Central

    Wolff, Phillip; Barbey, Aron K.

    2015-01-01

    Causal composition allows people to generate new causal relations by combining existing causal knowledge. We introduce a new computational model of such reasoning, the force theory, which holds that people compose causal relations by simulating the processes that join forces in the world, and compare this theory with the mental model theory (Khemlani et al., 2014) and the causal model theory (Sloman et al., 2009), which explain causal composition on the basis of mental models and structural equations, respectively. In one experiment, the force theory was uniquely able to account for people's ability to compose causal relationships from complex animations of real-world events. In three additional experiments, the force theory did as well as or better than the other two theories in explaining the causal compositions people generated from linguistically presented causal relations. Implications for causal learning and the hierarchical structure of causal knowledge are discussed. PMID:25653611

  13. Nano Sized Powder Additives of SiC and Diamond to MgB2 as Artificially Inductor of Pinning Force for the Dense Samples Obtained by High Pressure Technologies

    NASA Astrophysics Data System (ADS)

    Morawski, A.; Pachla, W.; Kuzmenko, D.; Łada, T.; Zaleski, A.; Eibl, O.; Haessler, W.; Kovac, P.

    2006-09-01

    The nano-powder additives of SiC (11nm) and diamond (6 nm) were mixed with Mg and amorphous B powders in the production route of MgB2 bulk and wires samples. Special attention was paid to the precursor powders with the respect to chemical purity, grain morphology and secondary phases. Commercially available MgB2 powders (ex-situ technology) and also mixtures of MgH2 and amorphous B powders (in-situ technology) were applied as the starting precursors. Electron microscopy was used extensively for the characterization of these powders applying both SEM and TEM analysis. Superconducting bulks and wires samples have been produced, by hot pressing, hot isostatic pressing and hydrostatic extrusion processes. High grain refinement and density in the final wire samples have been achieved by the severe plastic deformation (reduction over 99.98%) with the use of the cumulative (multi-step) hydrostatic extrusion. Superconducting properties of these samples were measured, with particular attention paid to the Jc(B) characteristics. Critical currents at lower and higher magnetic fields depended sensitively on the amount of the additives and grain refinement. TEM imaging and electron spectroscopic imaging were used to evaluate the size and distribution of the both of additives within the microstructure. The strain field of the additives resulted from the misfit in thermal expansion coefficient between the additives and the MgB2 matrix was imaged in bright and dark field TEM and is particularly important for the flux-pinning properties of these materials. Influence of such synthesis parameters as pressure, temperature and time on the superconducting properties and the morphology of the products were examined and obtained results were compared. This allowed to choose the optimal conditions for the improvement of the bulk MgB2 characteristics of the wire samples.

  14. Electrostatic patch potentials in Casimir force measurements

    NASA Astrophysics Data System (ADS)

    Garrett, Joseph; Somers, David; Munday, Jeremy

    2015-03-01

    Measurements of the Casimir force require the elimination of the electrostatic force between interacting surfaces. The force can be minimized by applying a potential to one of the two surfaces. However, electrostatic patch potentials remain and contribute an additional force which can obscure the Casimir force signal. We will discuss recent measurements of patch potentials made with Heterodyne Amplitude-Modulated Kelvin Probe Force Microscopy that suggest patches could be responsible for >1% of the signal in some Casimir force measurements, and thus make the distinction between different theoretical models of the Casimir force (e.g. a Drude-model or a plasma-model for the dielectric response) difficult to discern.

  15. Extension of the LOPLS-AA Force Field for Alcohols, Esters, and Monoolein Bilayers and its Validation by Neutron Scattering Experiments.

    PubMed

    Pluhackova, Kristyna; Morhenn, Humphrey; Lautner, Lisa; Lohstroh, Wiebke; Nemkovski, Kirill S; Unruh, Tobias; Böckmann, Rainer A

    2015-12-10

    The recently presented LOPLS-AA all-atom force field for long hydrocarbon chains, based on the OPLS-AA force field, was extended to alcohols, esters, and glyceryl monooleate (GMO) lipids as a model lipid. Dihedral angles were fitted against high level ab initio calculations, and ester charges were increased to improve their hydration properties. Additionally, the ester Lennard-Jones parameters were readjusted to reproduce experimental liquid bulk properties, densities, and heats of vaporization. This extension enabled the setup of LOPLS-AA parameters for GMO molecules. The properties of the lipid force field were tested for the liquid-crystalline phase of a GMO bilayer. The obtained area per lipid for GMO is in good agreement with experiment. Additionally, the lipid dynamics on the subpicosecond to the nanosecond time scale is in excellent agreement with results from time-of-flight (TOF) quasielastic neutron scattering (QENS) experiments on a multilamellar monoolein system, enabling here for the first time the critical evaluation of the short-time dynamics obtained from a molecular dynamics simulation of a membrane system. PMID:26537654

  16. Carbohydrate force fields

    PubMed Central

    Foley, B. Lachele; Tessier, Matthew B.; Woods, Robert J.

    2014-01-01

    Carbohydrates present a special set of challenges to the generation of force fields. First, the tertiary structures of monosaccharides are complex merely by virtue of their exceptionally high number of chiral centers. In addition, their electronic characteristics lead to molecular geometries and electrostatic landscapes that can be challenging to predict and model. The monosaccharide units can also interconnect in many ways, resulting in a large number of possible oligosaccharides and polysaccharides, both linear and branched. These larger structures contain a number of rotatable bonds, meaning they potentially sample an enormous conformational space. This article briefly reviews the history of carbohydrate force fields, examining and comparing their challenges, forms, philosophies, and development strategies. Then it presents a survey of recent uses of these force fields, noting trends, strengths, deficiencies, and possible directions for future expansion. PMID:25530813

  17. Surgical force detection probe

    NASA Technical Reports Server (NTRS)

    Tcheng, Ping; Roberts, Paul; Scott, Charles; Prass, Richard

    1991-01-01

    The development progress of a precision electro-mechanical instrument which allows the detection and documentation of the forces and moment applied to human tissue during surgery (under actual operation room conditions), is reported. The pen-shaped prototype probe which measures 1/2 inch in diameter and 7 inches in length was fabricated using an aerodynamic balance. The aerodynamic balance, a standard wind tunnel force and moment sensing transducer, measures the forces and the moments transmitted through the surgeon's hand to the human tissue during surgery. The prototype probe which was fabricated as a development tool was tested successfully. The final version of the surgical force detection probe will be designed based on additional laboratory tests in order to establish the full scale loads. It is expected that the final product will require a simplified aerodynamic balance with two or three force components and one moment component with lighter full scale loads. A signal conditioner was fabricated to process and display the outputs from the prototype probe. This unit will be interfaced with a PC-based data system to provide automatic data acquisition, data processing, and graphics display. The expected overall accuracy of the probe is better than one percent full scale.

  18. Radiative Forcing by Contrails

    NASA Technical Reports Server (NTRS)

    Meerkoetter, R.; Schumann, U.; Doelling, D. R.; Nakajima, T.; Tsushima, Y.

    1999-01-01

    A parametric study of the instantaneous radiative impact of contrails is presented using three different radiative transfer models for a series of model atmospheres and cloud parameters. Contrails are treated as geometrically and optically thin plane parallel homogeneous cirrus layers in a static atmospheres The ice water content is varied as a function of ambient temperature. The model atmospheres include tropical, mid-latitude, and subarctic summer and winter atmospheres Optically thin contrails cause a positive net forcing at top of the atmosphere. At the surface the radiative forcing is negative during daytime. The forcing increases with the optical depth and the amount of contrail cover. At the top of the atmosphere a mean contrail cover of 0.1% with average optical depth of 0.2 to 0.5 causes about 0.01 to 0.03 W/m(exp 2)a daily mean instantaneous radiative forcing. Contrails cool the surface during the day and heat the surface during the night, and hence reduce the daily temperature amplitude The net effect depends strongly on the daily variation of contrail cloud cover. The indirect radiative forcing due to particle changes in natural cirrus clouds may be of the same magnitude as the direct one due to additional cover.

  19. Current Status of Protein Force Fields for Molecular Dynamics

    PubMed Central

    Lopes, Pedro E.M.; Guvench, Olgun

    2015-01-01

    Summary The current status of classical force fields for proteins is reviewed. These include additive force fields as well as the latest developments in the Drude and AMOEBA polarizable force fields. Parametrization strategies developed specifically for the Drude force field are described and compared with the additive CHARMM36 force field. Results from molecular simulations of proteins and small peptides are summarized to illustrate the performance of the Drude and AMOEBA force fields. PMID:25330958

  20. Multistage Force Amplification of Piezoelectric Stacks

    NASA Technical Reports Server (NTRS)

    Xu, Tian-Bing (Inventor); Siochi, Emilie J. (Inventor); Zuo, Lei (Inventor); Jiang, Xiaoning (Inventor); Kang, Jin Ho (Inventor)

    2015-01-01

    Embodiments of the disclosure include an apparatus and methods for using a piezoelectric device, that includes an outer flextensional casing, a first cell and a last cell serially coupled to each other and coupled to the outer flextensional casing such that each cell having a flextensional cell structure and each cell receives an input force and provides an output force that is amplified based on the input force. The apparatus further includes a piezoelectric stack coupled to each cell such that the piezoelectric stack of each cell provides piezoelectric energy based on the output force for each cell. Further, the last cell receives an input force that is the output force from the first cell and the last cell provides an output apparatus force In addition, the piezoelectric energy harvested is based on the output apparatus force. Moreover, the apparatus provides displacement based on the output apparatus force.

  1. Communication: Multiple atomistic force fields in a single enhanced sampling simulation

    NASA Astrophysics Data System (ADS)

    Hoang Viet, Man; Derreumaux, Philippe; Nguyen, Phuong H.

    2015-07-01

    The main concerns of biomolecular dynamics simulations are the convergence of the conformational sampling and the dependence of the results on the force fields. While the first issue can be addressed by employing enhanced sampling techniques such as simulated tempering or replica exchange molecular dynamics, repeating these simulations with different force fields is very time consuming. Here, we propose an automatic method that includes different force fields into a single advanced sampling simulation. Conformational sampling using three all-atom force fields is enhanced by simulated tempering and by formulating the weight parameters of the simulated tempering method in terms of the energy fluctuations, the system is able to perform random walk in both temperature and force field spaces. The method is first demonstrated on a 1D system and then validated by the folding of the 10-residue chignolin peptide in explicit water.

  2. Communication: Multiple atomistic force fields in a single enhanced sampling simulation

    SciTech Connect

    Hoang Viet, Man; Derreumaux, Philippe; Nguyen, Phuong H.

    2015-07-14

    The main concerns of biomolecular dynamics simulations are the convergence of the conformational sampling and the dependence of the results on the force fields. While the first issue can be addressed by employing enhanced sampling techniques such as simulated tempering or replica exchange molecular dynamics, repeating these simulations with different force fields is very time consuming. Here, we propose an automatic method that includes different force fields into a single advanced sampling simulation. Conformational sampling using three all-atom force fields is enhanced by simulated tempering and by formulating the weight parameters of the simulated tempering method in terms of the energy fluctuations, the system is able to perform random walk in both temperature and force field spaces. The method is first demonstrated on a 1D system and then validated by the folding of the 10-residue chignolin peptide in explicit water.

  3. Radial force in a bearingless reluctance motor

    NASA Astrophysics Data System (ADS)

    Chiba, Akira; Rahman, M. A.; Fukao, Tadashi

    1991-03-01

    A four-pole reluctance synchronous machine with additional two-pole windings was constructed. The additional winding currents produce the radial force to act as a magnetic bearing. Expressions for the machine inductance functions are given. Inductance functions with respect to the eccentric displacement of the rotor were measured. The contribution of these inductances to the radial force production is established.

  4. The swim force as a body force

    NASA Astrophysics Data System (ADS)

    Yan, Wen; Brady, John

    2015-11-01

    Net (as opposed to random) motion of active matter results from an average swim (or propulsive) force. It is shown that the average swim force acts like a body force - an internal body force [Yan and Brady, Soft Matter, DOI:10.1039/C5SM01318F]. As a result, the particle-pressure exerted on a container wall is the sum of the swim pressure [Takatori et al., Phys. Rev. Lett., 2014, 113, 028103] and the `weight' of the active particles. A continuum mechanical description is possible when variations occur on scales larger than the run length of the active particles and gives a Boltzmann-like distribution from a balance of the swim force and the swim pressure. Active particles may also display `action at a distance' and accumulate adjacent to (or be depleted from) a boundary without any external forces. In the momentum balance for the suspension - the mixture of active particles plus fluid - only external body forces appear.

  5. 24 CFR 1710.216 - Additional information.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 24 Housing and Urban Development 5 2014-04-01 2014-04-01 false Additional information. 1710.216... § 1710.216 Additional information. (a) Property Owners' Association. (1) If the association has been..., information on such matters as to: (i) Whether the developer will employ his own sales force or will...

  6. 12 CFR 1010.216 - Additional information.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 12 Banks and Banking 8 2012-01-01 2012-01-01 false Additional information. 1010.216 Section 1010...) Reporting Requirements § 1010.216 Additional information. (a) Property Owners' Association. (1) If the..., information on such matters as to: (i) Whether the developer will employ his own sales force or will...

  7. 12 CFR 1010.216 - Additional information.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 12 Banks and Banking 8 2014-01-01 2014-01-01 false Additional information. 1010.216 Section 1010...) Reporting Requirements § 1010.216 Additional information. (a) Property Owners' Association. (1) If the..., information on such matters as to: (i) Whether the developer will employ his own sales force or will...

  8. Stochastically forced zonal flows

    NASA Astrophysics Data System (ADS)

    Srinivasan, Kaushik

    This thesis investigates the dynamics of multiple zonal jets, that spontaneously emerge on the barotropic beta-plane, driven by a homogenous and rapidly decorrelating forcing and damped by bottom drag. Decomposing the barotropic vorticity equation into the zonal-mean and eddy equations, and neglecting the eddy-eddy interactions, defines the quasi-linear (QL) system. Numerical solution of the QL system shows zonal jets with length scales comparable to jets obtained by solving the nonlinear (NL) system. Starting with the QL system, one can construct a deterministic equation for the evolution of the two-point single-time correlation function of the vorticity, from which one can obtain the Reynolds stress that drives the zonal mean flow. This deterministic system has an exact nonlinear solution, which is a homogenous eddy field with no jets. When the forcing is also isotropic in space, we characterize the linear stability of this jetless solution by calculating the critical stability curve in the parameter space and successfully comparing this analytic result with numerical solutions of the QL system. But the critical drag required for the onset of NL zonostrophic instability is up to a factor of six smaller than that for QL zonostrophic instability. The constraint of isotropic forcing is then relaxed and spatially anisotropic forcing is used to drive the jets. Meridionally drifting jets are observed whenever the forcing breaks an additional symmetry that we refer to as mirror, or reflexional symmetry. The magnitude of drift speed in our results shows a strong variation with both mu and beta: while the drift speed decreases almost linearly with decreasing mu, it actually increases as beta decreases. Similar drifting jets are also observed in QL, with the same direction (i.e. northward or southward) and similar magnitude as NL jet-drift. Starting from the laminar solution, and assuming a mean-flow that varies slowly with reference to the scale of the eddies, we obtain

  9. Theoretical Models for Surface Forces and Adhesion and Their Measurement Using Atomic Force Microscopy

    PubMed Central

    Leite, Fabio L.; Bueno, Carolina C.; Da Róz, Alessandra L.; Ziemath, Ervino C.; Oliveira, Osvaldo N.

    2012-01-01

    The increasing importance of studies on soft matter and their impact on new technologies, including those associated with nanotechnology, has brought intermolecular and surface forces to the forefront of physics and materials science, for these are the prevailing forces in micro and nanosystems. With experimental methods such as the atomic force spectroscopy (AFS), it is now possible to measure these forces accurately, in addition to providing information on local material properties such as elasticity, hardness and adhesion. This review provides the theoretical and experimental background of AFS, adhesion forces, intermolecular interactions and surface forces in air, vacuum and in solution. PMID:23202925

  10. Force field dependent solution properties of glycine oligomers

    PubMed Central

    Drake, Justin A.

    2015-01-01

    Molecular simulations can be used to study disordered polypeptide systems and to generate hypotheses on the underlying structural and thermodynamic mechanisms that govern their function. As the number of disordered protein systems investigated with simulations increase, it is important to understand how particular force fields affect the structural properties of disordered polypeptides in solution. To this end, we performed a comparative structural analysis of Gly3 and Gly10 in aqueous solution from all-atom, microsecond MD simulations using the CHARMM 27 (C27), CHARMM 36 (C36), and Amber ff12SB force fields. For each force field, Gly3 and Gly10 were simulated for at least 300 ns and 1 μs, respectively. Simulating oligoglycines of two different lengths allows us to evaluate how force field effects depend on polypeptide length. Using a variety of structural metrics (e.g. end-to-end distance, radius of gyration, dihedral angle distributions), we characterize the distribution of oligoglycine conformers for each force field and show that each sample conformation space differently, yielding considerably different structural tendencies of the same oligoglycine model in solution. Notably, we find that C36 samples more extended oligoglycine structures than both C27 and ff12SB. PMID:25952623

  11. Force field-dependent solution properties of glycine oligomers.

    PubMed

    Drake, Justin A; Pettitt, B Montgomery

    2015-06-30

    Molecular simulations can be used to study disordered polypeptide systems and to generate hypotheses on the underlying structural and thermodynamic mechanisms that govern their function. As the number of disordered protein systems investigated with simulations increase, it is important to understand how particular force fields affect the structural properties of disordered polypeptides in solution. To this end, we performed a comparative structural analysis of Gly(3) and Gly(10) in aqueous solution from all atom, microsecond molecular dynamics (MD) simulations using the CHARMM 27 (C27), CHARMM 36 (C36), and Amber ff12SB force fields. For each force field, Gly(3) and Gly(10) were simulated for at least 300 ns and 1 μs, respectively. Simulating oligoglycines of two different lengths allows us to evaluate how force field effects depend on polypeptide length. Using a variety of structural metrics (e.g., end-to-end distance, radius of gyration, dihedral angle distributions), we characterize the distribution of oligoglycine conformers for each force field and show that each sample conformation space differently, yielding considerably different structural tendencies of the same oligoglycine model in solution. Notably, we find that C36 samples more extended oligoglycine structures than both C27 and ff12SB. PMID:25952623

  12. Benchmarking of Force Fields for Molecule-Membrane Interactions.

    PubMed

    Paloncýová, Markéta; Fabre, Gabin; DeVane, Russell H; Trouillas, Patrick; Berka, Karel; Otyepka, Michal

    2014-09-01

    Studies of drug-membrane interactions witness an ever-growing interest, as penetration, accumulation, and positioning of drugs play a crucial role in drug delivery and metabolism in human body. Molecular dynamics simulations complement nicely experimental measurements and provide us with new insight into drug-membrane interactions; however, the quality of the theoretical data dramatically depends on the quality of the force field used. We calculated the free energy profiles of 11 molecules through a model dimyristoylphosphatidylcholine (DMPC) membrane bilayer using five force fields, namely Berger, Slipids, CHARMM36, GAFFlipids, and GROMOS 43A1-S3. For the sake of comparison, we also employed the semicontinuous tool COSMOmic. High correlation was observed between theoretical and experimental partition coefficients (log K). Partition coefficients calculated by all-atomic force fields (Slipids, CHARMM36, and GAFFlipids) and COSMOmic differed by less than 0.75 log units from the experiment and Slipids emerged as the best performing force field. This work provides the following recommendations (i) for a global, systematic and high throughput thermodynamic evaluations (e.g., log K) of drugs COSMOmic is a tool of choice due to low computational costs; (ii) for studies of the hydrophilic molecules CHARMM36 should be considered; and (iii) for studies of more complex systems, taking into account all pros and cons, Slipids is the force field of choice. PMID:26588554

  13. Force Augmentation for Relief Valve

    NASA Technical Reports Server (NTRS)

    Luger, J.

    1982-01-01

    Simple design change for poppet relief valve enables flow through valve to exert additional force to help keep valve open. Although originally intended for relief valves for liquid oxygen and liquid nitrogen in Space Shuttle orbiter, concept is applicable to pressure-or flow-actuated valves for wide range of fluids and temperatures.

  14. Calibration of frictional forces in atomic force microscopy

    SciTech Connect

    Ogletree, D.F.; Carpick, R.W.; Salmeron, M.

    1996-09-01

    The atomic force microscope can provide information on the atomic-level frictional properties of surfaces, but reproducible quantitative measurements are difficult to obtain. Parameters that are either unknown or difficult to precisely measure include the normal and lateral cantilever force constants (particularly with microfabricated cantilevers), the tip height, the deflection sensor response, and the tip structure and composition at the tip-surface contact. We present an {ital in} {ital situ} experimental procedure to determine the response of a cantilever to lateral forces in terms of its normal force response. This procedure is quite general. It will work with any type of deflection sensor and does not require the knowledge or direct measurement of the lever dimensions or the tip height. In addition, the shape of the tip apex can be determined. We also discuss a number of specific issues related to force and friction measurements using optical lever deflection sensing. We present experimental results on the lateral force response of commercially available V-shaped cantilevers. Our results are consistent with estimates of lever mechanical properties using continuum elasticity theory. {copyright} {ital 1996 American Institute of Physics.}

  15. Molecular dynamics simulations data of the twenty encoded amino acids in different force fields.

    PubMed

    Vitalini, F; Noé, F; Keller, B G

    2016-06-01

    We present extensive all-atom Molecular Dynamics (MD) simulation data of the twenty encoded amino acids in explicit water, simulated with different force fields. The termini of the amino acids have been capped to ensure that the dynamics of the Φ and ψ torsion angles are analogues to the dynamics within a peptide chain. We use representatives of each of the four major force field families: AMBER ff-99SBILDN [1], AMBER ff-03 [2], OPLS-AA/L [3], CHARMM27 [4] and GROMOS43a1 [5], [6]. Our data represents a library and test bed for method development for MD simulations and for force fields development. Part of the data set has been previously used for comparison of the dynamic properties of force fields (Vitalini et al., 2015) [7] and for the construction of peptide basis functions for the variational approach to molecular kinetics [8]. PMID:27054161

  16. Molecular dynamics simulations data of the twenty encoded amino acids in different force fields

    PubMed Central

    Vitalini, F.; Noé, F.; Keller, B.G.

    2016-01-01

    We present extensive all-atom Molecular Dynamics (MD) simulation data of the twenty encoded amino acids in explicit water, simulated with different force fields. The termini of the amino acids have been capped to ensure that the dynamics of the Φ and ψ torsion angles are analogues to the dynamics within a peptide chain. We use representatives of each of the four major force field families: AMBER ff-99SBILDN [1], AMBER ff-03 [2], OPLS-AA/L [3], CHARMM27 [4] and GROMOS43a1 [5], [6]. Our data represents a library and test bed for method development for MD simulations and for force fields development. Part of the data set has been previously used for comparison of the dynamic properties of force fields (Vitalini et al., 2015) [7] and for the construction of peptide basis functions for the variational approach to molecular kinetics [8]. PMID:27054161

  17. Grip force control during virtual object interaction: effect of force feedback,accuracy demands, and training.

    PubMed

    Gibo, Tricia L; Bastian, Amy J; Okamura, Allison M

    2014-03-01

    When grasping and manipulating objects, people are able to efficiently modulate their grip force according to the experienced load force. Effective grip force control involves providing enough grip force to prevent the object from slipping, while avoiding excessive force to avoid damage and fatigue. During indirect object manipulation via teleoperation systems or in virtual environments, users often receive limited somatosensory feedback about objects with which they interact. This study examines the effects of force feedback, accuracy demands, and training on grip force control during object interaction in a virtual environment. The task required subjects to grasp and move a virtual object while tracking a target. When force feedback was not provided, subjects failed to couple grip and load force, a capability fundamental to direct object interaction. Subjects also exerted larger grip force without force feedback and when accuracy demands of the tracking task were high. In addition, the presence or absence of force feedback during training affected subsequent performance, even when the feedback condition was switched. Subjects' grip force control remained reminiscent of their employed grip during the initial training. These results motivate the use of force feedback during telemanipulation and highlight the effect of force feedback during training. PMID:24845744

  18. Training program to prepare the U.S. DOE laboratories for the entry into force of the protocol additional to the agreement between the United States of America and the International Atomic Energy Agency for the application of safeguards in the United

    SciTech Connect

    Boyer, Brian David; Stevens, Rebecca C; Uribe, Eva C; Sandoval, M Analisa; Valente, John N; Valente, John U; Jo, Jae H; Sellen, Joana

    2009-01-01

    In 2008, a joint team from Brookhaven National Laboratory (BNL) and Los Alamos National Laboratory (LANL) consisting of specialists in training IAEA inspectors in the use of complementary access activities formulated a training program to prepare the U.S DOE laboratories for the entry into force of the U.S. Additional Protocol. Since the U.S. Additional Protocol would allow for IAEA access to the DOE laboratories under the aegis of complementary access activities, the DOE laboratories would need to prepare for such visits. The goal of the training was to ensure that the DOE laboratories would successfully host an IAEA complementary access. In doing so, the labs must be able to provide the IAEA with the information that the IAEA would need to resolve its questions about the U.S. Declaration and declared activities at the lab, and also protect certain equities, as provided under the U.S. Additional Protocol Article 1.b and c. which set forth a 'National Security Exclusion.' This 'NSE' states that the AP provisions apply within the United States 'excluding only instances where its application would result in access by the Agency to activities with direct national security significance to the United States or to location or information associated with such activities.' These activities are referred to collectively as DNSS-direct national security significance. Furthermore, the U.S. has a specific right to employ managed access, without prejudice to the right under Article 1.b, in connection with activities of DNSS. The provisions in Articles 1.b and 1.c are unique to the U.S. AP, and are additional to the more general right, under Article 7, to use managed access to protect from disclosure proprietary and/or proliferation-sensitive information, and to meet safety and security requirements, that is incorporated directly from the Model Additional Protocol. The BNL-LANL team performed training at Lawrence Livermore National Laboratory, Idaho National Laboratory, and Oak

  19. Elastodynamic image forces on dislocations

    PubMed Central

    Gurrutxaga-Lerma, Beñat; Balint, Daniel S.; Dini, Daniele; Sutton, Adrian P.

    2015-01-01

    The elastodynamic image forces on edge and screw dislocations in the presence of a planar-free surface are derived. The explicit form of the elastodynamic fields of an injected, quiescent screw dislocation are also derived. The resulting image forces are affected by retardation effects: the dislocations experience no image force for a period of time defined by the arrival and reflection at the free surface of the dislocation fields. For the case of injected, stationary dislocations, it is shown that the elastodynamic image force tends asymptotically to the elastotatic prediction. For the case of injected, moving dislocations, it is shown that the elastodynamic image force on both the edge and the screw dislocations is magnified by inertial effects, and becomes increasingly divergent with time; this additional effect, missing in the elastostatic description, is shown to be substantial even for slow moving dislocations. Finally, it is shown that the elastodynamic image force of an edge dislocation moving towards the surface at the Rayleigh wave speed becomes repulsive, rather than attractive; this is suggestive of instabilities at the core of the dislocation, and likely resonances with the free surface. PMID:26528080

  20. Unification of Fundamental Forces

    NASA Astrophysics Data System (ADS)

    Salam, Abdus

    1990-05-01

    This is an expanded version of the third Dirac Memorial Lecture, given in 1988 by the Nobel Laureate Abdus Salam. Salam's lecture presents an overview of the developments in modern particle physics from its inception at the turn of the century to the present theories seeking to unify all the fundamental forces. In addition, two previously unpublished lectures by Paul Dirac, and Werner Heisenberg are included. These lectures provide a fascinating insight into their approach to research and the developments in particle physics at that time. Nonspecialists, undergraduates and researchers will find this a fascinating book. It contains a clear introduction to the major themes of particle physics and cosmology by one of the most distinguished contemporary physicists.

  1. Finger Forces in Clarinet Playing

    PubMed Central

    Hofmann, Alex; Goebl, Werner

    2016-01-01

    Clarinettists close and open multiple tone holes to alter the pitch of the tones. Their fingering technique must be fast, precise, and coordinated with the tongue articulation. In this empirical study, finger force profiles and tongue techniques of clarinet students (N = 17) and professional clarinettists (N = 6) were investigated under controlled performance conditions. First, in an expressive-performance task, eight selected excerpts from the first Weber Concerto were performed. These excerpts were chosen to fit in a 2 × 2 × 2 design (register: low–high; tempo: slow–fast, dynamics: soft–loud). There was an additional condition controlled by the experimenter, which determined the expression levels (low–high) of the performers. Second, a technical-exercise task, an isochronous 23-tone melody was designed that required different effectors to produce the sequence (finger-only, tongue-only, combined tongue-finger actions). The melody was performed in three tempo conditions (slow, medium, fast) in a synchronization-continuation paradigm. Participants played on a sensor-equipped Viennese clarinet, which tracked finger forces and reed oscillations simultaneously. From the data, average finger force (Fmean) and peak force (Fmax) were calculated. The overall finger forces were low (Fmean = 1.17 N, Fmax = 3.05 N) compared to those on other musical instruments (e.g., guitar). Participants applied the largest finger forces during the high expression level performance conditions (Fmean = 1.21 N). For the technical exercise task, timing and articulation information were extracted from the reed signal. Here, the timing precision of the fingers deteriorated the timing precision of the tongue for combined tongue-finger actions, especially for faster tempi. Although individual finger force profiles were overlapping, the group of professional players applied less finger force overall (Fmean = 0.54 N). Such sensor instruments provide useful insights into player

  2. Automatic molecular structure perception for the universal force field.

    PubMed

    Artemova, Svetlana; Jaillet, Léonard; Redon, Stephane

    2016-05-15

    The Universal Force Field (UFF) is a classical force field applicable to almost all atom types of the periodic table. Such a flexibility makes this force field a potential good candidate for simulations involving a large spectrum of systems and, indeed, UFF has been applied to various families of molecules. Unfortunately, initializing UFF, that is, performing molecular structure perception to determine which parameters should be used to compute the UFF energy and forces, appears to be a difficult problem. Although many perception methods exist, they mostly focus on organic molecules, and are thus not well-adapted to the diversity of systems potentially considered with UFF. In this article, we propose an automatic perception method for initializing UFF that includes the identification of the system's connectivity, the assignment of bond orders as well as UFF atom types. This perception scheme is proposed as a self-contained UFF implementation integrated in a new module for the SAMSON software platform for computational nanoscience (http://www.samson-connect.net). We validate both the automatic perception method and the UFF implementation on a series of benchmarks. PMID:26927616

  3. Force propagation and force generation in cells.

    PubMed

    Jonas, Oliver; Duschl, Claus

    2010-09-01

    Determining how forces are produced by and propagated through the cytoskeleton (CSK) of the cell is of great interest as dynamic processes of the CSK are intimately correlated with many molecular signaling pathways. We are presenting a novel approach for integrating measurements on cell elasticity, transcellular force propagation, and cellular force generation to obtain a comprehensive description of dynamic and mechanical properties of the CSK under force loading. This approach uses a combination of scanning force microscopy (SFM) and Total Internal Reflection Fluorescence (TIRF) microscopy. We apply well-defined loading schemes onto the apical cell membrane of fibroblasts using the SFM and simultaneously use TIRF microscopy to image the topography of the basal cell membrane. The locally distinct changes of shape and depth of the cytoskeletal imprints onto the basal membrane are interpreted as results of force propagation through the cytoplasm. This observation provides evidence for the tensegrity model and demonstrates the usefulness of our approach that does not depend on potentially disturbing marker compounds. We confirm that the actin network greatly determines cell stiffness and represents the substrate that mediates force transduction through the cytoplasm of the cell. The latter is an essential feature of tensegrity. Most importantly, our new finding that, both intact actin and microtubule networks are required for enabling the cell to produce work, can only be understood within the framework of the tensegrity model. We also provide, for the first time, a direct measurement of the cell's mechanical power output under compression at two femtowatts. PMID:20607861

  4. [Food additives and healthiness].

    PubMed

    Heinonen, Marina

    2014-01-01

    Additives are used for improving food structure or preventing its spoilage, for example. Many substances used as additives are also naturally present in food. The safety of additives is evaluated according to commonly agreed principles. If high concentrations of an additive cause adverse health effects for humans, a limit of acceptable daily intake (ADI) is set for it. An additive is a risk only when ADI is exceeded. The healthiness of food is measured on the basis of nutrient density and scientifically proven effects. PMID:24772784

  5. Polyimide processing additives

    NASA Technical Reports Server (NTRS)

    Pratt, J. R.; St. Clair, T. L.; Burks, H. D.; Stoakley, D. M.

    1987-01-01

    A method has been found for enhancing the melt flow of thermoplastic polyimides during processing. A high molecular weight 422 copoly(amic acid) or copolyimide was fused with approximately 0.05 to 5 pct by weight of a low molecular weight amic acid or imide additive, and this melt was studied by capillary rheometry. Excellent flow and improved composite properties on graphite resulted from the addition of a PMDA-aniline additive to LARC-TPI. Solution viscosity studies imply that amic acid additives temporarily lower molecular weight and, hence, enlarge the processing window. Thus, compositions containing the additive have a lower melt viscosity for a longer time than those unmodified.

  6. The effect of patch potentials in Casimir force measurements determined by heterodyne Kelvin probe force microscopy

    NASA Astrophysics Data System (ADS)

    Garrett, Joseph L.; Somers, David; Munday, Jeremy N.

    2015-06-01

    Measurements of the Casimir force require the elimination of the electrostatic force between the surfaces. However, due to electrostatic patch potentials, the voltage required to minimize the total force may not be sufficient to completely nullify the electrostatic interaction. Thus, these surface potential variations cause an additional force, which can obscure the Casimir force signal. In this paper, we inspect the spatially varying surface potential of e-beamed, sputtered, sputtered and annealed, and template stripped gold surfaces with Heterodyne amplitude modulated Kelvin probe force microscopy (HAM-KPFM). It is demonstrated that HAM-KPFM improves the spatial resolution of surface potential measurements compared to amplitude modulated Kelvin probe force microscopy. We find that patch potentials vary depending on sample preparation, and that the calculated pressure can be similar to the pressure difference between Casimir force calculations employing the plasma and Drude models.

  7. The effect of patch potentials in Casimir force measurements determined by heterodyne Kelvin probe force microscopy.

    PubMed

    Garrett, Joseph L; Somers, David; Munday, Jeremy N

    2015-06-01

    Measurements of the Casimir force require the elimination of the electrostatic force between the surfaces. However, due to electrostatic patch potentials, the voltage required to minimize the total force may not be sufficient to completely nullify the electrostatic interaction. Thus, these surface potential variations cause an additional force, which can obscure the Casimir force signal. In this paper, we inspect the spatially varying surface potential of e-beamed, sputtered, sputtered and annealed, and template stripped gold surfaces with Heterodyne amplitude modulated Kelvin probe force microscopy (HAM-KPFM). It is demonstrated that HAM-KPFM improves the spatial resolution of surface potential measurements compared to amplitude modulated Kelvin probe force microscopy. We find that patch potentials vary depending on sample preparation, and that the calculated pressure can be similar to the pressure difference between Casimir force calculations employing the plasma and Drude models. PMID:25964997

  8. Aerodynamic Lifting Force.

    ERIC Educational Resources Information Center

    Weltner, Klaus

    1990-01-01

    Describes some experiments showing both qualitatively and quantitatively that aerodynamic lift is a reaction force. Demonstrates reaction forces caused by the acceleration of an airstream and the deflection of an airstream. Provides pictures of demonstration apparatus and mathematical expressions. (YP)

  9. A force field for tricalcium aluminate to characterize surface properties, initial hydration, and organically modified interfaces in atomic resolution.

    PubMed

    Mishra, Ratan K; Fernández-Carrasco, Lucia; Flatt, Robert J; Heinz, Hendrik

    2014-07-21

    Tricalcium aluminate (C3A) is a major phase of Portland cement clinker and some dental root filling cements. An accurate all-atom force field is introduced to examine structural, surface, and hydration properties as well as organic interfaces to overcome challenges using current laboratory instrumentation. Molecular dynamics simulation demonstrates excellent agreement of computed structural, thermal, mechanical, and surface properties with available experimental data. The parameters are integrated into multiple potential energy expressions, including the PCFF, CVFF, CHARMM, AMBER, OPLS, and INTERFACE force fields. This choice enables the simulation of a wide range of inorganic-organic interfaces at the 1 to 100 nm scale at a million times lower computational cost than DFT methods. Molecular models of dry and partially hydrated surfaces are introduced to examine cleavage, agglomeration, and the role of adsorbed organic molecules. Cleavage of crystalline tricalcium aluminate requires approximately 1300 mJ m(-2) and superficial hydration introduces an amorphous calcium hydroxide surface layer that reduces the agglomeration energy from approximately 850 mJ m(-2) to 500 mJ m(-2), as well as to lower values upon surface displacement. The adsorption of several alcohols and amines was examined to understand their role as grinding aids and as hydration modifiers in cement. The molecules mitigate local electric fields through complexation of calcium ions, hydrogen bonds, and introduction of hydrophobicity upon binding. Molecularly thin layers of about 0.5 nm thickness reduce agglomeration energies to between 100 and 30 mJ m(-2). Molecule-specific trends were found to be similar for tricalcium aluminate and tricalcium silicate. The models allow quantitative predictions and are a starting point to provide fundamental understanding of the role of C3A and organic additives in cement. Extensions to impure phases and advanced hydration stages are feasible. PMID:24828263

  10. Ab initio based force field and molecular dynamics simulations of crystalline TATB.

    PubMed

    Gee, Richard H; Roszak, Szczepan; Balasubramanian, Krishnan; Fried, Laurence E

    2004-04-15

    An all-atom force field for 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) is presented. The classical intermolecular interaction potential for TATB is based on single-point energies determined from high-level ab initio calculations of TATB dimers. The newly developed potential function is used to examine bulk crystalline TATB via molecular dynamics simulations. The isobaric thermal expansion and isothermal compression under hydrostatic pressures obtained from the molecular dynamics simulations are in good agreement with experiment. The calculated volume-temperature expansion is almost one dimensional along the c crystallographic axis, whereas under compression, all three unit cell axes participate, albeit unequally. PMID:15267608

  11. Fluid force transducer

    DOEpatents

    Jendrzejczyk, Joseph A.

    1982-01-01

    An electrical fluid force transducer for measuring the magnitude and direction of fluid forces caused by lateral fluid flow, includes a movable sleeve which is deflectable in response to the movement of fluid, and a rod fixed to the sleeve to translate forces applied to the sleeve to strain gauges attached to the rod, the strain gauges being connected in a bridge circuit arrangement enabling generation of a signal output indicative of the magnitude and direction of the force applied to the sleeve.

  12. Submolecular Resolution Imaging of Molecules by Atomic Force Microscopy: The Influence of the Electrostatic Force

    NASA Astrophysics Data System (ADS)

    van der Lit, Joost; Di Cicco, Francesca; Hapala, Prokop; Jelinek, Pavel; Swart, Ingmar

    2016-03-01

    The forces governing the contrast in submolecular resolution imaging of molecules with atomic force microscopy (AFM) have recently become a topic of intense debate. Here, we show that the electrostatic force is essential to understand the contrast in atomically resolved AFM images of polar molecules. Specifically, we image strongly polarized molecules with negatively and positively charged tips. A contrast inversion is observed above the polar groups. By taking into account the electrostatic forces between tip and molecule, the observed contrast differences can be reproduced using a molecular mechanics model. In addition, we analyze the height dependence of the various force components contributing to the high-resolution AFM contrast.

  13. [Atomic force field FFsol for calculation of molecular interactions of in water environment].

    PubMed

    Pereiaslavets, L B; Finkel'shtein, A V

    2010-01-01

    Detailed calculations of protein interactions with explicitly considered water takes enormous computer time. The calculation becomes faster if water is considered implicitly (as a continuous media rather than as molecules); however, these calculations are much less precise, unless one uses an additional (and also volumes) computation of the solvent-accessible areas of protein atoms. The aim of our study was to obtain parameters for non-bonded atom-atom interactions for the case when water surrounding is considered implicitly and the solvent-accessible areas are not computed. Since the "in-vacuum" interactions of atoms are obtained from experimental structures of crystals and enthalpies of their sublimation, the "in-water" interactions of atoms must be corrected using solvation free energies of molecules, which can be obtained from the Henry constants. Taken 58 structures of molecular crystals and thermodynamic data on their sublimation and solubility, we obtained parameters for "in-water" attraction and repulsion of atoms typical of protein structures (H, C, N, O, S) in various covalently-bonded states, as well as parameters for electrostatic interactions. All necessary for calculations parameters of covalent interactions have been taken from the ENCAD force field, and partial charges of all atoms of separate molecules of a crystal have been obtained from quantum-mechanical calculations. The sought parameters of the "in-water" van der Waals and electrostatic interactions were optimized so as to achieve the best description of equilibrium crystal structures and their sublimation and solvation at the room temperature. With the optimized parameters, the average error in calculation of the effective cohesion energy of molecules in crystals was less than 10% both in the "in-vacuum" and "in-water" cases. PMID:20586195

  14. Detailed Per-residue Energetic Analysis Explains the Driving Force for Microtubule Disassembly

    PubMed Central

    Ayoub, Ahmed T.; Klobukowski, Mariusz; Tuszynski, Jack A.

    2015-01-01

    Microtubules are long filamentous hollow cylinders whose surfaces form lattice structures of αβ-tubulin heterodimers. They perform multiple physiological roles in eukaryotic cells and are targets for therapeutic interventions. In our study, we carried out all-atom molecular dynamics simulations for arbitrarily long microtubules that have either GDP or GTP molecules in the E-site of β-tubulin. A detailed energy balance of the MM/GBSA inter-dimer interaction energy per residue contributing to the overall lateral and longitudinal structural stability was performed. The obtained results identified the key residues and tubulin domains according to their energetic contributions. They also identified the molecular forces that drive microtubule disassembly. At the tip of the plus end of the microtubule, the uneven distribution of longitudinal interaction energies within a protofilament generates a torque that bends tubulin outwardly with respect to the cylinder's axis causing disassembly. In the presence of GTP, this torque is opposed by lateral interactions that prevent outward curling, thus stabilizing the whole microtubule. Once GTP hydrolysis reaches the tip of the microtubule (lateral cap), lateral interactions become much weaker, allowing tubulin dimers to bend outwards, causing disassembly. The role of magnesium in the process of outward curling has also been demonstrated. This study also showed that the microtubule seam is the most energetically labile inter-dimer interface and could serve as a trigger point for disassembly. Based on a detailed balance of the energetic contributions per amino acid residue in the microtubule, numerous other analyses could be performed to give additional insights into the properties of microtubule dynamic instability. PMID:26030285

  15. Debunking Coriolis Force Myths

    ERIC Educational Resources Information Center

    Shakur, Asif

    2014-01-01

    Much has been written and debated about the Coriolis force. Unfortunately, this has done little to demystify the paradoxes surrounding this fictitious force invoked by an observer in a rotating frame of reference. It is the purpose of this article to make another valiant attempt to slay the dragon of the Coriolis force! This will be done without…

  16. Forces in General Relativity

    ERIC Educational Resources Information Center

    Ridgely, Charles T.

    2010-01-01

    Many textbooks dealing with general relativity do not demonstrate the derivation of forces in enough detail. The analyses presented herein demonstrate straightforward methods for computing forces by way of general relativity. Covariant divergence of the stress-energy-momentum tensor is used to derive a general expression of the force experienced…

  17. Additive usage levels.

    PubMed

    Langlais, R

    1996-01-01

    With the adoption of the European Parliament and Council Directives on sweeteners, colours and miscellaneous additives the Commission is now embarking on the project of coordinating the activities of the European Union Member States in the collection of the data that are to make up the report on food additive intake requested by the European Parliament. This presentation looks at the inventory of available sources on additive use levels and concludes that for the time being national legislation is still the best source of information considering that the directives have yet to be transposed into national legislation. Furthermore, this presentation covers the correlation of the food categories as found in the additives directives with those used by national consumption surveys and finds that in a number of instances this correlation still leaves a lot to be desired. The intake of additives via food ingestion and the intake of substances which are chemically identical to additives but which occur naturally in fruits and vegetables is found in a number of cases to be higher than the intake of additives added during the manufacture of foodstuffs. While the difficulties are recognized in contributing to the compilation of food additive intake data, industry as a whole, i.e. the food manufacturing and food additive manufacturing industries, are confident that in a concerted effort, use data on food additives by industry can be made available. Lastly, the paper points out that with the transportation of the additives directives into national legislation and the time by which the food industry will be able to make use of the new food legislative environment several years will still go by; food additives use data by the food industry will thus have to be reviewed at the beginning of the next century. PMID:8792135

  18. An additional middle cuneiform?

    PubMed Central

    Brookes-Fazakerley, S.D.; Jackson, G.E.; Platt, S.R.

    2015-01-01

    Additional cuneiform bones of the foot have been described in reference to the medial bipartite cuneiform or as small accessory ossicles. An additional middle cuneiform has not been previously documented. We present the case of a patient with an additional ossicle that has the appearance and location of an additional middle cuneiform. Recognizing such an anatomical anomaly is essential for ruling out second metatarsal base or middle cuneiform fractures and for the preoperative planning of arthrodesis or open reduction and internal fixation procedures in this anatomical location. PMID:26224890

  19. 76 FR 65501 - Procurement List Additions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-21

    ...: Grounds Maintenance, Air Force Research Laboratory Stockbridge Test Facility, 5251 Burleson Road, Oneida... INFORMATION: Additions On 8/19/2011 (76 FR 51955-51956) and 8/26/2011 (76 FR 53419-53420), the Committee for..., FA8751 AFRL RIKO, Rome, NY. Patricia Briscoe, Deputy Director, Business Operations, Pricing...

  20. Cell adhesion force microscopy

    PubMed Central

    Sagvolden, G.; Giaever, I.; Pettersen, E. O.; Feder, J.

    1999-01-01

    The adhesion forces of cervical carcinoma cells in tissue culture were measured by using the manipulation force microscope, a novel atomic force microscope. The forces were studied as a function of time and temperature for cells cultured on hydrophilic and hydrophobic polystyrene substrates with preadsorbed proteins. The cells attached faster and stronger at 37°C than at 23°C and better on hydrophilic than on hydrophobic substrates, even though proteins adsorb much better to the hydrophobic substrates. Because cell adhesion serves to control several stages in the cell cycle, we anticipate that the manipulation force microscope can help clarify some cell-adhesion related issues. PMID:9892657

  1. Efficacy of climate forcings

    NASA Astrophysics Data System (ADS)

    Hansen, J.; Sato, M.; Ruedy, R.; Nazarenko, L.; Lacis, A.; Schmidt, G. A.; Russell, G.; Aleinov, I.; Bauer, M.; Bauer, S.; Bell, N.; Cairns, B.; Canuto, V.; Chandler, M.; Cheng, Y.; Del Genio, A.; Faluvegi, G.; Fleming, E.; Friend, A.; Hall, T.; Jackman, C.; Kelley, M.; Kiang, N.; Koch, D.; Lean, J.; Lerner, J.; Lo, K.; Menon, S.; Miller, R.; Minnis, P.; Novakov, T.; Oinas, V.; Perlwitz, Ja.; Perlwitz, Ju.; Rind, D.; Romanou, A.; Shindell, D.; Stone, P.; Sun, S.; Tausnev, N.; Thresher, D.; Wielicki, B.; Wong, T.; Yao, M.; Zhang, S.

    2005-09-01

    We use a global climate model to compare the effectiveness of many climate forcing agents for producing climate change. We find a substantial range in the "efficacy" of different forcings, where the efficacy is the global temperature response per unit forcing relative to the response to CO2 forcing. Anthropogenic CH4 has efficacy ˜110%, which increases to ˜145% when its indirect effects on stratospheric H2O and tropospheric O3 are included, yielding an effective climate forcing of ˜0.8 W/m2 for the period 1750-2000 and making CH4 the largest anthropogenic climate forcing other than CO2. Black carbon (BC) aerosols from biomass burning have a calculated efficacy ˜58%, while fossil fuel BC has an efficacy ˜78%. Accounting for forcing efficacies and for indirect effects via snow albedo and cloud changes, we find that fossil fuel soot, defined as BC + OC (organic carbon), has a net positive forcing while biomass burning BC + OC has a negative forcing. We show that replacement of the traditional instantaneous and adjusted forcings, Fi and Fa, with an easily computed alternative, Fs, yields a better predictor of climate change, i.e., its efficacies are closer to unity. Fs is inferred from flux and temperature changes in a fixed-ocean model run. There is remarkable congruence in the spatial distribution of climate change, normalized to the same forcing Fs, for most climate forcing agents, suggesting that the global forcing has more relevance to regional climate change than may have been anticipated. Increasing greenhouse gases intensify the Hadley circulation in our model, increasing rainfall in the Intertropical Convergence Zone (ITCZ), Eastern United States, and East Asia, while intensifying dry conditions in the subtropics including the Southwest United States, the Mediterranean region, the Middle East, and an expanding Sahel. These features survive in model simulations that use all estimated forcings for the period 1880-2000. Responses to localized forcings, such

  2. Force reflecting hand controller for manipulator teleoperation

    NASA Technical Reports Server (NTRS)

    Bryfogle, Mark D.

    1991-01-01

    A force reflecting hand controller based upon a six degree of freedom fully parallel mechanism, often termed a Stewart Platform, has been designed, constructed, and tested as an integrated system with a slave robot manipulator test bed. A force reflecting hand controller comprises a kinesthetic device capable of transmitting position and orientation commands to a slave robot manipulator while simultaneously representing the environmental interaction forces of the slave manipulator back to the operator through actuators driving the hand controller mechanism. The Stewart Platform was chosen as a novel approach to improve force reflecting teleoperation because of its inherently high ratio of load generation capability to system mass content and the correspondingly high dynamic bandwidth. An additional novelty of the program was to implement closed loop force and torque control about the hand controller mechanism by equipping the handgrip with a six degree of freedom force and torque measuring cell. The mechanical, electrical, computer, and control systems are discussed and system tests are presented.

  3. Casimir-Polder forces on moving atoms

    SciTech Connect

    Scheel, Stefan; Buhmann, Stefan Yoshi

    2009-10-15

    Polarizable atoms and molecules experience the Casimir-Polder force near magnetoelectric bodies, a force that is induced by quantum fluctuations of the electromagnetic field and the matter. Atoms and molecules in relative motion to a magnetoelectric surface experience an additional velocity-dependent force. We present a full quantum-mechanical treatment of this force and identify a generalized Doppler effect, the time delay between photon emission and reabsorption, and the Roentgen interaction as its three sources. For ground-state atoms, the force is very small and always decelerating, hence commonly known as quantum friction. For atoms and molecules in electronically excited states, on the contrary, both decelerating and accelerating forces can occur depending on the magnitude of the atomic transition frequency relative to the surface-plasmon frequency.

  4. Force reflecting hand controller for manipulator teleoperation

    NASA Astrophysics Data System (ADS)

    Bryfogle, Mark D.

    1991-12-01

    A force reflecting hand controller based upon a six degree of freedom fully parallel mechanism, often termed a Stewart Platform, has been designed, constructed, and tested as an integrated system with a slave robot manipulator test bed. A force reflecting hand controller comprises a kinesthetic device capable of transmitting position and orientation commands to a slave robot manipulator while simultaneously representing the environmental interaction forces of the slave manipulator back to the operator through actuators driving the hand controller mechanism. The Stewart Platform was chosen as a novel approach to improve force reflecting teleoperation because of its inherently high ratio of load generation capability to system mass content and the correspondingly high dynamic bandwidth. An additional novelty of the program was to implement closed loop force and torque control about the hand controller mechanism by equipping the handgrip with a six degree of freedom force and torque measuring cell. The mechanical, electrical, computer, and control systems are discussed and system tests are presented.

  5. Carbamate deposit control additives

    SciTech Connect

    Honnen, L.R.; Lewis, R.A.

    1980-11-25

    Deposit control additives for internal combustion engines are provided which maintain cleanliness of intake systems without contributing to combustion chamber deposits. The additives are poly(oxyalkylene) carbamates comprising a hydrocarbyloxyterminated poly(Oxyalkylene) chain of 2-5 carbon oxyalkylene units bonded through an oxycarbonyl group to a nitrogen atom of ethylenediamine.

  6. Forces in molecules.

    PubMed

    Hernández-Trujillo, Jesús; Cortés-Guzmán, Fernando; Fang, De-Chai; Bader, Richard F W

    2007-01-01

    Chemistry is determined by the electrostatic forces acting within a collection of nuclei and electrons. The attraction of the nuclei for the electrons is the only attractive force in a molecule and is the force responsible for the bonding between atoms. This is the attractive force acting on the electrons in the Ehrenfest force and on the nuclei in the Feynman force, one that is countered by the repulsion between the electrons in the former and by the repulsion between the nuclei in the latter. The virial theorem relates these forces to the energy changes resulting from interactions between atoms. All bonding, as signified by the presence of a bond path, has a common origin in terms of the mechanics determined by the Ehrenfest, Feynman and virial theorems. This paper is concerned in particular with the mechanics of interaction encountered in what are classically described as 'nonbonded interactions'--are atoms that 'touch' bonded or repelling one another? PMID:17328425

  7. Magnus force in superfluids and superconductors

    SciTech Connect

    Sonin, E.B. |

    1997-01-01

    The forces on the vortex, transverse to its velocity, are considered. In addition to the superfluid Magnus force from the condensate (superfluid component), there are transverse forces from thermal quasiparticles and external fields violating the Galilean invariance. The forces between quasiparticles and the vortex originate from interference of quasiparticles with trajectories on the left and on the right from the vortex like similar forces for electrons interacting with the thin magnetic-flux tube (the Aharonov-Bohm effect). These forces are derived for phonons from the equations of superfluid hydrodynamics, and for BCS quasiparticles from the Bogolyubov{endash}de Gennes equations. The effect of external fields breaking Galilean invariance is analyzed for vortices in the two-dimensional Josephson junction array. The symmetry analysis of the classical equations for the array shows that the total transverse force on the vortex vanishes. Therefore the Hall effect which is linear in the transverse force is absent also. This means that the Magnus force from the superfluid component {ital exactly} cancels with the transverse force from the external fields. The results of other approaches are also brought together for discussion. {copyright} {ital 1997} {ital The American Physical Society}

  8. Force Limited Vibration Testing

    NASA Technical Reports Server (NTRS)

    Scharton, Terry; Chang, Kurng Y.

    2005-01-01

    This slide presentation reviews the concept and applications of Force Limited Vibration Testing. The goal of vibration testing of aerospace hardware is to identify problems that would result in flight failures. The commonly used aerospace vibration tests uses artificially high shaker forces and responses at the resonance frequencies of the test item. It has become common to limit the acceleration responses in the test to those predicted for the flight. This requires an analysis of the acceleration response, and requires placing accelerometers on the test item. With the advent of piezoelectric gages it has become possible to improve vibration testing. The basic equations have are reviewed. Force limits are analogous and complementary to the acceleration specifications used in conventional vibration testing. Just as the acceleration specification is the frequency spectrum envelope of the in-flight acceleration at the interface between the test item and flight mounting structure, the force limit is the envelope of the in-flight force at the interface . In force limited vibration tests, both the acceleration and force specifications are needed, and the force specification is generally based on and proportional to the acceleration specification. Therefore, force limiting does not compensate for errors in the development of the acceleration specification, e.g., too much conservatism or the lack thereof. These errors will carry over into the force specification. Since in-flight vibratory force data are scarce, force limits are often derived from coupled system analyses and impedance information obtained from measurements or finite element models (FEM). Fortunately, data on the interface forces between systems and components are now available from system acoustic and vibration tests of development test models and from a few flight experiments. Semi-empirical methods of predicting force limits are currently being developed on the basis of the limited flight and system test

  9. Polyimide processing additives

    NASA Technical Reports Server (NTRS)

    Fletcher, James C. (Inventor); Pratt, J. Richard (Inventor); St.clair, Terry L. (Inventor); Stoakley, Diane M. (Inventor); Burks, Harold D. (Inventor)

    1992-01-01

    A process for preparing polyimides having enhanced melt flow properties is described. The process consists of heating a mixture of a high molecular weight poly-(amic acid) or polyimide with a low molecular weight amic acid or imide additive in the range of 0.05 to 15 percent by weight of additive. The polyimide powders so obtained show improved processability, as evidenced by lower melt viscosity by capillary rheometry. Likewise, films prepared from mixtures of polymers with additives show improved processability with earlier onset of stretching by TMA.

  10. Polyimide processing additives

    NASA Technical Reports Server (NTRS)

    Pratt, J. Richard (Inventor); St.clair, Terry L. (Inventor); Stoakley, Diane M. (Inventor); Burks, Harold D. (Inventor)

    1993-01-01

    A process for preparing polyimides having enhanced melt flow properties is described. The process consists of heating a mixture of a high molecular weight poly-(amic acid) or polyimide with a low molecular weight amic acid or imide additive in the range of 0.05 to 15 percent by weight of the additive. The polyimide powders so obtained show improved processability, as evidenced by lower melt viscosity by capillary rheometry. Likewise, films prepared from mixtures of polymers with additives show improved processability with earlier onset of stretching by TMA.

  11. Smog control fuel additives

    SciTech Connect

    Lundby, W.

    1993-06-29

    A method is described of controlling, reducing or eliminating, ozone and related smog resulting from photochemical reactions between ozone and automotive or industrial gases comprising the addition of iodine or compounds of iodine to hydrocarbon-base fuels prior to or during combustion in an amount of about 1 part iodine per 240 to 10,000,000 parts fuel, by weight, to be accomplished by: (a) the addition of these inhibitors during or after the refining or manufacturing process of liquid fuels; (b) the production of these inhibitors for addition into fuel tanks, such as automotive or industrial tanks; or (c) the addition of these inhibitors into combustion chambers of equipment utilizing solid fuels for the purpose of reducing ozone.

  12. Food Additives and Hyperkinesis

    ERIC Educational Resources Information Center

    Wender, Ester H.

    1977-01-01

    The hypothesis that food additives are causally associated with hyperkinesis and learning disabilities in children is reviewed, and available data are summarized. Available from: American Medical Association 535 North Dearborn Street Chicago, Illinois 60610. (JG)

  13. Additional Types of Neuropathy

    MedlinePlus

    ... A A Listen En Español Additional Types of Neuropathy Charcot's Joint Charcot's Joint, also called neuropathic arthropathy, ... can stop bone destruction and aid healing. Cranial Neuropathy Cranial neuropathy affects the 12 pairs of nerves ...

  14. The Bichromatic Optical Force on the Atomic Life- time Scale

    NASA Astrophysics Data System (ADS)

    Corder, Christopher; Arnold, Brian; Metcalf, Harold

    2013-05-01

    Our experimental and theoretical studies of the bichromatic force (BF) have shown that its strength and velocity range are very much larger than those of the usual radiative force. Since the BF relies on stimulated effects, the role of spontaneous emission in laser cooling has come into question. We drive the 23 S -->33 P transition of He at λ = 389 nm with laser frequencies ωl =ωa +/- δ , where ωa is the atomic transition frequency and δ ~ 30 MHz. Thus the velocity range of the force is Δv ~ δ / 2 k = 6 m/s. Because of the large and nearly constant strength of the BF, F ~ ℏkδ / π , all atoms can reach the velocity limit in a time <= MΔv / F = π / 4ωr = 380 ns, where ωr is the atomic recoil frequency. In our experiment a beam of He atoms crosses perpendicular through the BF laser beams in 380 ns so the relatively long lifetime of the excited state (τ = 106 ns) allows one or at most two spontaneous emission events, despite Δv of many tens of recoils. We will present our initial measurements of the BF in this new domain. Supported by ONR and Dept. of Ed. GAANN.

  15. Coulomb force as an entropic force

    NASA Astrophysics Data System (ADS)

    Wang, Tower

    2010-05-01

    Motivated by Verlinde’s theory of entropic gravity, we give a tentative explanation to the Coulomb’s law with an entropic force. When trying to do this, we find the equipartition rule should be extended to charges and the concept of temperature should be reinterpreted. If one accepts the holographic principle as well as our generalizations and reinterpretations, then Coulomb’s law, the Poisson equation, and the Maxwell equations can be derived smoothly. Our attempt can be regarded as a new way to unify the electromagnetic force with gravity, from the entropic origin. Possibly some of our postulates are related to the D-brane picture of black hole thermodynamics.

  16. Coulomb force as an entropic force

    SciTech Connect

    Wang Tower

    2010-05-15

    Motivated by Verlinde's theory of entropic gravity, we give a tentative explanation to the Coulomb's law with an entropic force. When trying to do this, we find the equipartition rule should be extended to charges and the concept of temperature should be reinterpreted. If one accepts the holographic principle as well as our generalizations and reinterpretations, then Coulomb's law, the Poisson equation, and the Maxwell equations can be derived smoothly. Our attempt can be regarded as a new way to unify the electromagnetic force with gravity, from the entropic origin. Possibly some of our postulates are related to the D-brane picture of black hole thermodynamics.

  17. Effective Forces Between Colloidal Particles

    NASA Technical Reports Server (NTRS)

    Tehver, Riina; Banavar, Jayanth R.; Koplik, Joel

    1999-01-01

    Colloidal suspensions have proven to be excellent model systems for the study of condensed matter and its phase behavior. Many of the properties of colloidal suspensions can be investigated with a systematic variation of the characteristics of the systems and, in addition, the energy, length and time scales associated with them allow for experimental probing of otherwise inaccessible regimes. The latter property also makes colloidal systems vulnerable to external influences such as gravity. Experiments performed in micro-ravity by Chaikin and Russell have been invaluable in extracting the true behavior of the systems without an external field. Weitz and Pusey intend to use mixtures of colloidal particles with additives such as polymers to induce aggregation and form weak, tenuous, highly disordered fractal structures that would be stable in the absence of gravitational forces. When dispersed in a polarizable medium, colloidal particles can ionize, emitting counterions into the solution. The standard interaction potential in these charged colloidal suspensions was first obtained by Derjaguin, Landau, Verwey and Overbeek. The DLVO potential is obtained in the mean-field linearized Poisson-Boltzmann approximation and thus has limited applicability. For more precise calculations, we have used ab initio density functional theory. In our model, colloidal particles are charged hard spheres, the counterions are described by a continuum density field and the solvent is treated as a homogeneous medium with a specified dielectric constant. We calculate the effective forces between charged colloidal particles by integrating over the solvent and counterion degrees of freedom, taking into account the direct interactions between the particles as well as particle-counterion, counterion-counterion Coulomb, counterion entropic and correlation contributions. We obtain the effective interaction potential between charged colloidal particles in different configurations. We evaluate two

  18. Inversion of radial distribution functions to pair forces by solving the Yvon-Born-Green equation iteratively.

    PubMed

    Cho, Hyung Min; Chu, Jhih-Wei

    2009-10-01

    We develop a new method to invert the target profiles of radial distribution functions (RDFs) to the pair forces between particles. The target profiles of RDFs can be obtained from all-atom molecular dynamics (MD) simulations or experiments and the inverted pair forces can be used in molecular simulations at a coarse-grained (CG) scale. Our method is based on a variational principle that determines the mean forces between CG sites after integrating out the unwanted degrees of freedom. The solution of this variational principle has been shown to correspond to the Yvon-Born-Green (YBG) equation [Noid et al., J. Phys. Chem. B 111, 4116 (2007)]. To invert RDFs, we solve the YBG equation iteratively by running a CG MD simulation at each step of iteration. A novelty of the iterative-YBG method is that during iteration, CG forces are updated according to the YBG equation without imposing any approximation as is required by other methods. As a result, only three to ten iterations are required to achieve convergence for all cases tested in this work. Furthermore, we show that not only are the target RDFs reproduced by the iterative solution; the profiles of the three-body correlation function in the YBG equation computed from all-atom and CG simulations also have a better agreement. The iterative-YBG method is applied to compute the CG forces of four molecular liquids to illustrate its efficiency and robustness: water, ethane, ethanol, and a water/methanol mixture. Using the resulting CG forces, all of the target RDFs observed in all-atom MD simulations are reproduced. We also show that the iterative-YBG method can be applied with a virial constraint to expand the representability of a CG force field. The iterative-YBG method thus provides a general and robust framework for computing CG forces from RDFs and could be systematically generalized to go beyond pairwise forces and to include higher-body interactions in a CG force field by applying the aforementioned variational

  19. Debunking Coriolis Force Myths

    NASA Astrophysics Data System (ADS)

    Shakur, Asif

    2014-11-01

    Much has been written and debated about the Coriolis force.1-8 Unfortunately, this has done little to demystify the paradoxes surrounding this fictitious force invoked by an observer in a rotating frame of reference. It is the purpose of this article to make another valiant attempt to slay the dragon of the Coriolis force! This will be done without unleashing the usual mathematical apparatus, which we believe is more of a hindrance than a help.

  20. Lathe tool force

    SciTech Connect

    Emery, J.D.

    1993-02-01

    This report describes a computer program that computes the forces exerted on a lathe tool as a part is being machined. The program is based on a mechanistic model which assumes that the normal force on the tool face is proportional to the cross-sectional area of the chip that is being removed from the part. This report gives transcripts of program runs, a comparison with experimentally measured forces, a bibliography, and a listing of the program.

  1. Additive Manufacturing Infrared Inspection

    NASA Technical Reports Server (NTRS)

    Gaddy, Darrell

    2014-01-01

    Additive manufacturing is a rapid prototyping technology that allows parts to be built in a series of thin layers from plastic, ceramics, and metallics. Metallic additive manufacturing is an emerging form of rapid prototyping that allows complex structures to be built using various metallic powders. Significant time and cost savings have also been observed using the metallic additive manufacturing compared with traditional techniques. Development of the metallic additive manufacturing technology has advanced significantly over the last decade, although many of the techniques to inspect parts made from these processes have not advanced significantly or have limitations. Several external geometry inspection techniques exist such as Coordinate Measurement Machines (CMM), Laser Scanners, Structured Light Scanning Systems, or even traditional calipers and gages. All of the aforementioned techniques are limited to external geometry and contours or must use a contact probe to inspect limited internal dimensions. This presentation will document the development of a process for real-time dimensional inspection technique and digital quality record of the additive manufacturing process using Infrared camera imaging and processing techniques.

  2. Mechanotransduction: use the force(s).

    PubMed

    Paluch, Ewa K; Nelson, Celeste M; Biais, Nicolas; Fabry, Ben; Moeller, Jens; Pruitt, Beth L; Wollnik, Carina; Kudryasheva, Galina; Rehfeldt, Florian; Federle, Walter

    2015-01-01

    Mechanotransduction - how cells sense physical forces and translate them into biochemical and biological responses - is a vibrant and rapidly-progressing field, and is important for a broad range of biological phenomena. This forum explores the role of mechanotransduction in a variety of cellular activities and highlights intriguing questions that deserve further attention. PMID:26141078

  3. No fifth force?

    NASA Astrophysics Data System (ADS)

    Maggs, William Ward

    Hopes that geophysicists might be able to document a fifth force of nature have diminished, as new measurements and analyses of earlier geodetic experiments have yielded no solid evidence of a non-Newtonian component of gravity.Modern physics recognizes four fundamental forces with distinct spheres of influence: The strong and weak nuclear forces operate over the range of one atom, while gravity and electromagnetism have an infinite range. Gravity measurements over a few centimeters in laboratories and over millions of kilometers in space continue to buttress Issac Newton's conclusion that the gravitational force between two objects decreases as the square of the distance between them.

  4. Electrodynamic force law controversy.

    PubMed

    Graneau, P; Graneau, N

    2001-05-01

    Cavalleri et al. [Phys. Rev. E 52, 2505 (1998); Eur. J. Phys. 17, 205 (1996)] have attempted to resolve the electrodynamic force law controversy. This attempt to prove the validity of either the Ampère or Lorentz force law by theory and experiment has revealed only that the two are equivalent when predicting the force on part of a circuit due to the current in the complete circuit. However, in our analysis of internal stresses, only Ampère's force law agrees with experiment. PMID:11415053

  5. Finger Forces in Clarinet Playing.

    PubMed

    Hofmann, Alex; Goebl, Werner

    2016-01-01

    Clarinettists close and open multiple tone holes to alter the pitch of the tones. Their fingering technique must be fast, precise, and coordinated with the tongue articulation. In this empirical study, finger force profiles and tongue techniques of clarinet students (N = 17) and professional clarinettists (N = 6) were investigated under controlled performance conditions. First, in an expressive-performance task, eight selected excerpts from the first Weber Concerto were performed. These excerpts were chosen to fit in a 2 × 2 × 2 design (register: low-high; tempo: slow-fast, dynamics: soft-loud). There was an additional condition controlled by the experimenter, which determined the expression levels (low-high) of the performers. Second, a technical-exercise task, an isochronous 23-tone melody was designed that required different effectors to produce the sequence (finger-only, tongue-only, combined tongue-finger actions). The melody was performed in three tempo conditions (slow, medium, fast) in a synchronization-continuation paradigm. Participants played on a sensor-equipped Viennese clarinet, which tracked finger forces and reed oscillations simultaneously. From the data, average finger force (F mean ) and peak force (F max ) were calculated. The overall finger forces were low (F mean = 1.17 N, F max = 3.05 N) compared to those on other musical instruments (e.g., guitar). Participants applied the largest finger forces during the high expression level performance conditions (F mean = 1.21 N). For the technical exercise task, timing and articulation information were extracted from the reed signal. Here, the timing precision of the fingers deteriorated the timing precision of the tongue for combined tongue-finger actions, especially for faster tempi. Although individual finger force profiles were overlapping, the group of professional players applied less finger force overall (F mean = 0.54 N). Such sensor instruments provide useful insights into player

  6. Phenylethynyl Containing Reactive Additives

    NASA Technical Reports Server (NTRS)

    Connell, John W. (Inventor); Smith, Joseph G., Jr. (Inventor); Hergenrother, Paul M. (Inventor)

    2002-01-01

    Phenylethynyl containing reactive additives were prepared from aromatic diamine, containing phenylethvnvl groups and various ratios of phthalic anhydride and 4-phenylethynviphthalic anhydride in glacial acetic acid to form the imide in one step or in N-methyl-2-pvrrolidinone to form the amide acid intermediate. The reactive additives were mixed in various amounts (10% to 90%) with oligomers containing either terminal or pendent phenylethynyl groups (or both) to reduce the melt viscosity and thereby enhance processability. Upon thermal cure, the additives react and become chemically incorporated into the matrix and effect an increase in crosslink density relative to that of the host resin. This resultant increase in crosslink density has advantageous consequences on the cured resin properties such as higher glass transition temperature and higher modulus as compared to that of the host resin.

  7. Additives in plastics.

    PubMed Central

    Deanin, R D

    1975-01-01

    The polymers used in plastics are generally harmless. However, they are rarely used in pure form. In almost all commercial plastics, they are "compounded" with monomeric ingredients to improve their processing and end-use performance. In order of total volume used, these monomeric additives may be classified as follows: reinforcing fibers, fillers, and coupling agents; plasticizers; colorants; stabilizers (halogen stabilizers, antioxidants, ultraviolet absorbers, and biological preservatives); processing aids (lubricants, others, and flow controls); flame retardants, peroxides; and antistats. Some information is already available, and much more is needed, on potential toxicity and safe handling of these additives during processing and manufacture of plastics products. PMID:1175566

  8. Inhomogeneous radiative forcing of homogeneous greenhouse gases

    NASA Astrophysics Data System (ADS)

    Huang, Yi; Tan, Xiaoxiao; Xia, Yan

    2016-03-01

    Radiative forcing of a homogeneous greenhouse gas (HGG) can be very inhomogeneous because the forcing is dependent on other atmospheric and surface variables. In the case of doubling CO2, the monthly mean instantaneous forcing at the top of the atmosphere is found to vary geographically and temporally from positive to negative values, with the range (-2.5-5.1 W m-2) being more than 3 times the magnitude of the global mean value (2.3 W m-2). The vertical temperature change across the atmospheric column (temperature lapse rate) is found to be the best single predictor for explaining forcing variation. In addition, the masking effects of clouds and water vapor also contribute to forcing inhomogeneity. A regression model that predicts forcing from geophysical variables is constructed. This model can explain more than 90% of the variance of the forcing. Applying this model to analyzing the forcing variation in the Climate Model Intercomparison Project Phase 5 models, we find that intermodel discrepancy in CO2 forcing caused by model climatology leads to considerable discrepancy in their projected change in poleward energy transport.

  9. Climate forcings and feedbacks

    NASA Technical Reports Server (NTRS)

    Hansen, James

    1993-01-01

    Global temperature has increased significantly during the past century. Understanding the causes of observed global temperature change is impossible in the absence of adequate monitoring of changes in global climate forcings and radiative feedbacks. Climate forcings are changes imposed on the planet's energy balance, such as change of incoming sunlight or a human-induced change of surface properties due to deforestation. Radiative feedbacks are radiative changes induced by climate change, such as alteration of cloud properties or the extent of sea ice. Monitoring of global climate forcings and feedbacks, if sufficiently precise and long-term, can provide a very strong constraint on interpretation of observed temperature change. Such monitoring is essential to eliminate uncertainties about the relative importance of various climate change mechanisms including tropospheric sulfate aerosols from burning of coal and oil smoke from slash and burn agriculture, changes of solar irradiance changes of several greenhouse gases, and many other mechanisms. The considerable variability of observed temperature, together with evidence that a substantial portion of this variability is unforced indicates that observations of climate forcings and feedbacks must be continued for decades. Since the climate system responds to the time integral of the forcing, a further requirement is that the observations be carried out continuously. However, precise observations of forcings and feedbacks will also be able to provide valuable conclusions on shorter time scales. For example, knowledge of the climate forcing by increasing CFC's relative to the forcing by changing ozone is important to policymakers, as is information on the forcing by CO2 relative to the forcing by sulfate aerosols. It will also be possible to obtain valuable tests of climate models on short time scales, if there is precise monitoring of all forcings and feedbacks during and after events such as a large volcanic eruption

  10. Biobased lubricant additives

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fully biobased lubricants are those formulated using all biobased ingredients, i.e. biobased base oils and biobased additives. Such formulations provide the maximum environmental, safety, and economic benefits expected from a biobased product. Currently, there are a number of biobased base oils that...

  11. Multifunctional fuel additives

    SciTech Connect

    Baillargeon, D.J.; Cardis, A.B.; Heck, D.B.

    1991-03-26

    This paper discusses a composition comprising a major amount of a liquid hydrocarbyl fuel and a minor low-temperature flow properties improving amount of an additive product of the reaction of a suitable diol and product of a benzophenone tetracarboxylic dianhydride and a long-chain hydrocarbyl aminoalcohol.

  12. Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment.

    PubMed

    Rauscher, Sarah; Gapsys, Vytautas; Gajda, Michal J; Zweckstetter, Markus; de Groot, Bert L; Grubmüller, Helmut

    2015-11-10

    Intrinsically disordered proteins (IDPs) are notoriously challenging to study both experimentally and computationally. The structure of IDPs cannot be described by a single conformation but must instead be described as an ensemble of interconverting conformations. Atomistic simulations are increasingly used to obtain such IDP conformational ensembles. Here, we have compared the IDP ensembles generated by eight all-atom empirical force fields against primary small-angle X-ray scattering (SAXS) and NMR data. Ensembles obtained with different force fields exhibit marked differences in chain dimensions, hydrogen bonding, and secondary structure content. These differences are unexpectedly large: changing the force field is found to have a stronger effect on secondary structure content than changing the entire peptide sequence. The CHARMM 22* ensemble performs best in this force field comparison: it has the lowest error in chemical shifts and J-couplings and agrees well with the SAXS data. A high population of left-handed α-helix is present in the CHARMM 36 ensemble, which is inconsistent with measured scalar couplings. To eliminate inadequate sampling as a reason for differences between force fields, extensive simulations were carried out (0.964 ms in total); the remaining small sampling uncertainty is shown to be much smaller than the observed differences. Our findings highlight how IDPs, with their rugged energy landscapes, are highly sensitive test systems that are capable of revealing force field deficiencies and, therefore, contributing to force field development. PMID:26574339

  13. Force distribution in a semiflexible loop

    NASA Astrophysics Data System (ADS)

    Waters, James T.; Kim, Harold D.

    2016-04-01

    Loops undergoing thermal fluctuations are prevalent in nature. Ringlike or cross-linked polymers, cyclic macromolecules, and protein-mediated DNA loops all belong to this category. Stability of these molecules are generally described in terms of free energy, an average quantity, but it may also be impacted by local fluctuating forces acting within these systems. The full distribution of these forces can thus give us insights into mechanochemistry beyond the predictive capability of thermodynamics. In this paper, we study the force exerted by an inextensible semiflexible polymer constrained in a looped state. By using a simulation method termed "phase-space sampling," we generate the equilibrium distribution of chain conformations in both position and momentum space. We compute the constraint forces between the two ends of the loop in this chain ensemble using Lagrangian mechanics, and show that the mean of these forces is equal to the thermodynamic force. By analyzing kinetic and potential contributions to the forces, we find that the mean force acts in the direction of increasing extension not because of bending stress, but in spite of it. Furthermore, we obtain a distribution of constraint forces as a function of chain length, extension, and stiffness. Notably, increasing contour length decreases the average force, but the additional freedom allows fluctuations in the constraint force to increase. The force distribution is asymmetric and falls off less sharply than a Gaussian distribution. Our work exemplifies a system where large-amplitude fluctuations occur in a way unforeseen by a purely thermodynamic framework, and offers computational tools useful for efficient, unbiased simulation of a constrained system.

  14. Forces in yeast flocculation

    PubMed Central

    El-Kirat-Chatel, Sofiane; Beaussart, Audrey; Vincent, Stéphane P.; Flos, Marta Abellán; Hols, Pascal; Lipke, Peter N.; Dufrêne, Yves F.

    2014-01-01

    In the baker's yeast Saccharomyces cerevisiae, cell-cell adhesion (“flocculation”) is conferred by a family of lectin-like proteins known as the flocculin (Flo) proteins. Knowledge of the adhesive and mechanical properties of flocculins is important for understanding the mechanisms of yeast adhesion, and may help controlling yeast behaviour in biotechnology. We use single-molecule and single-cell atomic force microscopy (AFM) to explore the nanoscale forces engaged in yeast flocculation, focusing on the role of Flo1 as a prototype of flocculins. Using AFM tips labelled with mannose, we detect single flocculins on Flo1-expressing cells, showing they are widely exposed on the cell surface. When subjected to force, individual Flo1 proteins display two distinct force responses, i.e. weak lectin binding forces and strong unfolding forces reflecting the force-induced extension of hydrophobic tandem repeats. We demonstrate that cell-cell adhesion bonds also involve multiple weak lectin interactions together with strong unfolding forces, both associated with Flo1 molecules. Single-molecule and single-cell data correlate with microscale cell adhesion behaviour, suggesting strongly that Flo1 mechanics is critical for yeast flocculation. These results favour a model in which not only weak lectin-sugar interactions are involved in yeast flocculation but also strong hydrophobic interactions resulting from protein unfolding. PMID:25515338

  15. SCM-Forcing Data

    DOE Data Explorer

    Xie, Shaocheng; Tang,Shuaiqi; Zhang,Yunyan; Zhang,Minghua

    2016-07-01

    Single-Column Model (SCM) Forcing Data are derived from the ARM facility observational data using the constrained variational analysis approach (Zhang and Lin 1997 and Zhang et al., 2001). The resulting products include both the large-scale forcing terms and the evaluation fields, which can be used for driving the SCMs and Cloud Resolving Models (CRMs) and validating model simulations.

  16. Elementary Particles and Forces.

    ERIC Educational Resources Information Center

    Quigg, Chris

    1985-01-01

    Discusses subatomic particles (quarks, leptons, and others) revealed by higher accelerator energies. A connection between forces at this subatomic level has been established, and prospects are good for a description of forces that encompass binding atomic nuclei. Colors, fundamental interactions, screening, camouflage, electroweak symmetry, and…

  17. Forces in yeast flocculation

    NASA Astrophysics Data System (ADS)

    El-Kirat-Chatel, Sofiane; Beaussart, Audrey; Vincent, Stéphane P.; Abellán Flos, Marta; Hols, Pascal; Lipke, Peter N.; Dufrêne, Yves F.

    2015-01-01

    In the baker's yeast Saccharomyces cerevisiae, cell-cell adhesion (``flocculation'') is conferred by a family of lectin-like proteins known as the flocculin (Flo) proteins. Knowledge of the adhesive and mechanical properties of flocculins is important for understanding the mechanisms of yeast adhesion, and may help controlling yeast behaviour in biotechnology. We use single-molecule and single-cell atomic force microscopy (AFM) to explore the nanoscale forces engaged in yeast flocculation, focusing on the role of Flo1 as a prototype of flocculins. Using AFM tips labelled with mannose, we detect single flocculins on Flo1-expressing cells, showing they are widely exposed on the cell surface. When subjected to force, individual Flo1 proteins display two distinct force responses, i.e. weak lectin binding forces and strong unfolding forces reflecting the force-induced extension of hydrophobic tandem repeats. We demonstrate that cell-cell adhesion bonds also involve multiple weak lectin interactions together with strong unfolding forces, both associated with Flo1 molecules. Single-molecule and single-cell data correlate with microscale cell adhesion behaviour, suggesting strongly that Flo1 mechanics is critical for yeast flocculation. These results favour a model in which not only weak lectin-sugar interactions are involved in yeast flocculation but also strong hydrophobic interactions resulting from protein unfolding.

  18. Force Concept Inventory.

    ERIC Educational Resources Information Center

    Hestenes, David; And Others

    1992-01-01

    Reports the rationale, design, validation, and uses of the "Force Concept Inventory," an instrument to assess the students' beliefs on force. Includes results and implications of two studies that compared the inventory with the "Mechanics Baseline." Includes a copy of the instrument. (MDH)

  19. 49 CFR 192.935 - What additional preventive and mitigative measures must an operator take?

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    .... (2) Outside force damage. If an operator determines that outside force (e.g., earth movement, floods... implementing additional inspection and maintenance programs. (b) Third party damage and outside force damage... measures to minimize the consequences to the covered segment from outside force damage. These...

  20. 49 CFR 192.935 - What additional preventive and mitigative measures must an operator take?

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    .... (2) Outside force damage. If an operator determines that outside force (e.g., earth movement, floods... implementing additional inspection and maintenance programs. (b) Third party damage and outside force damage... measures to minimize the consequences to the covered segment from outside force damage. These...

  1. 49 CFR 192.935 - What additional preventive and mitigative measures must an operator take?

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... implementing additional inspection and maintenance programs. (b) Third party damage and outside force damage.... (2) Outside force damage. If an operator determines that outside force (e.g., earth movement, floods... measures to minimize the consequences to the covered segment from outside force damage. These......

  2. Lorentz force velocimetry.

    PubMed

    Thess, A; Votyakov, E V; Kolesnikov, Y

    2006-04-28

    We describe a noncontact technique for velocity measurement in electrically conducting fluids. The technique, which we term Lorentz force velocimetry (LFV), is based on exposing the fluid to a magnetic field and measuring the drag force acting upon the magnetic field lines. Two series of measurements are reported, one in which the force is determined through the angular velocity of a rotary magnet system and one in which the force on a fixed magnet system is measured directly. Both experiments confirm that the measured signal is a linear function of the flow velocity. We then derive the scaling law that relates the force on a localized distribution of magnetized material to the velocity of an electrically conducting fluid. This law shows that LFV, if properly designed, has a wide range of potential applications in metallurgy, semiconductor crystal growth, and glass manufacturing. PMID:16712237

  3. Feeble forces and gravity.

    NASA Astrophysics Data System (ADS)

    Bars, Itzhak; Visser, Matt

    1987-03-01

    We develop a scenario in which feeble intermediate range forces emerge as an effect resulting from the compactification (à la Kaluza-Klein) of multidimensional theories. These feeble forces compete with gravity and in general permit different bodies to fall to earth with different accelerations. We show that these feeble forces are mediated by vectors (V) and/or scalars (S), whose dimensionless coupling constants are typically of order gv ≈ gs ≈ 10-10 Under certain plausible assumptions the ranges of these feeble forces are expected to be of order 1 m to 1 km. It is conjectured that the general strategy will prove applicable to realistic multidimensional theories such as the 10-dimensional superstring theories. We speculate that deviations from the standard gravitational force-similar to the ones reported recently as a “fifth force”-may be interpreted as evidence for higher dimensions.

  4. Conservative entropic forces

    NASA Astrophysics Data System (ADS)

    Visser, Matt

    2011-10-01

    Entropic forces have recently attracted considerable attention as ways to reformulate, retrodict, and perhaps even "explain" classical Newtonian gravity from a rather specific thermodynamic perspective. In this article I point out that if one wishes to reformulate classical Newtonian gravity in terms of an entropic force, then the fact that Newtonian gravity is described by a conservative force places significant constraints on the form of the entropy and temperature functions. (These constraints also apply to entropic reinterpretations of electromagnetism, and indeed to any conservative force derivable from a potential.) The constraints I will establish are sufficient to present real and significant problems for any reasonable variant of Verlinde's entropic gravity proposal, though for technical reasons the constraints established herein do not directly impact on either Jacobson'sor Padmanabhan's versions of entropic gravity. In an attempt to resolve these issues, I will extend the usual notion of entropic force to multiple heat baths with multiple "temperatures" and multiple "entropies".

  5. Boron addition to alloys

    SciTech Connect

    Coad, B. C.

    1985-08-20

    A process for addition of boron to an alloy which involves forming a melt of the alloy and a reactive metal, selected from the group consisting of aluminum, titanium, zirconium and mixtures thereof to the melt, maintaining the resulting reactive mixture in the molten state and reacting the boric oxide with the reactive metal to convert at least a portion of the boric oxide to boron which dissolves in the resulting melt, and to convert at least portion of the reactive metal to the reactive metal oxide, which oxide remains with the resulting melt, and pouring the resulting melt into a gas stream to form a first atomized powder which is subsequently remelted with further addition of boric oxide, re-atomized, and thus reprocessed to convert essentially all the reactive metal to metal oxide to produce a powdered alloy containing specified amounts of boron.

  6. Tackifier for addition polyimides

    NASA Technical Reports Server (NTRS)

    Butler, J. M.; St.clair, T. L.

    1980-01-01

    A modification to the addition polyimide, LaRC-160, was prepared to improve tack and drape and increase prepeg out-time. The essentially solventless, high viscosity laminating resin is synthesized from low cost liquid monomers. The modified version takes advantage of a reactive, liquid plasticizer which is used in place of solvent and helps solve a major problem of maintaining good prepeg tack and drape, or the ability of the prepeg to adhere to adjacent plies and conform to a desired shape during the lay up process. This alternate solventless approach allows both longer life of the polymer prepeg and the processing of low void laminates. This approach appears to be applicable to all addition polyimide systems.

  7. Vinyl capped addition polyimides

    NASA Technical Reports Server (NTRS)

    Vannucci, Raymond D. (Inventor); Malarik, Diane C. (Inventor); Delvigs, Peter (Inventor)

    1991-01-01

    Polyimide resins (PMR) are generally useful where high strength and temperature capabilities are required (at temperatures up to about 700 F). Polyimide resins are particularly useful in applications such as jet engine compressor components, for example, blades, vanes, air seals, air splitters, and engine casing parts. Aromatic vinyl capped addition polyimides are obtained by reacting a diamine, an ester of tetracarboxylic acid, and an aromatic vinyl compound. Low void materials with improved oxidative stability when exposed to 700 F air may be fabricated as fiber reinforced high molecular weight capped polyimide composites. The aromatic vinyl capped polyimides are provided with a more aromatic nature and are more thermally stable than highly aliphatic, norbornenyl-type end-capped polyimides employed in PMR resins. The substitution of aromatic vinyl end-caps for norbornenyl end-caps in addition polyimides results in polymers with improved oxidative stability.

  8. [Biologically active food additives].

    PubMed

    Velichko, M A; Shevchenko, V P

    1998-07-01

    More than half out of 40 projects for the medical science development by the year of 2000 have been connected with the bio-active edible additives that are called "the food of XXI century", non-pharmacological means for many diseases. Most of these additives--nutricevtics and parapharmacevtics--are intended for the enrichment of food rations for the sick or healthy people. The ecologicaly safest and most effective are combined domestic adaptogens with immuno-modulating and antioxidating action that give anabolic and stimulating effect,--"leveton", "phytoton" and "adapton". The MKTs-229 tablets are residue discharge means. For atherosclerosis and general adiposis they recommend "tsar tablets" and "aiconol (ikhtien)"--on the base of cod-liver oil or "splat" made out of seaweed (algae). All these preparations have been clinically tested and received hygiene certificates from the Institute of Dietology of the Russian Academy of Medical Science. PMID:9752776

  9. Electrophilic addition of astatine

    SciTech Connect

    Norseev, Yu.V.; Vasaros, L.; Nhan, D.D.; Huan, N.K.

    1988-03-01

    It has been shown for the first time that astatine is capable of undergoing addition reactions to unsaturated hydrocarbons. A new compound of astatine, viz., ethylene astatohydrin, has been obtained, and its retention numbers of squalane, Apiezon, and tricresyl phosphate have been found. The influence of various factors on the formation of ethylene astatohydrin has been studied. It has been concluded on the basis of the results obtained that the univalent cations of astatine in an acidic medium is protonated hypoastatous acid.

  10. Hydrocarbon fuel additive

    SciTech Connect

    Ambrogio, S.

    1989-02-28

    This patent describes the method of fuel storage or combustion, wherein the fuel supply contains small amounts of water, the step of adding to the fuel supply an additive comprising a blend of a hydrophilic agent chosen from the group of ethylene glycol, n-butyl alcohol, and cellosolve in the range of 22-37% by weight; ethoxylated nonylphenol in the range of 26-35% by weight; nonylphenol polyethylene glycol ether in the range of 32-43% by weight.

  11. Functional Generalized Additive Models.

    PubMed

    McLean, Mathew W; Hooker, Giles; Staicu, Ana-Maria; Scheipl, Fabian; Ruppert, David

    2014-01-01

    We introduce the functional generalized additive model (FGAM), a novel regression model for association studies between a scalar response and a functional predictor. We model the link-transformed mean response as the integral with respect to t of F{X(t), t} where F(·,·) is an unknown regression function and X(t) is a functional covariate. Rather than having an additive model in a finite number of principal components as in Müller and Yao (2008), our model incorporates the functional predictor directly and thus our model can be viewed as the natural functional extension of generalized additive models. We estimate F(·,·) using tensor-product B-splines with roughness penalties. A pointwise quantile transformation of the functional predictor is also considered to ensure each tensor-product B-spline has observed data on its support. The methods are evaluated using simulated data and their predictive performance is compared with other competing scalar-on-function regression alternatives. We illustrate the usefulness of our approach through an application to brain tractography, where X(t) is a signal from diffusion tensor imaging at position, t, along a tract in the brain. In one example, the response is disease-status (case or control) and in a second example, it is the score on a cognitive test. R code for performing the simulations and fitting the FGAM can be found in supplemental materials available online. PMID:24729671

  12. Numerical analysis of randomly forced glycolitic oscillations

    SciTech Connect

    Ryashko, Lev

    2015-03-10

    Randomly forced glycolytic oscillations in Higgins model are studied both numerically and analytically. Numerical analysis is based on the direct simulation of the solutions of stochastic system. Non-uniformity of the stochastic bundle along the deterministic cycle is shown. For the analytical investigation of the randomly forced Higgins model, the stochastic sensitivity function technique and confidence domains method are applied. Results of the influence of additive noise on the cycle of this model are given.

  13. Sensing Current and Forces with SPM

    SciTech Connect

    Park, Jeong Y.; Maier, Sabine; Hendriksen, Bas; Salmeron, Miquel

    2010-07-02

    Atomic force microscopy (AFM) and scanning tunneling microscopy (STM) are well established techniques to image surfaces and to probe material properties at the atomic and molecular scale. In this review, we show hybrid combinations of AFM and STM that bring together the best of two worlds: the simultaneous detection of atomic scale forces and conduction properties. We illustrate with several examples how the detection of forces during STM and the detection of currents during AFM can give valuable additional information of the nanoscale material properties.

  14. 2. Southeast side of addition. View to northwest. Offutt ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    2. Southeast side of addition. View to northwest. - Offutt Air Force Base, Looking Glass Airborne Command Post, Aerospace Ground Equipment (AGE) Storage Facility, Far Northwest end of Project Looking Glass Historic District, Bellevue, Sarpy County, NE

  15. 5. General interior overview of addition. View to south. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. General interior overview of addition. View to south. - Offutt Air Force Base, Looking Glass Airborne Command Post, Aerospace Ground Equipment (AGE) Storage Facility, Far Northwest end of Project Looking Glass Historic District, Bellevue, Sarpy County, NE

  16. 6. General interior overview of addition. View to northwest. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    6. General interior overview of addition. View to northwest. - Offutt Air Force Base, Looking Glass Airborne Command Post, Aerospace Ground Equipment (AGE) Storage Facility, Far Northwest end of Project Looking Glass Historic District, Bellevue, Sarpy County, NE

  17. 3. Northwest side and southwest rear of addition. View to ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    3. Northwest side and southwest rear of addition. View to east. - Offutt Air Force Base, Looking Glass Airborne Command Post, Aerospace Ground Equipment (AGE) Storage Facility, Far Northwest end of Project Looking Glass Historic District, Bellevue, Sarpy County, NE

  18. Interior view of addition pharmacy showing dutch door and security ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Interior view of addition pharmacy showing dutch door and security ceiling grate, facing north. - Albrook Air Force Station, Dispensary, East side of Canfield Avenue, Balboa, Former Panama Canal Zone, CZ

  19. Linearly Forced Isotropic Turbulence

    NASA Technical Reports Server (NTRS)

    Lundgren, T. S.

    2003-01-01

    Stationary isotropic turbulence is often studied numerically by adding a forcing term to the Navier-Stokes equation. This is usually done for the purpose of achieving higher Reynolds number and longer statistics than is possible for isotropic decaying turbulence. It is generally accepted that forcing the Navier-Stokes equation at low wave number does not influence the small scale statistics of the flow provided that there is wide separation between the largest and smallest scales. It will be shown, however, that the spectral width of the forcing has a noticeable effect on inertial range statistics. A case will be made here for using a broader form of forcing in order to compare computed isotropic stationary turbulence with (decaying) grid turbulence. It is shown that using a forcing function which is directly proportional to the velocity has physical meaning and gives results which are closer to both homogeneous and non-homogeneous turbulence. Section 1 presents a four part series of motivations for linear forcing. Section 2 puts linear forcing to a numerical test with a pseudospectral computation.

  20. Turbomachinery rotor forces

    NASA Technical Reports Server (NTRS)

    Arndt, Norbert

    1988-01-01

    The fluid-induced forces, both steady and unsteady, acting upon an impeller of a centrifugal pump, and impeller blade-diffuser vane interaction in centrifugal pumps with vaned radial diffusers were evaluated experimentally and theoretically. Knowledge of the steady and unsteady forces, and the associated rotordynamic coefficients are required to effectively model the rotor dynamics of the High Pressure Fuel Turbopump (HPFTP) of the Space Shuttle Main Engine (SSME). These forces and rotordynamic coefficients were investigated using different impellers in combination with volutes and vaned diffusers, and axial inducers. These rotor forces are global. Local forces and pressures are also important in impeller-diffuser interaction, for they may cause cavitation damage and even vane failures. Thus, in a separate investigation, impeller wake, and impeller blade and diffuser vane pressure measurements were made. The nature of the rotordynamic forces is discussed, the experimental facility is described, and the measurements of unsteady forces and pressure are reported together with a brief and incomplete attempt to calculate these flows.

  1. Stable dynamics in forced systems with sufficiently high/low forcing frequency.

    PubMed

    Bartuccelli, M; Gentile, G; Wright, J A

    2016-08-01

    We consider parametrically forced Hamiltonian systems with one-and-a-half degrees of freedom and study the stability of the dynamics when the frequency of the forcing is relatively high or low. We show that, provided the frequency is sufficiently high, Kolmogorov-Arnold-Moser (KAM) theorem may be applied even when the forcing amplitude is far away from the perturbation regime. A similar result is obtained for sufficiently low frequency, but in that case we need the amplitude of the forcing to be not too large; however, we are still able to consider amplitudes which are outside of the perturbation regime. In addition, we find numerically that the dynamics may be stable even when the forcing amplitude is very large, well beyond the range of validity of the analytical results, provided the frequency of the forcing is taken correspondingly low. PMID:27586604

  2. OOTW Force Design Tools

    SciTech Connect

    Bell, R.E.; Hartley, D.S.III; Packard, S.L.

    1999-05-01

    This report documents refined requirements for tools to aid the process of force design in Operations Other Than War (OOTWs). It recommends actions for the creation of one tool and work on other tools relating to mission planning. It also identifies the governmental agencies and commands with interests in each tool, from whom should come the user advisory groups overseeing the respective tool development activities. The understanding of OOTWs and their analytical support requirements has matured to the point where action can be taken in three areas: force design, collaborative analysis, and impact analysis. While the nature of the action and the length of time before complete results can be expected depends on the area, in each case the action should begin immediately. Force design for OOTWs is not a technically difficult process. Like force design for combat operations, it is a process of matching the capabilities of forces against the specified and implied tasks of the operation, considering the constraints of logistics, transport and force availabilities. However, there is a critical difference that restricts the usefulness of combat force design tools for OOTWs: the combat tools are built to infer non-combat capability requirements from combat capability requirements and cannot reverse the direction of the inference, as is required for OOTWs. Recently, OOTWs have played a larger role in force assessment, system effectiveness and tradeoff analysis, and concept and doctrine development and analysis. In the first Quadrennial Defense Review (QDR), each of the Services created its own OOTW force design tool. Unfortunately, the tools address different parts of the problem and do not coordinate the use of competing capabilities. These tools satisfied the immediate requirements of the QDR, but do not provide a long-term cost-effective solution.

  3. Manual discrimination of force

    NASA Technical Reports Server (NTRS)

    Pang, Xiao-Dong; Tan, HONG-Z.; Durlach, Nathaniel I.

    1991-01-01

    Optimal design of human-machine interfaces for teleoperators and virtual-environment systems which involve the tactual and kinesthetic modalities requires knowledge of the human's resolving power in these modalities. The resolution of the interface should be appropriately matched to that of the human operator. We report some preliminary results on the ability of the human hand to distinguish small differences in force under a variety of conditions. Experiments were conducted on force discrimination with the thumb pushing an interface that exerts a constant force over the pushing distance and the index finger pressing against a fixed support. The dependence of the sensitivity index d' on force increment can be fit by a straight line through the origin and the just-noticeable difference (JND) in force can thus be described by the inverse of the slope of this line. The receiver operating characteristic (ROC) was measured by varying the a priori probabilities of the two alternatives, reference force and reference force plus an increment, in one-interval, two-alternative, forced-choice experiments. When plotted on normal deviate coordinates, the ROC's were roughly straight lines of unit slope, thus supporting the assumption of equal-variance normal distributions and the use of the conventional d' measure. The JND was roughly 6-8 percent for reference force ranging from 2.5 to 10 newtons, pushing distance from 5 to 30 mm, and initial finger-span from 45 to 125 mm. Also, the JND remained the same when the subjects were instructed to change the average speed of pushing from 23 to 153 mm/sec. The pushing was terminated by reaching either a wall or a well, and the JND's were essentially the same in both cases.

  4. Siloxane containing addition polyimides

    NASA Technical Reports Server (NTRS)

    Maudgal, S.; St. Clair, T. L.

    1984-01-01

    Addition polyimide oligomers have been synthesized from bis(gamma-aminopropyl) tetramethyldisiloxane and 3, 3', 4, 4'-benzophenonetetracarboxylic dianhydride using a variety of latent crosslinking groups as endcappers. The prepolymers were isolated and characterized for solubility (in amide, chlorinated and ether solvents), melt flow and cure properties. The most promising systems, maleimide and acetylene terminated prepolymers, were selected for detailed study. Graphite cloth reinforced composites were prepared and properties compared with those of graphite/Kerimid 601, a commercially available bismaleimide. Mixtures of the maleimide terminated system with Kerimid 601, in varying proportions, were also studied.

  5. Oil additive process

    SciTech Connect

    Bishop, H.

    1988-10-18

    This patent describes a method of making an additive comprising: (a) adding 2 parts by volume of 3% sodium hypochlorite to 45 parts by volume of diesel oil fuel to form a sulphur free fuel, (b) removing all water and foreign matter formed by the sodium hypochlorite, (c) blending 30 parts by volume of 24% lead naphthanate with 15 parts by volume of the sulphur free fuel, 15 parts by volume of light-weight material oil to form a blended mixture, and (d) heating the blended mixture slowly and uniformly to 152F.

  6. Dilatonic Entropic Force

    NASA Astrophysics Data System (ADS)

    Sakalli, I.

    2011-08-01

    We show in detail that the entropic force of the static spherically symmetric spacetimes with unusual asymptotics can be calculated through the Verlinde's arguments. We introduce three different holographic screen candidates, which are first employed thoroughly by Myung and Kim [Phys. Rev. D 81, 105012 (2010)] for Schwarzschild black hole solutions, in order to identify the entropic force arising between a charged dilaton black hole and a test particle. The significance of the dilaton parameter on the entropic force is highlighted, and shown graphically.

  7. Quantized Casimir force.

    PubMed

    Tse, Wang-Kong; MacDonald, A H

    2012-12-01

    We investigate the Casimir effect between two-dimensional electron systems driven to the quantum Hall regime by a strong perpendicular magnetic field. In the large-separation (d) limit where retardation effects are essential, we find (i) that the Casimir force is quantized in units of 3ħcα(2)/8π(2)d(4) and (ii) that the force is repulsive for mirrors with the same type of carrier and attractive for mirrors with opposite types of carrier. The sign of the Casimir force is therefore electrically tunable in ambipolar materials such as graphene. The Casimir force is suppressed when one mirror is a charge-neutral graphene system in a filling factor ν=0 quantum Hall state. PMID:23368242

  8. Forces in Motion.

    ERIC Educational Resources Information Center

    Goodsell, David; And Others

    1995-01-01

    Describes an activity to give students experience with the variables and forces impacting a moving body on an inclined plane by observing a ball as it rolls down an inclined PVC pipe of fixed length. Includes a student worksheet. (MKR)

  9. Force Field Development and Molecular Dynamics of [NiFe] Hydrogenase

    SciTech Connect

    Smith, Dayle MA; Xiong, Yijia; Straatsma, TP; Rosso, Kevin M.; Squier, Thomas C.

    2012-05-09

    Classical molecular force-field parameters describing the structure and motion of metal clusters in [NiFe] hydrogenase enzymes can be used to compare the dynamics and thermodynamics of [NiFe] under different oxidation, protonation, and ligation circumstances. Using density functional theory (DFT) calculations of small model clusters representative of the active site and the proximal, medial, and distal Fe/S metal centers and their attached protein side chains, we have calculated classical force-field parameters for [NiFe] in reduced and oxidized states, including internal coordinates, force constants, and atom-centered charges. Derived force constants revealed that cysteinate ligands bound to the metal ions are more flexible in the Ni-B active site, which has a bridging hydroxide ligand, than in the Ni-C active site, which has a bridging hydride. Ten nanosecond all-atom, explicit-solvent MD simulations of [NiFe] hydrogenase in oxidized and reduced catalytic states established the stability of the derived force-field parameters in terms of C{alpha} and metal cluster fluctuations. Average active site structures from the protein MD simulations are consistent with [NiFe] structures from the Protein Data Bank, suggesting that the derived force-field parameters are transferrable to other hydrogenases beyond the structure used for testing. A comparison of experimental H{sub 2}-production rates demonstrated a relationship between cysteinate side chain rotation and activity, justifying the use of a fully dynamic model of [NiFe] metal cluster motion.

  10. Measurement of the Bichromatic Force in 1-D

    NASA Astrophysics Data System (ADS)

    Williams, M. R.; Chi, F.; Cashen, M. T.; Metcalf, H. J.

    1998-05-01

    We have demonstrated atomic beam steering using the bichromatic force(J. Söding et al)., Phys. Rev. Lett. 78, 1420 (1997).. This force is large and has the same sign for all velocities between v \\cong ± δ / 2 k for counterpropagating laser beams each having frequencies ω ± δ. Thus, all atoms with |v| < δ / 2 k are eventually accelerated to v \\cong δ/ 2 k. With a frequency shift Δ of both components of one laser beam relative to the other, this description is appropriate for a reference frame moving at v=Δ/2k. A terminal velocity of v=0 in the lab frame can be achieved by choosing Δ=δ. The four frequencies needed for this scheme can be generated with a single AOM (at drive frequency δ) with almost no wasted light. This is done by equalizing the power in the unshifted and 1^st order up-shifted beams, and then retroreflecting both through the AOM. Two spatially separated output beams are created, one with ω ± δ and the other with ω and ω + 2δ. With these frequencies, the moving frame has velocity v=δ / 2 k which is just what is needed to produce a beam at v=0 in the lab frame. Using δ=2π × 50 MHz the capture angle for Rb at 350 m/s is 0.1 radian.

  11. Repulsive force actuated rotary micromirror

    NASA Astrophysics Data System (ADS)

    He, Siyuan; Ben Mrad, Ridha

    2004-09-01

    In this paper, a novel repulsive force based rotary micromirror is proposed. A repulsive force is produced in the rotary micromirror and the mirror plate is pushed up and away from the substrate. Therefore the rotation angle of the micromirror is not limited to the space underneath the mirror plate and thus the "pull-in" effect is completely circumvented. The novel rotary micromirror can achieve a large rotation angle with a large mirror plate. In addition the novel micromirror has a very simple structure and can be fabricated by standard surface micromachining technology. Numerical simulation is used to verify the working principle of the novel micromirror. A prototype of the novel rotary micromirror is fabricated by a commercially available surface microfabrication process called MUMPs. The prototype has a mirror size of 300μm x 300μm. The experimental measurements show that the prototype can achieve a mechanical rotation of 2.25 degrees (an optical angle of 4.5 degrees) at a driving voltage of 170 volts. A conventional surface micromachined attractive force based rotary micromirror of the same size can only achieve an angle of 0.1~0.2 degree.

  12. Performance Boosting Additive

    NASA Technical Reports Server (NTRS)

    1999-01-01

    Mainstream Engineering Corporation was awarded Phase I and Phase II contracts from Goddard Space Flight Center's Small Business Innovation Research (SBIR) program in early 1990. With support from the SBIR program, Mainstream Engineering Corporation has developed a unique low cost additive, QwikBoost (TM), that increases the performance of air conditioners, heat pumps, refrigerators, and freezers. Because of the energy and environmental benefits of QwikBoost, Mainstream received the Tibbetts Award at a White House Ceremony on October 16, 1997. QwikBoost was introduced at the 1998 International Air Conditioning, Heating, and Refrigeration Exposition. QwikBoost is packaged in a handy 3-ounce can (pressurized with R-134a) and will be available for automotive air conditioning systems in summer 1998.

  13. Sewage sludge additive

    NASA Technical Reports Server (NTRS)

    Kalvinskas, J. J.; Mueller, W. A.; Ingham, J. D. (Inventor)

    1980-01-01

    The additive is for a raw sewage treatment process of the type where settling tanks are used for the purpose of permitting the suspended matter in the raw sewage to be settled as well as to permit adsorption of the dissolved contaminants in the water of the sewage. The sludge, which settles down to the bottom of the settling tank is extracted, pyrolyzed and activated to form activated carbon and ash which is mixed with the sewage prior to its introduction into the settling tank. The sludge does not provide all of the activated carbon and ash required for adequate treatment of the raw sewage. It is necessary to add carbon to the process and instead of expensive commercial carbon, coal is used to provide the carbon supplement.

  14. Perspectives on Additive Manufacturing

    NASA Astrophysics Data System (ADS)

    Bourell, David L.

    2016-07-01

    Additive manufacturing (AM) has skyrocketed in visibility commercially and in the public sector. This article describes the development of this field from early layered manufacturing approaches of photosculpture, topography, and material deposition. Certain precursors to modern AM processes are also briefly described. The growth of the field over the last 30 years is presented. Included is the standard delineation of AM technologies into seven broad categories. The economics of AM part generation is considered, and the impacts of the economics on application sectors are described. On the basis of current trends, the future outlook will include a convergence of AM fabricators, mass-produced AM fabricators, enabling of topology optimization designs, and specialization in the AM legal arena. Long-term developments with huge impact are organ printing and volume-based printing.

  15. New addition curing polyimides

    NASA Technical Reports Server (NTRS)

    Frimer, Aryeh A.; Cavano, Paul

    1991-01-01

    In an attempt to improve the thermal-oxidative stability (TOS) of PMR-type polymers, the use of 1,4-phenylenebis (phenylmaleic anhydride) PPMA, was evaluated. Two series of nadic end-capped addition curing polyimides were prepared by imidizing PPMA with either 4,4'-methylene dianiline or p-phenylenediamine. The first resulted in improved solubility and increased resin flow while the latter yielded a compression molded neat resin sample with a T(sub g) of 408 C, close to 70 C higher than PME-15. The performance of these materials in long term weight loss studies was below that of PMR-15, independent of post-cure conditions. These results can be rationalized in terms of the thermal lability of the pendant phenyl groups and the incomplete imidization of the sterically congested PPMA. The preparation of model compounds as well as future research directions are discussed.

  16. Strategic forces briefing

    SciTech Connect

    Bing, G.; Chrzanowski, P.; May, M.; Nordyke, M.

    1989-04-06

    The Strategic Forces Briefing'' is our attempt, accomplished over the past several months, to outline and highlight the more significant strategic force issues that must be addressed in the near future. Some issues are recurrent: the need for an effective modernized Triad and a constant concern for force survivability. Some issues derive from arms control: the Strategic Arms Reduction Talks (SALT) are sufficiently advanced to set broad numerical limits on forces, but not so constraining as to preclude choices among weapon systems and deployment modes. Finally, a new administration faced with serious budgetary problems must strive for the most effective strategic forces limited dollars can buy and support. A review of strategic forces logically begins with consideration of the missions the forces are charged with. We begin the briefing with a short review of targeting policy and implementation within the constraints of available unclassified information. We then review each element of the Triad with sections on SLBMs, ICBMs, and Air-Breathing (bomber and cruise missile) systems. A short section at the end deals with the potential impact of strategic defense on offensive force planning. We consider ABM, ASAT, and air defense; but we do not attempt to address the technical issues of strategic defense per se. The final section gives a brief overview of the tritium supply problem. We conclude with a summary of recommendations that emerge from our review. The results of calculation on the effectiveness of various weapon systems as a function of cost that are presented in the briefing are by Paul Chrzanowski.

  17. Force-Measuring Clamp

    NASA Technical Reports Server (NTRS)

    Nunnelee, Mark (Inventor)

    2004-01-01

    A precision clamp that accurately measures force over a wide range of conditions is described. Using a full bridge or other strain gage configuration. the elastic deformation of the clamp is measured or detected by the strain gages. Thc strain gages transmit a signal that corresponds to the degree of stress upon the clamp. Thc strain gage signal is converted to a numeric display. Calibration is achieved by ero and span potentiometers which enable accurate measurements by the force-measuring clamp.

  18. Force user's manual, revised

    NASA Technical Reports Server (NTRS)

    Jordan, Harry F.; Benten, Muhammad S.; Arenstorf, Norbert S.; Ramanan, Aruna V.

    1987-01-01

    A methodology for writing parallel programs for shared memory multiprocessors has been formalized as an extension to the Fortran language and implemented as a macro preprocessor. The extended language is known as the Force, and this manual describes how to write Force programs and execute them on the Flexible Computer Corporation Flex/32, the Encore Multimax and the Sequent Balance computers. The parallel extension macros are described in detail, but knowledge of Fortran is assumed.

  19. Van der Waals Forces

    NASA Astrophysics Data System (ADS)

    Parsegian, V. Adrian

    2006-03-01

    This should prove to be the definitive work explaining van der Waals forces, how to calculate them and take account of their impact under any circumstances and conditions. These weak intermolecular forces are of truly pervasive impact, and biologists, chemists, physicists and engineers will profit greatly from the thorough grounding in these fundamental forces that this book offers. Parsegian has organized his book at three successive levels of mathematical sophistication, to satisfy the needs and interests of readers at all levels of preparation. The Prelude and Level 1 are intended to give everyone an overview in words and pictures of the modern theory of van der Waals forces. Level 2 gives the formulae and a wide range of algorithms to let readers compute the van der Waals forces under virtually any physical or physiological conditions. Level 3 offers a rigorous basic formulation of the theory. Author is among the most highly respected biophysicists Van der Waals forces are significant for a wide range of questions and problems in the life sciences, chemistry, physics, and engineering, ranging up to the macro level No other book that develops the subject vigorously, and this book also makes the subject intuitively accessible to students who had not previously been mathematically sophisticated enough to calculate them

  20. Optical Bernoulli forces

    NASA Astrophysics Data System (ADS)

    Movassagh, Ramis; Johnson, Steven G.

    2013-08-01

    By Bernoulli's law, an increase in the relative speed of a fluid around a body is accompanied by a decrease in the pressure. Therefore, a rotating body in a fluid stream experiences a force perpendicular to the motion of the fluid because of the unequal relative speed of the fluid across its surface. It is well known that light has a constant speed irrespective of the relative motion. Does a rotating body immersed in a stream of photons experience a Bernoulli-like force? We show that, indeed, a rotating dielectric cylinder experiences such a lateral force from an electromagnetic wave. In fact, the sign of the lateral force is the same as that of the fluid-mechanical analog as long as the electric susceptibility is positive (ɛ>ɛ0), but for negative-susceptibility materials (e.g., metals) we show that the lateral force is in the opposite direction. Because these results are derived from a classical electromagnetic scattering problem, Mie-resonance enhancements that occur in other scattering phenomena also enhance the lateral force.

  1. Forced wetting and hydrodynamic assist

    NASA Astrophysics Data System (ADS)

    Blake, Terence D.; Fernandez-Toledano, Juan-Carlos; Doyen, Guillaume; De Coninck, Joël

    2015-11-01

    Wetting is a prerequisite for coating a uniform layer of liquid onto a solid. Wetting failure and air entrainment set the ultimate limit to coating speed. It is well known in the coating art that this limit can be postponed by manipulating the coating flow to generate what has been termed "hydrodynamic assist," but the underlying mechanism is unclear. Experiments have shown that the conditions that postpone air entrainment also reduce the apparent dynamic contact angle, suggesting a direct link, but how the flow might affect the contact angle remains to be established. Here, we use molecular dynamics to compare the outcome of steady forced wetting with previous results for the spontaneous spreading of liquid drops and apply the molecular-kinetic theory of dynamic wetting to rationalize our findings and place them on a quantitative footing. The forced wetting simulations reveal significant slip at the solid-liquid interface and details of the flow immediately adjacent to the moving contact line. Our results confirm that the local, microscopic contact angle is dependent not simply only on the velocity of wetting but also on the nature of the flow that drives it. In particular, they support an earlier suggestion that during forced wetting, an intense shear stress in the vicinity of the contact line can assist surface tension forces in promoting dynamic wetting, thus reducing the velocity-dependence of the contact angle. Hydrodynamic assist then appears as a natural consequence of wetting that emerges when the contact line is driven by a strong and highly confined flow. Our theoretical approach also provides a self-consistent model of molecular slip at the solid-liquid interface that enables its magnitude to be estimated from dynamic contact angle measurements. In addition, the model predicts how hydrodynamic assist and slip may be influenced by liquid viscosity and solid-liquid interactions.

  2. Feedback Control of Floor Reaction Force Based on Force-Reflecting-Type Multilateral Control

    NASA Astrophysics Data System (ADS)

    Nagase, Kazuki; Katsura, Seiichiro

    Real-world haptics is being studied not only for improving feedback on real-world haptic information in teleoperation but also for developing key technologies for future human support. For the remote operating of systems at distant places, haptic information is required in addition to visual information. The haptic information around a work environment can be the floor reaction force, which can be obtained using a movement-type haptic device. The floor reaction force from the environment that the mobile haptic device touches is fed back accurately to the operator. First, this paper proposes a general force-reflecting-type multilateral control. Second, this paper extends the control to feedback control of the floor reaction force by using force-reflecting-type multilateral control and a novel haptic device employing a biped robot with a slave system. The position response of a master system is transformed to a leg tip position command for the biped-type haptic device. In addition, the floor reaction force determined by the biped-type haptic device is fed back to the master system. The proposed method can determine the force feedback to the sole of the foot, which is not possible with a conventional stationary system. As a result, the floor reaction force from a large area can be obtained, and the operability of the control system is improved by using the proposed system.

  3. Forces between silica particles in the presence of multivalent cations.

    PubMed

    Valmacco, Valentina; Elzbieciak-Wodka, Magdalena; Herman, David; Trefalt, Gregor; Maroni, Plinio; Borkovec, Michal

    2016-06-15

    Forces between negatively charged silica particles in aqueous electrolyte solutions were measured with the colloidal probe technique based on the atomic force microscope (AFM). The present study focuses on the comparison of monovalent and multivalent counterions, namely K(+), Mg(2+), and La(3+). The force profiles can be well described with the theory of Derjaguin, Landau, Verwey, and Overbeek (DLVO) down to distances of about 4nm. At smaller distances, the forces become strongly repulsive due to additional non-DLVO repulsion. In the presence of La(3+), one observes an additional attractive force with a range of about 1nm at intermediate salt concentrations. This force is probably related to ion-ion correlations, but could also be influenced by surface charge heterogeneities or charge fluctuation forces. PMID:27016916

  4. Backbone additivity in the transfer model of protein solvation

    PubMed Central

    Hu, Char Y; Kokubo, Hironori; Lynch, Gillian C; Bolen, D Wayne; Pettitt, B Montgomery

    2010-01-01

    The transfer model implying additivity of the peptide backbone free energy of transfer is computationally tested. Molecular dynamics simulations are used to determine the extent of change in transfer free energy (ΔGtr) with increase in chain length of oligoglycine with capped end groups. Solvation free energies of oligoglycine models of varying lengths in pure water and in the osmolyte solutions, 2M urea and 2M trimethylamine N-oxide (TMAO), were calculated from simulations of all atom models, and ΔGtr values for peptide backbone transfer from water to the osmolyte solutions were determined. The results show that the transfer free energies change linearly with increasing chain length, demonstrating the principle of additivity, and provide values in reasonable agreement with experiment. The peptide backbone transfer free energy contributions arise from van der Waals interactions in the case of transfer to urea, but from electrostatics on transfer to TMAO solution. The simulations used here allow for the calculation of the solvation and transfer free energy of longer oligoglycine models to be evaluated than is currently possible through experiment. The peptide backbone unit computed transfer free energy of −54 cal/mol/M compares quite favorably with −43 cal/mol/M determined experimentally. PMID:20306490

  5. Backbone Additivity in the Transfer Model of Protein Solvation

    SciTech Connect

    Hu, Char Y.; Kokubo, Hironori; Lynch, Gillian C.; Bolen, D Wayne; Pettitt, Bernard M.

    2010-05-01

    The transfer model implying additivity of the peptide backbone free energy of transfer is computationally tested. Molecular dynamics simulations are used to determine the extent of change in transfer free energy (ΔGtr) with increase in chain length of oligoglycine with capped end groups. Solvation free energies of oligoglycine models of varying lengths in pure water and in the osmolyte solutions, 2M urea and 2M trimethylamine N-oxide (TMAO), were calculated from simulations of all atom models, and ΔGtr values for peptide backbone transfer from water to the osmolyte solutions were determined. The results show that the transfer free energies change linearly with increasing chain length, demonstrating the principle of additivity, and provide values in reasonable agreement with experiment. The peptide backbone transfer free energy contributions arise from van der Waals interactions in the case of transfer to urea, but from electrostatics on transfer to TMAO solution. The simulations used here allow for the calculation of the solvation and transfer free energy of longer oligoglycine models to be evaluated than is currently possible through experiment. The peptide backbone unit computed transfer free energy of –54 cal/mol/Mcompares quite favorably with –43 cal/mol/M determined experimentally.

  6. Satellite Remote Sensing of Aerosol Forcing

    NASA Technical Reports Server (NTRS)

    Remer, Lorraine; Kaufman, Yoram; Ramaprasad, Jaya; Procopio, Aline; Levin, Zev

    1999-01-01

    The role of aerosol forcing remains one of the largest uncertainties in estimating man's impact on the global climate system. One school of thought suggests that remote sensing by satellite sensors will provide the data necessary to narrow these uncertainties. While satellite measurements of direct aerosol forcing appear to be straightforward, satellite measurements of aerosol indirect forcing will be more complicated. Pioneering studies identified indirect aerosol forcing using AVHRR data in the biomass burning regions of Brazil. We have expanded this analysis with AVHRR to include an additional year of data and assimilated water vapor fields. The results show similar latitudinal dependence as reported by Kaufman and Fraser, but by using water vapor observations we conclude that latitude is not a proxy for water vapor and the strength of the indirect effect is not correlated to water vapor amounts. In addition to the AVHRR study we have identified indirect aerosol forcing in Brazil at much smaller spatial scales using the MODIS Airborne Simulator. The strength of the indirect effect appears to be related to cloud type and cloud dynamics. There is a suggestion that some of the cloud dynamics may be influenced by smoke destabilization of the atmospheric column. Finally, this study attempts to quantify remote sensing limitations due to the accuracy limits of the retrieval algorithms. We use a combination of numerical aerosol transport models, ground-based AERONET data and ISCCP cloud climatology to determine how much of the forcing occurs in regions too clean to determine from satellite retrievals.

  7. Lenz's Law: Feel the Force.

    ERIC Educational Resources Information Center

    Sawicki, Charles A.

    1996-01-01

    Describes a simple, inexpensive system that allows students to have hands-on contact with simple experiments involving forces generated by induced currents. Discusses the use of a dynamic force sensor in making quantitative measurements of the forces generated. (JRH)

  8. Piezoresistive cantilever force-clamp system

    SciTech Connect

    Park, Sung-Jin; Petzold, Bryan C.; Pruitt, Beth L.; Goodman, Miriam B.

    2011-04-15

    We present a microelectromechanical device-based tool, namely, a force-clamp system that sets or ''clamps'' the scaled force and can apply designed loading profiles (e.g., constant, sinusoidal) of a desired magnitude. The system implements a piezoresistive cantilever as a force sensor and the built-in capacitive sensor of a piezoelectric actuator as a displacement sensor, such that sample indentation depth can be directly calculated from the force and displacement signals. A programmable real-time controller operating at 100 kHz feedback calculates the driving voltage of the actuator. The system has two distinct modes: a force-clamp mode that controls the force applied to a sample and a displacement-clamp mode that controls the moving distance of the actuator. We demonstrate that the system has a large dynamic range (sub-nN up to tens of {mu}N force and nm up to tens of {mu}m displacement) in both air and water, and excellent dynamic response (fast response time, <2 ms and large bandwidth, 1 Hz up to 1 kHz). In addition, the system has been specifically designed to be integrated with other instruments such as a microscope with patch-clamp electronics. We demonstrate the capabilities of the system by using it to calibrate the stiffness and sensitivity of an electrostatic actuator and to measure the mechanics of a living, freely moving Caenorhabditis elegans nematode.

  9. Piezoresistive cantilever force-clamp system

    PubMed Central

    Park, Sung-Jin; Petzold, Bryan C.; Goodman, Miriam B.; Pruitt, Beth L.

    2011-01-01

    We present a microelectromechanical device-based tool, namely, a force-clamp system that sets or “clamps” the scaled force and can apply designed loading profiles (e.g., constant, sinusoidal) of a desired magnitude. The system implements a piezoresistive cantilever as a force sensor and the built-in capacitive sensor of a piezoelectric actuator as a displacement sensor, such that sample indentation depth can be directly calculated from the force and displacement signals. A programmable real-time controller operating at 100 kHz feedback calculates the driving voltage of the actuator. The system has two distinct modes: a force-clamp mode that controls the force applied to a sample and a displacement-clamp mode that controls the moving distance of the actuator. We demonstrate that the system has a large dynamic range (sub-nN up to tens of μN force and nm up to tens of μm displacement) in both air and water, and excellent dynamic response (fast response time, <2 ms and large bandwidth, 1 Hz up to 1 kHz). In addition, the system has been specifically designed to be integrated with other instruments such as a microscope with patch-clamp electronics. We demonstrate the capabilities of the system by using it to calibrate the stiffness and sensitivity of an electrostatic actuator and to measure the mechanics of a living, freely moving Caenorhabditis elegans nematode. PMID:21529009

  10. Brief: Field measurements of casing tension forces

    SciTech Connect

    Quigley, M.S.; Lewis, D.B.; Boswell, R.S.

    1995-02-01

    Tension forces acting on individual casing joints were accurately measured during installation of 10,158 ft of 9 5/8-in. {times} 47-lbm/ft casing and 11,960 ft of 11 7/8-in. {times} 71.8-lbm/ft casing. A unique casing load table (CLT) weighed the casing string after the addition of each casing joint. Strain gauges attached inside the pin ends of instrumented casing joints (ICJ`s) directly measured tension force on those joints. A high-speed computer data-acquisition system (DAS) automatically recorded data from all the sensors. Several casing joints were intentionally subjected to extreme deceleration to determine upper limits for dynamic tension forces. Data from these tests clearly show effects of wellbore friction and casing handling conditions. In every case, tension forces in the casing during maximum deceleration were considerably less than expected. In some cases, the highest tension forces occurred when the casing lifted out of the slips. Peak tension forces caused by setting the casing slips were typically no more than 5% greater than tension forces in the casing at rest. This dynamic amplification was far less than the 60% value used in the previous casing design method. Reducing the safety factor for installation loads has permitted use of lighter, less-expensive casing than dictated by older design criteria.

  11. Impulsive Enzymes: A New Force in Mechanobiology

    PubMed Central

    Butler, Peter J.; Dey, Krishna K.; Sen, Ayusman

    2015-01-01

    We review studies that quantify newly discovered forces from single enzymatic reactions. These forces arise from the conversion of chemical energy to kinetic energy, which can be harnessed to direct diffusion of the enzyme up a concentration gradient of substrate, a novel phenomenon of molecular chemotaxis. When immobilized, enzymes can move fluid around them and perform directional pumping in microfluidic chambers. Because of the extensive array of enzymes in biological cells, we also develop three new hypotheses: that enzymatic self diffusion can assist in organizing signaling pathways in cells, can assist in pumping of fluid in cells, and can impose biologically significant forces on organelles, which will be manifested as stochastic motion not explained by thermal forces or myosin II. Such mechanochemical phenomena open up new directions in research in mechanobiology in which all enzymes, in addition to their primary function as catalysts for reactions, may have secondary functions as initiators of mechanosensitive transduction pathways. PMID:26019728

  12. Casimir Forces On A Silicon Micromechanical Chip

    SciTech Connect

    Zou, J.; Marset, zsolt; Rodriguez, A.W.; Reid, M. T.H.; McCauley, A. P.; Kravchenko, Ivan I; Bao, Y.; Johnson, S. G.; Chan, Ho Bun

    2013-01-01

    Quantum fluctuations give rise to van der Waals and Casimir forces that dominate the interaction between electrically neutral objects at sub-micron separations. Under the trend of miniaturization, such quantum electrodynamical effects are expected to play an important role in micro- and nano-mechanical devices. Nevertheless, so far the Casimir force has been experimentally observed only in situations involving an external object manually positioned close to a micromechanical element on a silicon chip. Here, we demonstrate the Casimir effect between two silicon components on the same substrate. In addition to providing an integrated and compact platform for Casimir force measurements, this scheme also opens the possibility of tailoring the Casimir force using lithographically defined components of non-conventional shapes on a single micromechanical chip.

  13. Contact Forces between TiO2 Nanoparticles Governed by an Interplay of Adsorbed Water Layers and Roughness.

    PubMed

    Laube, Jens; Salameh, Samir; Kappl, Michael; Mädler, Lutz; Colombi Ciacchi, Lucio

    2015-10-20

    Interparticle forces govern the mechanical behavior of granular matter and direct the hierarchical assembling of nanoparticles into supramolecular structures. Understanding how these forces change under different ambient conditions would directly benefit industrial-scale nanoparticle processing units such as filtering and fluidization. Here we rationalize and quantify the contributions of dispersion, capillary, and solvation forces between hydrophilic TiO2 nanoparticles with sub-10 nm diameter and show that the humidity dependence of the interparticle forces is governed by a delicate interplay between the structure of adsorbed water layers and the surface roughness. All-atom molecular dynamics modeling supported by force-spectroscopy experiments reveals an unexpected decrease in the contact forces at increasing humidity for nearly spherical particles, while the forces between rough particles are insensitive to strong humidity changes. Our results also frame the limits of applicability of discrete solvation and continuum capillary theories in a regime where interparticle forces are dominated by the molecular nature of surface adsorbates. PMID:26414448

  14. Linear force device

    NASA Technical Reports Server (NTRS)

    Clancy, John P.

    1988-01-01

    The object of the invention is to provide a mechanical force actuator which is lightweight and manipulatable and utilizes linear motion for push or pull forces while maintaining a constant overall length. The mechanical force producing mechanism comprises a linear actuator mechanism and a linear motion shaft mounted parallel to one another. The linear motion shaft is connected to a stationary or fixed housing and to a movable housing where the movable housing is mechanically actuated through actuator mechanism by either manual means or motor means. The housings are adapted to releasably receive a variety of jaw or pulling elements adapted for clamping or prying action. The stationary housing is adapted to be pivotally mounted to permit an angular position of the housing to allow the tool to adapt to skewed interfaces. The actuator mechanisms is operated by a gear train to obtain linear motion of the actuator mechanism.

  15. [Forced spirometry procedure].

    PubMed

    Cortés Aguilera, Antonio Javier

    2008-11-01

    Forced spirometry consists in a complementary test which is carried out in a health office in a workplace in order to determine the lung capacity of workers exposed to determined professional risks or those susceptible to determined working conditions which could lead to the development of respiratory problems. This test has been developed based on health vigilance laws under Article 22 of the Law for Prevention of Risks in the Workplace and requires that the technician, a nurse in a workplace, who performs it have some knowledge and skills regarding its use, following the norms for forced spirometry set by the Spanish Association for Pneumatology and Thoracic Surgery (SEPAR). PMID:19203116

  16. Air Force Seal Programs

    NASA Technical Reports Server (NTRS)

    Mayhew, Ellen R.

    1996-01-01

    Seal technology development is an important part of the Air Force's participation in the Integrated High Performance Turbine Engine Technology (IHPTET) initiative, the joint DOD, NASA, ARPA, and industry endeavor to double turbine engine capabilities by the turn of the century. Significant performance and efficiency improvements can be obtained through reducing internal flow system leakage, but seal environment requirements continue to become more extreme as the engine thermodynamic cycles advance towards these IHPTET goals. Seal technology continues to be pursued by the Air Force to control leakage at the required conditions. This presentation briefly describes current seal research and development programs and gives a summary of seal applications in demonstrator and developmental engines.

  17. Friction force measurements relevant to de-inking by means of atomic force microscope.

    PubMed

    Theander, Katarina; Pugh, Robert J; Rutland, Mark W

    2005-11-15

    In the pulping step of the de-inking process, the ink detaches from the fibers due to shear and physical chemical interaction. In order to get a better understanding of the forces involved between cellulose and ink, the atomic force microscope and the colloidal probe technique have been used in the presence of a model chemical dispersant (hexa-ethyleneglycol mono n-dodecyl ether, C12E6). A cellulose bead was used as the colloidal probe and three different lower surfaces have been used, an alkyd resin, mica and a cellulose sphere. The normal and lateral forces have been measured at a range of nonionic concentrations. It was found that the lateral sliding friction forces deceased with increasing surfactant concentration for both the alkyd resin and mica while no differences were observed for the cellulose surface. In addition, only a very small change in normal force could be detected for the alkyd surface as the concentration changed. PMID:15961095

  18. Radiative Forcing of Climate Change

    SciTech Connect

    Ramaswamy, V.; Boucher, Olivier; Haigh, J.; Hauglustaine, D.; Haywood, J.; Myhre, G.; Nakajima, Takahito; Shi, Guangyu; Solomon, S.; Betts, Robert E.; Charlson, R.; Chuang, C. C.; Daniel, J. S.; Del Genio, Anthony D.; Feichter, J.; Fuglestvedt, J.; Forster, P. M.; Ghan, Steven J.; Jones, A.; Kiehl, J. T.; Koch, D.; Land, C.; Lean, J.; Lohmann, Ulrike; Minschwaner, K.; Penner, Joyce E.; Roberts, D. L.; Rodhe, H.; Roelofs, G.-J.; Rotstayn, Leon D.; Schneider, T. L.; Schumann, U.; Schwartz, Stephen E.; Schwartzkopf, M. D.; Shine, K. P.; Smith, Steven J.; Stevenson, D. S.; Stordal, F.; Tegen, I.; van Dorland, R.; Zhang, Y.; Srinivasan, J.; Joos, Fortunat

    2001-10-01

    Chapter 6 of the IPCC Third Assessment Report Climate Change 2001: The Scientific Basis. Sections include: Executive Summary 6.1 Radiative Forcing 6.2 Forcing-Response Relationship 6.3 Well-Mixed Greenhouse Gases 6.4 Stratospheric Ozone 6.5 Radiative Forcing By Tropospheric Ozone 6.6 Indirect Forcings due to Chemistry 6.7 The Direct Radiative Forcing of Tropospheric Aerosols 6.8 The Indirect Radiative Forcing of Tropospheric Aerosols 6.9 Stratospheric Aerosols 6.10 Land-use Change (Surface Albedo Effect) 6.11 Solar Forcing of Climate 6.12 Global Warming Potentials hydrocarbons 6.13 Global Mean Radiative Forcings 6.14 The Geographical Distribution of the Radiative Forcings 6.15 Time Evolution of Radiative Forcings Appendix 6.1 Elements of Radiative Forcing Concept References.

  19. Parameterization and optimization of the menthol force field for molecular dynamics simulations.

    PubMed

    Jasik, Mateusz; Szefczyk, Borys

    2016-10-01

    Menthol's various biological properties render it a useful component for medical and cosmetological applications, while its three centers of asymmetry mean that it can be used in a range of organic reactions. Menthol-substituted ionic liquids (ILs) have been found to exhibit promising antimicrobial and antielectrostatic properties, as well as being useful in organic catalysis and biochemical studies. However, so far, a force field designed and validated specifically for the menthol molecule has not been constructed. In the present work, the validation and optimization of force field parameters with regard to the ability to reproduce the macroscopic properties of menthol is presented. The set of optimized potentials for liquid simulations all atom (OPLS-AA) compatible parameters was tested and carefully tuned. The refinement of parameters included fitting of partial atomic charges, optimization of Lennard-Jones parameters, and recalculation of the dihedral angle parameters needed to reproduce quantum energy profiles. To validate the force field, a variety of physicochemical properties were calculated for liquid menthol. Both thermodynamic and kinetic properties were taken into account, including density, surface tension, enthalpy of vaporization, and shear viscosity. The obtained force field was proven to accurately reproduce the properties of the investigated compound while being fully compatible with the OPLS-AA force field. PMID:27604277

  20. Imaging and force probing RNA by atomic force microscopy.

    PubMed

    Schön, Peter

    2016-07-01

    In the past 30years, the atomic force microscope (AFM) has become a true enabling platform in the life sciences opening entire novel avenues for structural and dynamic studies of biological systems. It enables visualization, probing and manipulation across the length scales, from single molecules to living cells in buffer solution under physiological conditions without the need for labeling or staining of the specimen. In particular, for structural studies of nucleic acids and assemblies thereof, the AFM has matured into a routinely used tool providing nanometer spatial resolution. This includes ssRNA, dsRNA and nucleoprotein complexes thereof, as well as RNA aggregates and 2D RNA assemblies. By AFM unique information can be obtained on RNA based assemblies which are becoming increasingly important as novel unique building blocks in the emerging field of RNA nanotechnology. In addition, the AFM is of fundamental relevance to study biological relevant RNA interactions and dynamics. In this short review first the basic functioning principles of commonly used AFM modes including AFM based force spectroscopy will be briefly described. Next a brief overview will be given on structural studies that have been done related to AFM topographic imaging of RNA, RNA assemblies and aggregates. Finally, an overview on AFM beyond imaging will be provided. This includes force spectroscopy of RNA under physiological conditions in aqueous buffer to probe RNA interaction with proteins and ligands as well as other AFM tip based RNA probing. The main intention of this short review to give the reader a flavor of what AFM contributes to RNA research and engineering. PMID:27222101

  1. SOLVENT RECOVERY AT VANDENBERG AIR FORCE BASE

    EPA Science Inventory

    The report gives results of a feasibility study of the addition of vapor recovery and solvent purification equipment for Vandenberg Air Force Base (VAFB) to reuse the large quantities of waste solvent generated in space shuttle preparation operations. (NOTE: Operation of VAFB as ...

  2. Dynamic force matching: A method for constructing dynamical coarse-grained models with realistic time dependence

    SciTech Connect

    Davtyan, Aram; Dama, James F.; Voth, Gregory A.; Andersen, Hans C.

    2015-04-21

    Coarse-grained (CG) models of molecular systems, with fewer mechanical degrees of freedom than an all-atom model, are used extensively in chemical physics. It is generally accepted that a coarse-grained model that accurately describes equilibrium structural properties (as a result of having a well constructed CG potential energy function) does not necessarily exhibit appropriate dynamical behavior when simulated using conservative Hamiltonian dynamics for the CG degrees of freedom on the CG potential energy surface. Attempts to develop accurate CG dynamic models usually focus on replacing Hamiltonian motion by stochastic but Markovian dynamics on that surface, such as Langevin or Brownian dynamics. However, depending on the nature of the system and the extent of the coarse-graining, a Markovian dynamics for the CG degrees of freedom may not be appropriate. In this paper, we consider the problem of constructing dynamic CG models within the context of the Multi-Scale Coarse-graining (MS-CG) method of Voth and coworkers. We propose a method of converting a MS-CG model into a dynamic CG model by adding degrees of freedom to it in the form of a small number of fictitious particles that interact with the CG degrees of freedom in simple ways and that are subject to Langevin forces. The dynamic models are members of a class of nonlinear systems interacting with special heat baths that were studied by Zwanzig [J. Stat. Phys. 9, 215 (1973)]. The properties of the fictitious particles can be inferred from analysis of the dynamics of all-atom simulations of the system of interest. This is analogous to the fact that the MS-CG method generates the CG potential from analysis of equilibrium structures observed in all-atom simulation data. The dynamic models generate a non-Markovian dynamics for the CG degrees of freedom, but they can be easily simulated using standard molecular dynamics programs. We present tests of this method on a series of simple examples that demonstrate that

  3. 20. Photographic copy of an asconstructed site plan for additions ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    20. Photographic copy of an as-constructed site plan for additions to North Base: Job No. A(8-1), Military Construction, Materiel Command Flight Test Base, Muroc, California; Additional Construction, Location Plan, Sheet No. 2, October 1943. Reproduced from the holdings of the National Archives, Pacific Southwest Region - Edwards Air Force Base, North Base, North Base Road, Boron, Kern County, CA

  4. The Force of Ideas

    ERIC Educational Resources Information Center

    Ascher, Carol

    2005-01-01

    "The Force of Ideas" describes a little-known aspect of both educational history and Viennese psychoanalysis during the interwar years: the movement for psychoanalytic pedagogy. The author traces her father's own story, beginning with his application to the Vienna Psychoanalytic Society for training as a psychoanalytic pedagogue, as a way to…

  5. Unification of Fundamental Forces

    NASA Astrophysics Data System (ADS)

    Salam, Abdus; Taylor, Foreword by John C.

    2005-10-01

    Foreword John C. Taylor; 1. Unification of fundamental forces Abdus Salam; 2. History unfolding: an introduction to the two 1968 lectures by W. Heisenberg and P. A. M. Dirac Abdus Salam; 3. Theory, criticism, and a philosophy Werner Heisenberg; 4. Methods in theoretical physics Paul Adrian Maurice Dirac.

  6. Reduction in Force.

    ERIC Educational Resources Information Center

    Wood, R. Craig

    This chapter of "Principles of School Business Management" reviews several concerns that must be addressed by school business administrators in districts facing declining enrollments and the need for reductions in force. The chapter first looks at the business administrator's significant role in planning for retrenchment. The chapter then…

  7. Reduction in Force.

    ERIC Educational Resources Information Center

    Phay, Robert

    Chapter 2 in a book on school law discusses the reasons for reduction in force (RIF) and presents a set of model regulations for school districts as the best means of minimizing legal problems resulting from RIF. The reasons for RIF include declining student enrollments; reduced turnover among teachers; changes in programs; and more constrained…

  8. Wearing Forces Spectacles

    ERIC Educational Resources Information Center

    Perrin, Graham

    2012-01-01

    When providing training to teachers struggling with the concept of forces, the author encourages them to start with something within the experience of the children they are teaching. For example, show them photographs taken on windy days, such as that of a tree, and ask them to explain what is happening. This encourages the children to focus on…

  9. Forces in nonlinear media

    NASA Astrophysics Data System (ADS)

    Milgrom, Mordehai

    2002-02-01

    I investigate the properties of forces on bodies in theories governed by the generalized Poisson equation μ(|ϕ| /a0)ϕ] ∝ Gρ, for the potential ϕ produced by a distribution of sources ρ. This equation describes, inter alia, media with a response coefficient, μ, that depends on the field strength, such as in nonlinear, dielectric or diamagnetic, media; nonlinear transport problems with field-strength-dependent conductivity or diffusion coefficient; nonlinear electrostatics, as in the Born-Infeld theory; certain stationary potential flows in compressible fluids, in which case the forces act on sources or obstacles in the flow. The expressions for the force on a point charge are derived exactly for the limits of very low and very high charge. The force on an arbitrary body in an external field of asymptotically constant gradient, -g0, is shown to be F = Qg0, where Q is the total effective charge of the body. The corollary Q = 0 → F = 0 is a generalization of d'Alembert's paradox. I show that for G > 0 (as in Newtonian gravity) two point charges of the same (opposite) sign still attract (repel). The opposite is true for G < 0. I discuss its generalization to extended bodies and derive virial relations.

  10. Force limited vibration testing

    NASA Technical Reports Server (NTRS)

    Scharton, Terry D.

    1991-01-01

    A new method of conducting lab vibration tests of spacecraft equipment was developed to more closely simulate the vibration environment experienced when the spacecraft is launched on a rocket. The improved tests are tailored to identify equipment design and workmanship problems without inducing artificial failures that would not have occurred at launch. These new, less destructive types of vibration tests are essential to JPL's protoflight test approach in which lab testing is conducted using the flight equipment, often one of a kind, to save time and money. In conventional vibration tests, only the input vibratory motion is specified; the feedback, or reaction force, between the test item and the vibration machine is ignored. Most test failures occur when the test item goes into resonance, and the reaction force becomes very large. It has long been recognized that the large reaction force is a test artifact which does not occur with the lightweight, flexible mounting structures characteristic of spacecraft and space vehicles. In new vibration tests, both the motion and the force provided to the test item by the vibration machine are controlled, so that the vibration ride experienced by the test item is as in flight.

  11. Direct Aerosol Forcing Uncertainty

    DOE Data Explorer

    Mccomiskey, Allison

    2008-01-15

    Understanding sources of uncertainty in aerosol direct radiative forcing (DRF), the difference in a given radiative flux component with and without aerosol, is essential to quantifying changes in Earth's radiation budget. We examine the uncertainty in DRF due to measurement uncertainty in the quantities on which it depends: aerosol optical depth, single scattering albedo, asymmetry parameter, solar geometry, and surface albedo. Direct radiative forcing at the top of the atmosphere and at the surface as well as sensitivities, the changes in DRF in response to unit changes in individual aerosol or surface properties, are calculated at three locations representing distinct aerosol types and radiative environments. The uncertainty in DRF associated with a given property is computed as the product of the sensitivity and typical measurement uncertainty in the respective aerosol or surface property. Sensitivity and uncertainty values permit estimation of total uncertainty in calculated DRF and identification of properties that most limit accuracy in estimating forcing. Total uncertainties in modeled local diurnally averaged forcing range from 0.2 to 1.3 W m-2 (42 to 20%) depending on location (from tropical to polar sites), solar zenith angle, surface reflectance, aerosol type, and aerosol optical depth. The largest contributor to total uncertainty in DRF is usually single scattering albedo; however decreasing measurement uncertainties for any property would increase accuracy in DRF. Comparison of two radiative transfer models suggests the contribution of modeling error is small compared to the total uncertainty although comparable to uncertainty arising from some individual properties.

  12. The Dynamic Force Table

    ERIC Educational Resources Information Center

    Geddes, John B.; Black, Kelly

    2008-01-01

    We examine an experimental apparatus that is used to motivate the connections between the basic properties of vectors, potential functions, systems of nonlinear equations, and Newton's method for nonlinear systems of equations. The apparatus is an adaptation of a force table where we remove the center-pin and allow the center-ring to move freely.…

  13. Mining Task Force Report.

    ERIC Educational Resources Information Center

    Saskatchewan Inst. of Applied Science and Technology, Saskatoon.

    In fall 1988, the Board of Directors of the Saskatchewan Institute of Applied Science and Technology (SIAST) created a task force to study the training needs of the mining industry in the province and evaluate SIAST's responsiveness to those needs. After assessing the technological changes taking place in the industry, surveying manpower needs,…

  14. Lorentz force particle analyzer

    NASA Astrophysics Data System (ADS)

    Wang, Xiaodong; Thess, André; Moreau, René; Tan, Yanqing; Dai, Shangjun; Tao, Zhen; Yang, Wenzhi; Wang, Bo

    2016-07-01

    A new contactless technique is presented for the detection of micron-sized insulating particles in the flow of an electrically conducting fluid. A transverse magnetic field brakes this flow and tends to become entrained in the flow direction by a Lorentz force, whose reaction force on the magnetic-field-generating system can be measured. The presence of insulating particles suspended in the fluid produce changes in this Lorentz force, generating pulses in it; these pulses enable the particles to be counted and sized. A two-dimensional numerical model that employs a moving mesh method demonstrates the measurement principle when such a particle is present. Two prototypes and a three-dimensional numerical model are used to demonstrate the feasibility of a Lorentz force particle analyzer (LFPA). The findings of this study conclude that such an LFPA, which offers contactless and on-line quantitative measurements, can be applied to an extensive range of applications. These applications include measurements of the cleanliness of high-temperature and aggressive molten metal, such as aluminum and steel alloys, and the clean manufacturing of semiconductors.

  15. Chiral drag force

    NASA Astrophysics Data System (ADS)

    Rajagopal, Krishna; Sadofyev, Andrey V.

    2015-10-01

    We provide a holographic evaluation of novel contributions to the drag force acting on a heavy quark moving through strongly interacting plasma. The new contributions are chiral in the sense that they act in opposite directions in plasmas containing an excess of left- or right-handed quarks. The new contributions are proportional to the coefficient of the axial anomaly, and in this sense also are chiral. These new contributions to the drag force act either parallel to or antiparallel to an external magnetic field or to the vorticity of the fluid plasma. In all these respects, these contributions to the drag force felt by a heavy quark are analogous to the chiral magnetic effect (CME) on light quarks. However, the new contribution to the drag force is independent of the electric charge of the heavy quark and is the same for heavy quarks and antiquarks, meaning that these novel effects do not in fact contribute to the CME current. We show that although the chiral drag force can be non-vanishing for heavy quarks that are at rest in the local fluid rest frame, it does vanish for heavy quarks that are at rest in a suitably chosen frame. In this frame, the heavy quark at rest sees counterpropagating momentum and charge currents, both proportional to the axial anomaly coefficient, but feels no drag force. This provides strong concrete evidence for the absence of dissipation in chiral transport, something that has been predicted previously via consideration of symmetries. Along the way to our principal results, we provide a general calculation of the corrections to the drag force due to the presence of gradients in the flowing fluid in the presence of a nonzero chemical potential. We close with a consequence of our result that is at least in principle observable in heavy ion collisions, namely an anticorrelation between the direction of the CME current for light quarks in a given event and the direction of the kick given to the momentum of all the heavy quarks and

  16. Solvation forces between rough surfaces

    SciTech Connect

    Frink, L.J.; van Swol, F.

    1998-04-01

    We investigate the role of surface roughness on solvation forces and solvation free energies. Roughness is introduced by dividing a surface into an array of square tiles that are then randomly displaced in the direction perpendicular to the wall. The integrated wall strength of these tiled surfaces is independent of the surface roughness and hence this class of rough walls is ideally suited for isolating roughness effects. We use grand canonical Monte Carlo simulations of a Lennard-Jones fluid confined in a slit pore with rough walls to generate the solvation interactions as a function of roughness, tile size, and surface area. The simulation data are compared to a simple superposition approximation of smooth wall solvation interactions (obtained from simulation or density functional theory), based on a distribution of wall separations. We find that this approximation provides a surprisingly accurate route to the solvation interaction of rough surfaces. In general, increased roughness leads to a reduction of oscillations in the solvation forces and surface free energies. However, nonmonotonic behavior of the oscillation amplitude with roughness can be observed for finite surfaces. The washing out of the oscillations found for large surface roughness produces a solvation force that exhibits a broad repulsive peak with separation. The broad repulsion is a consequence of the resistance to squeezing out fluid from the smallest gaps between two opposing rough surfaces. It is as much a reflection of packing effects as are the solvation oscillations for perfectly smooth pores. In addition, we present results for patterned and undulating surfaces produced by an analogous modification of the one-body external field for smooth walls. Finally, we discuss the implications of our results for a number of experimental systems including self-assembled monolayers, microporous materials, protein solutions, and DNA crystals. {copyright} {ital 1998 American Institute of Physics.}

  17. Mechanical design and force calibration of dual-axis micromechanical probe for friction force microscopy

    NASA Astrophysics Data System (ADS)

    Fukuzawa, Kenji; Terada, Satoshi; Shikida, Mitsuhiro; Amakawa, Hiroaki; Zhang, Hedong; Mitsuya, Yasunaga

    2007-02-01

    A dual-axis micromechanical probe that combines a double cantilever and torsion beams is presented. This probe can reduce the mechanical cross-talk between the lateral and vertical force detections. In addition, dual-axis forces can be detected by measuring the dual-axis displacement of the probe end using the optical lever-based method used in conventional friction force microscopes (FFMs). In this paper, the mechanical design of the probe, the details of the fabrication method, FFM performance, and calibration of the friction force are discussed. The mechanical design and the microfabrication method for probes that can provide a force resolution of the order of 1nN without mechanical cross-talk are presented. Calibration of the lateral force signal is possible by using the relationship between the lateral force and the piezodisplacement at the onset of the probe scanning. The micromechanical probe enables simultaneous and independent detection of atomic and friction forces. This leads to accurate investigation of nanotribological phenomena and visualization of the distribution of the friction properties, which helps the identification of the material properties.

  18. Mechanical design and force calibration of dual-axis micromechanical probe for friction force microscopy

    SciTech Connect

    Fukuzawa, Kenji; Terada, Satoshi; Shikida, Mitsuhiro; Amakawa, Hiroaki; Zhang, Hedong; Mitsuya, Yasunaga

    2007-02-01

    A dual-axis micromechanical probe that combines a double cantilever and torsion beams is presented. This probe can reduce the mechanical cross-talk between the lateral and vertical force detections. In addition, dual-axis forces can be detected by measuring the dual-axis displacement of the probe end using the optical lever-based method used in conventional friction force microscopes (FFMs). In this paper, the mechanical design of the probe, the details of the fabrication method, FFM performance, and calibration of the friction force are discussed. The mechanical design and the microfabrication method for probes that can provide a force resolution of the order of 1 nN without mechanical cross-talk are presented. Calibration of the lateral force signal is possible by using the relationship between the lateral force and the piezodisplacement at the onset of the probe scanning. The micromechanical probe enables simultaneous and independent detection of atomic and friction forces. This leads to accurate investigation of nanotribological phenomena and visualization of the distribution of the friction properties, which helps the identification of the material properties.

  19. Quantitative 3D-KPFM imaging with simultaneous electrostatic force and force gradient detection

    NASA Astrophysics Data System (ADS)

    Collins, L.; Okatan, M. B.; Li, Q.; Kravenchenko, I. I.; Lavrik, N. V.; Kalinin, S. V.; Rodriguez, B. J.; Jesse, S.

    2015-05-01

    Kelvin probe force microscopy (KPFM) is a powerful characterization technique for imaging local electrochemical and electrostatic potential distributions and has been applied across a broad range of materials and devices. Proper interpretation of the local KPFM data can be complicated, however, by convolution of the true surface potential under the tip with additional contributions due to long range capacitive coupling between the probe (e.g. cantilever, cone, tip apex) and the sample under test. In this work, band excitation (BE)-KPFM is used to negate such effects. In contrast to traditional single frequency KPFM, multifrequency BE-KPFM is shown to afford dual sensitivity to both the electrostatic force and the force gradient detection, analogous to simultaneous amplitude modulated and frequency modulated KPFM imaging. BE-KPFM is demonstrated on a Pt/Au/SiOx test structure and electrostatic force gradient detection is found to lead to an improved lateral resolution compared to electrostatic force detection. Finally, a 3D-KPFM imaging technique is developed. Force volume (FV) BE-KPFM allows the tip-sample distance dependence of the electrostatic interactions (force and force gradient) to be recorded at each point across the sample surface. As such, FVBE-KPFM provides a much needed pathway towards complete tip-sample capacitive de-convolution in KPFM measurements and will enable quantitative surface potential measurements with nanoscale resolution.

  20. Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer's peptides

    NASA Astrophysics Data System (ADS)

    Tran, Thanh Thuy; Nguyen, Phuong H.; Derreumaux, Philippe

    2016-05-01

    Coarse-grained protein lattice models approximate atomistic details and keep the essential interactions. They are, therefore, suitable for capturing generic features of protein folding and amyloid formation at low computational cost. As our aim is to study the critical nucleus sizes of two experimentally well-characterized peptide fragments Aβ16-22 and Aβ37-42 of the full length Aβ1-42 Alzheimer's peptide, it is important that simulations with the lattice model reproduce all-atom simulations. In this study, we present a comprehensive force field parameterization based on the OPEP (Optimized Potential for Efficient protein structure Prediction) force field for an on-lattice protein model, which incorporates explicitly the formation of hydrogen bonds and directions of side-chains. Our bottom-up approach starts with the determination of the best lattice force parameters for the Aβ16-22 dimer by fitting its equilibrium parallel and anti-parallel β-sheet populations to all-atom simulation results. Surprisingly, the calibrated force field is transferable to the trimer of Aβ16-22 and the dimer and trimer of Aβ37-42. Encouraged by this finding, we characterized the free energy landscapes of the two decamers. The dominant structure of the Aβ16-22 decamer matches the microcrystal structure. Pushing the simulations for aggregates between 4-mer and 12-mer suggests a nucleus size for fibril formation of 10 chains. In contrast, the Aβ37-42 decamer is largely disordered with mixed by parallel and antiparallel chains, suggesting that the nucleus size is >10 peptides. Our refined force field coupled to this on-lattice model should provide useful insights into the critical nucleation number associated with neurodegenerative diseases.

  1. Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer's peptides.

    PubMed

    Tran, Thanh Thuy; Nguyen, Phuong H; Derreumaux, Philippe

    2016-05-28

    Coarse-grained protein lattice models approximate atomistic details and keep the essential interactions. They are, therefore, suitable for capturing generic features of protein folding and amyloid formation at low computational cost. As our aim is to study the critical nucleus sizes of two experimentally well-characterized peptide fragments Aβ16-22 and Aβ37-42 of the full length Aβ1-42 Alzheimer's peptide, it is important that simulations with the lattice model reproduce all-atom simulations. In this study, we present a comprehensive force field parameterization based on the OPEP (Optimized Potential for Efficient protein structure Prediction) force field for an on-lattice protein model, which incorporates explicitly the formation of hydrogen bonds and directions of side-chains. Our bottom-up approach starts with the determination of the best lattice force parameters for the Aβ16-22 dimer by fitting its equilibrium parallel and anti-parallel β-sheet populations to all-atom simulation results. Surprisingly, the calibrated force field is transferable to the trimer of Aβ16-22 and the dimer and trimer of Aβ37-42. Encouraged by this finding, we characterized the free energy landscapes of the two decamers. The dominant structure of the Aβ16-22 decamer matches the microcrystal structure. Pushing the simulations for aggregates between 4-mer and 12-mer suggests a nucleus size for fibril formation of 10 chains. In contrast, the Aβ37-42 decamer is largely disordered with mixed by parallel and antiparallel chains, suggesting that the nucleus size is >10 peptides. Our refined force field coupled to this on-lattice model should provide useful insights into the critical nucleation number associated with neurodegenerative diseases. PMID:27250331

  2. Probing adhesion forces at the molecular scale

    SciTech Connect

    Thomas, R.C.; Houston, J.E.; Michalske, T.A.

    1996-12-31

    Measurements of adhesion forces at the molecular scale, such as those discussed here, are necessary to understand macroscopic boundary-layer behavior such as adhesion, friction, wear, lubrication, and many other important phenomena. The authors` recent interfacial force microscopy (IFM) studies have provided detailed information about the mechanical response of both self-assembled monolayer (SAM) films and the underlying substrates. In addition, they recently demonstrated that the IFM is useful for studying the chemical nature of such films. In this talk, the authors discuss a new method for studying surface interactions and chemical reactions using the IFM. To quantitatively measure the work of adhesion and bond energies between two organic thin films, they modify both a Au substrate and a Au probe with self-assembling organomercaptan molecules having either the same or different end groups (-CH{sub 3}, -NH{sub 2}, and -COOH), and then analyze the force-versus-displacement curves (force profiles) that result from the approach to contact of the two surfaces. Their results show that the magnitude of the adhesive forces measured between methyl-methyl interactions are in excellent agreement with van der Waals calculations using Lifshitz theory and previous experimentally determined values. Moreover, the measured peak adhesive forces scale as expected for van der Waals, hydrogen-bonding, and acid-base interactions.

  3. Labyrinth seal forces on a whirling rotor

    NASA Technical Reports Server (NTRS)

    Wright, D. V.

    1983-01-01

    An experimental investigation of air labyrinth seal forces on a subsynchronously whirling model rotor is described and test results are given for diverging, converging, and straight two-strip seals. The effects of pressure drop, provide basic experimental data needed in the development of design methods for predicting and preventing self-excited whirl of turbine rotors and other machines having labyrinth seals. The total dynamic seal forces on the whirling model rotor are measured accurately by means of an active damping and stiffness system that is adjusted to obtain neutral whirl stability of the model rotor system. In addition, the whirling pressure pattern in the seal annulus is measured for a few test conditions and the corresponding pressure forces on the rotor are compared with the total measured forces. This comparison shows that either radial and axial pressure gradients in the seal annulus or drag forces on the rotor are significant. Comparisons made between the measured seal forces and theoretical results show that present theory is inadequate.

  4. Finding forced trends in oceanic oxygen

    NASA Astrophysics Data System (ADS)

    Long, Matthew C.; Deutsch, Curtis; Ito, Taka

    2016-02-01

    Anthropogenically forced trends in oceanic dissolved oxygen are evaluated in Earth system models in the context of natural variability. A large ensemble of a single Earth system model is used to clearly identify the forced component of change in interior oxygen distributions and to evaluate the magnitude of this signal relative to noise generated by internal climate variability. The time of emergence of forced trends is quantified on the basis of anomalies in oxygen concentrations and trends. We find that the forced signal should already be evident in the southern Indian Ocean and parts of the eastern tropical Pacific and Atlantic basins; widespread detection of forced deoxygenation is possible by 2030-2040. In addition to considering spatially discrete metrics of detection, we evaluate the similarity of the spatial structures associated with natural variability and the forced trend. Outside of the subtropics, these patterns are not wholly distinct on the isopycnal surfaces considered, and therefore, this approach does not provide significantly advanced detection. Our results clearly demonstrate the strong impact of natural climate variability on interior oxygen distributions, providing an important context for interpreting observations.

  5. Investigation of Calibrating Force Transducer Using Sinusoidal Force

    SciTech Connect

    Zhang Li; Wang Yu; Zhang Lizhe

    2010-05-28

    Sinusoidal force calibration method was studied several years before at Physikalisch-Technische Bundesanstalt (PTB). A similar dynamic force calibration system is developed at Changcheng Institute of Metrology and Measurement (CIMM). It uses electro-dynamic shakers to generate dynamic force in the range from 1 N to 20 kN, and heterodyne laser interferometers are used for acceleration measurement. The force transducer to be calibrated is mounted on the shaker, and a mass block is screwed on the top of force transducer, the sinusoidal forces realized by accelerated load masses are traceable to acceleration and mass according to the force definition. The methods of determining Spatial-dependent acceleration on mass block and measuring the end mass of force transducer in dynamic force calibration are discussed in this paper.

  6. Force control in chronic stroke.

    PubMed

    Kang, Nyeonju; Cauraugh, James H

    2015-05-01

    Force control deficits are common dysfunctions after a stroke. This review concentrates on various force control variables associated with motor impairments and suggests new approaches to quantifying force control production and modulation. Moreover, related neurophysiological mechanisms were addressed to determine variables that affect force control capabilities. Typically, post stroke force control impairments include: (a) decreased force magnitude and asymmetrical forces between hands, (b) higher task error, (c) greater force variability, (d) increased force regularity, and (e) greater time-lag between muscular forces. Recent advances in force control analyses post stroke indicated less bimanual motor synergies and impaired low-force frequency structure. Brain imaging studies demonstrate possible neurophysiological mechanisms underlying force control impairments: (a) decreased activation in motor areas of the ipsilesional hemisphere, (b) increased activation in secondary motor areas between hemispheres, (c) cerebellum involvement, and (d) relatively greater interhemispheric inhibition from the contralesional hemisphere. Consistent with identifying neurophysiological mechanisms, analyzing bimanual motor synergies as well as low-force frequency structure will advance our understanding of post stroke force control. PMID:25704075

  7. Dark Forces At The Tevatron

    DOE PAGESBeta

    Buckley, Matt; Fileviez Perez, Pavel; Hooper, Dan; Neil, Ethan

    2011-08-19

    A simple explanation of the W + dijet excess recently reported by the CDF collaboration involves the introduction of a new gauge boson with sizable couplings to quarks, but with no or highly suppressed couplings to leptons. Anomaly-free theories which include such a leptophobic gauge boson must also include additional particle content, which may include a stable and otherwise viable candidate for dark matter. Based on the couplings and mass of the Z` required to generate the CDF excess, we predict such a dark matter candidate to possess an elastic scattering cross section with nucleons on the order of σmore » ~ 10-40 cm2, providing a natural explanation for the signals reported by the CoGeNT and DAMA/LIBRA collaborations. In this light, CDF may be observing the gauge boson responsible for the force which mediates the interactions between the dark and visible matter of our universe.« less

  8. Ultrasensitive hysteretic force sensing with parametric nonlinear oscillators

    NASA Astrophysics Data System (ADS)

    Papariello, Luca; Zilberberg, Oded; Eichler, Alexander; Chitra, R.

    2016-08-01

    We propose a method for linear detection of weak forces using parametrically driven nonlinear resonators. The method is based on a peculiar feature in the response of the resonator to a near resonant periodic external force. This feature stems from a complex interplay among the parametric drive, external force, and nonlinearities. For weak parametric drive, the response exhibits the standard Duffing-like single jump hysteresis. For stronger drive amplitudes, we find a qualitatively new double jump hysteresis which arises from stable solutions generated by the cubic Duffing nonlinearity. The additional jump exists only if the external force is present and the frequency at which it occurs depends linearly on the amplitude of the external force, permitting a straightforward ultrasensitive detection of weak forces. With state-of-the-art nanomechanical resonators, our scheme should permit force detection in the attonewton range.

  9. Force-chain identification in quasi-2D granular systems

    NASA Astrophysics Data System (ADS)

    Zhang, Ling; Wu, Jun-Qi; Zhang, Jie

    2013-06-01

    Understanding the properties of force-chains is essential in understanding the physical and mechanical properties of granular materials. The key is to identify force-chains. In this study, we describe a systematic method to identify individual force-chains in 2D granular systems under different external load-pure shear or isotropic compression, where bi-disperse photo-elastic particles were used in order to measure vector contact forces between particles. Using this method, we studied the statistics of force-chain size distribution in these two systems: in pure shear, the distribution shows a fat tail that deviates from an exponential distribution function, whereas in isotropic compression, the distribution decays exponentially. In addition, we also investigated the dependence of various force-chain statistics on two main parameters defined in the force-chain identification algorithm.

  10. Force Feedback Joystick

    NASA Technical Reports Server (NTRS)

    1997-01-01

    I-FORCE, a computer peripheral from Immersion Corporation, was derived from virtual environment and human factors research at the Advanced Displays and Spatial Perception Laboratory at Ames Research Center in collaboration with Stanford University Center for Design Research. Entrepreneur Louis Rosenberg, a former Stanford researcher, now president of Immersion, collaborated with Dr. Bernard Adelstein at Ames on studies of perception in virtual reality. The result was an inexpensive way to incorporate motors and a sophisticated microprocessor into joysticks and other game controllers. These devices can emulate the feel of a car on the skid, a crashing plane, the bounce of a ball, compressed springs, or other physical phenomenon. The first products incorporating I-FORCE technology include CH- Products' line of FlightStick and CombatStick controllers.

  11. Force Modulator System

    SciTech Connect

    Redmond Clark

    2009-04-30

    Many metal parts manufacturers use large metal presses to shape sheet metal into finished products like car body parts, jet wing and fuselage surfaces, etc. These metal presses take sheet metal and - with enormous force - reshape the metal into a fully formed part in a manner of seconds. Although highly efficient, the forces involved in forming metal parts also damage the press itself, limit the metals used in part production, slow press operations and, when not properly controlled, cause the manufacture of large volumes of defective metal parts. To date, the metal-forming industry has not been able to develop a metal-holding technology that allows full control of press forces during the part forming process. This is of particular importance in the automotive lightweighting efforts under way in the US automotive manufacturing marketplace. Metalforming Controls Technology Inc. (MC2) has developed a patented press control system called the Force Modulator that has the ability to control these press forces, allowing a breakthrough in stamping process control. The technology includes a series of hydraulic cylinders that provide controlled tonnage at all points in the forming process. At the same time, the unique cylinder design allows for the generation of very high levels of clamping forces (very high tonnages) in very small spaces; a requirement for forming medium and large panels out of HSS and AHSS. Successful production application of these systems testing at multiple stamping operations - including Ford and Chrysler - has validated the capabilities and economic benefits of the system. Although this technology has been adopted in a number of stamping operations, one of the primary barriers to faster adoption and application of this technology in HSS projects is system cost. The cost issue has surfaced because the systems currently in use are built for each individual die as a custom application, thus driving higher tooling costs. This project proposed to better

  12. Suicide and Forced Marriage

    PubMed Central

    Pridmore, Saxby; Walter, Garry

    2013-01-01

    Background: The prevailing view that the vast majority of those who complete suicide have an underlying psychiatric disorder has been recently challenged by research on the contribution of “predicaments”, in the absence of mental illness, to suicide. In this paper, we sought data to support the notion that forced marriage may lead to suicide without the presence of psychiatric disorder. Methods: Historical records, newspapers, and the electronic media were searched for examples. Results: Two examples from ancient times and six from the last hundred years were located and described. Conclusion: These cases suggest that forced marriage may lead to suicide and complements earlier findings that loss of fortune, health, liberty, and reputation may lead to suicide in the absence of mental disorder. PMID:23983577

  13. Forces Driving Chaperone Action.

    PubMed

    Koldewey, Philipp; Stull, Frederick; Horowitz, Scott; Martin, Raoul; Bardwell, James C A

    2016-07-14

    It is still unclear what molecular forces drive chaperone-mediated protein folding. Here, we obtain a detailed mechanistic understanding of the forces that dictate the four key steps of chaperone-client interaction: initial binding, complex stabilization, folding, and release. Contrary to the common belief that chaperones recognize unfolding intermediates by their hydrophobic nature, we discover that the model chaperone Spy uses long-range electrostatic interactions to rapidly bind to its unfolded client protein Im7. Short-range hydrophobic interactions follow, which serve to stabilize the complex. Hydrophobic collapse of the client protein then drives its folding. By burying hydrophobic residues in its core, the client's affinity to Spy decreases, which causes client release. By allowing the client to fold itself, Spy circumvents the need for client-specific folding instructions. This mechanism might help explain how chaperones can facilitate the folding of various unrelated proteins. PMID:27293188

  14. Miniature drag force anemometer

    NASA Technical Reports Server (NTRS)

    Krause, L. N.; Fralick, G. C.

    1977-01-01

    A miniature drag force anemometer is described which is capable of measuring dynamic velocity head and flow direction. The anemometer consists of a silicon cantilevered beam 2.5 mm long, 1.5 mm wide, and 0.25 mm thick with an integrated diffused strain gage bridge, located at the base of the beam, as the force measuring element. The dynamics of the beam are like that of a second order system with a natural frequency of about 42 kHz and a damping coefficient of 0.007. The anemometer can be used in both forward and reversed flow. Measured flow characteristics up to Mach 0.6 are presented along with application examples including turbulence measurements.

  15. Air Force seal activities

    NASA Technical Reports Server (NTRS)

    Mayhew, Ellen R.

    1994-01-01

    Seal technology development is an important part of the Air Force's participation in the Integrated High Performance Turbine Engine Technology (IHPTET) initiative, the joint DOD, NASA, ARPA, and industry endeavor to double turbine engine capabilities by the turn of the century. Significant performance and efficiency improvements can be obtained through reducing internal flow system leakage, but seal environment requirements continue to become more extreme as the engine thermodynamic cycles advance towards these IHPTET goals. Brush seal technology continues to be pursued by the Air Force to reduce leakage at the required conditions. Likewise, challenges in engine mainshaft air/oil seals are also being addressed. Counter-rotating intershaft applications within the IHPTET initiative involve very high rubbing velocities. This viewgraph presentation briefly describes past and current seal research and development programs and gives a summary of seal applications in demonstrator and developmental engine testing.

  16. Giving a second thought to brisement force - a case report.

    PubMed

    Thakur, R; Shigli, A L; Thakur, G; Ahuja, R

    2015-01-01

    Fractures of temporomandibular joint (TMJ) may be caused by indirect trauma where force of trauma is transmitted to the mandibular condyle from a blow elsewhere or in other situations may also result from direct trauma. TMJ trauma in children is usually accompanied with pain, swelling, limited jaw movement and other additional findings. This report highlights a case of post traumatic trismus successfully managed with Brisement force - gradual tractional forces applied to the temporomandibular joint. PMID:25951309

  17. Fidelity imaging for atomic force microscopy

    SciTech Connect

    Ghosal, Sayan Salapaka, Murti

    2015-01-05

    Atomic force microscopy is widely employed for imaging material at the nanoscale. However, real-time measures on image reliability are lacking in contemporary atomic force microscopy literature. In this article, we present a real-time technique that provides an image of fidelity for a high bandwidth dynamic mode imaging scheme. The fidelity images define channels that allow the user to have additional authority over the choice of decision threshold that facilitates where the emphasis is desired, on discovering most true features on the sample with the possible detection of high number of false features, or emphasizing minimizing instances of false detections. Simulation and experimental results demonstrate the effectiveness of fidelity imaging.

  18. Force/Torque Display For Telerobotic Systems

    NASA Technical Reports Server (NTRS)

    Wise, Marion A.

    1989-01-01

    Pictorial cathode-ray-tube (CRT) display of force and/or torque (F/T) data for telerobotic systems used as output monitor from multiaxis sensor or as command display. Relative positions of two circles represent forces and torques acting on object, derived from signals from F/T sensor composed of strain gauges. Graphical presentation generated on two different graphics systems, one in color and one in black and white. High-level programming facilitates use of additional convenient features in software extending usefulness of sensor data and display. Useful in laboratory experiments, monitoring performance of automated system and for present data on status of system to operator at control station.

  19. Modified entropic force

    SciTech Connect

    Gao Changjun

    2010-04-15

    The theory of statistical thermodynamics tells us the equipartition law of energy does not hold in the limit of very low temperatures. It is found the Debye model is very successful in explaining the experimental results for most of the solid objects. Motivated by this fact, we modify the entropic force formula which is proposed very recently. Since the Unruh temperature is proportional to the strength of the gravitational field, so the modified entropic force formula is an extension of the Newtonian gravity to the weak field. On the contrary, general relativity extends Newtonian gravity to the strong field case. Corresponding to Debye temperature, there exists a Debye acceleration g{sub D}. It is found the Debye acceleration is g{sub D}=10{sup -15} N kg{sup -1}. This acceleration is very much smaller than the gravitational acceleration 10{sup -4} N kg{sup -1} which is felt by Neptune and the gravitational acceleration 10{sup -10} N kg{sup -1} felt by the Sun. Therefore, the modified entropic force can be very well approximated by the Newtonian gravity in the Solar System and in the Galaxy. With this Debye acceleration, we find the current cosmic speeding up can be explained without invoking any kind of dark energy.

  20. Finger force perception during ipsilateral and contralateral force matching tasks

    PubMed Central

    Park, Woo-Hyung; Leonard, Charles T.; Li, Sheng

    2010-01-01

    The aims of the present study were to compare matching performance between ipsilateral and contralateral finger force matching tasks and to examine the effect of handedness on finger force perception. Eleven subjects were instructed to produce reference forces by an instructed finger (index – I or little – L finger) and to reproduce the same amount force by the same or a different finger within the hand (i.e., ipsilateral matching task), or by a finger of the other hand (i.e., contralateral matching task). The results of the ipsilateral and contralateral tasks in the present study commonly showed that 1) the reference and matching forces were matched closely when the two forces were produced by the same or homologous finger(s) such as I/I task; 2) the weaker little finger underestimated the magnitude of reference force of the index finger (I/L task), even with the higher level of effort (relative force), but the two forces were matched when considering total finger forces; 3) the stronger index finger closely matched the reference force of the little finger with the lower level of relative force (i.e., L/I task); 4) when considering the constant errors, I/L tasks showed an underestimation and L/I tasks showed an overestimation compared to I/I tasks. There was no handedness effect during ipsilateral tasks. During the contralateral task, the dominant hand overestimated the force of the non-dominant hand, while the non-dominant hand attempted to match the absolute force of the dominant hand. The overall results support the notion that the absolute, rather than relative, finger force is perceived and reproduced during ipsilateral and contralateral finger force matching tasks, indicating the uniqueness of finger force perception. PMID:18488212

  1. Force reflection with compliance control

    NASA Technical Reports Server (NTRS)

    Kim, Won S. (Inventor)

    1993-01-01

    Two types of systems for force-reflecting control, which enables high force-reflection gain, are presented: position-error-based force reflection and low-pass-filtered force reflection. Both of the systems are combined with shared compliance control. In the position-error-based class, the position error between the commanded and the actual position of a compliantly controlled robot is used to provide force reflection. In the low-pass-filtered force reflection class, the low-pass-filtered output of the compliance control is used to provide force reflection. The increase in force reflection gain can be more than 10-fold as compared to a conventional high-bandwidth pure force reflection system, when high compliance values are used for the compliance control.

  2. The forces and moments on airplane engine mounts

    NASA Technical Reports Server (NTRS)

    Donely, Philip

    1936-01-01

    A resume of the equations and formulas for the forces and moments on an aircraft-engine mount is presented. In addition, available experimental data have been included to permit the computation of these forces and moments. A sample calculation is made and compared with present design conditions for engine mounts.

  3. Adding Value to Force Diagrams: Representing Relative Force Magnitudes

    NASA Astrophysics Data System (ADS)

    Wendel, Paul

    2011-05-01

    Nearly all physics instructors recognize the instructional value of force diagrams, and this journal has published several collections of exercises to improve student skill in this area.1-4 Yet some instructors worry that too few students perceive the conceptual and problem-solving utility of force diagrams,4-6 and over recent years a rich variety of approaches has been proposed to add value to force diagrams. Suggestions include strategies for identifying candidate forces,6,7 emphasizing the distinction between "contact" and "noncontact" forces,5,8 and the use of computer-based tutorials.9,10 Instructors have suggested a variety of conventions for constructing force diagrams, including approaches to arrow placement and orientation2,11-13 and proposed notations for locating forces or marking action-reaction force pairs.8,11,14,15

  4. Frictional properties of lubrication greases with the addition of nickel nanoparticles in pneumatic cylinder

    NASA Astrophysics Data System (ADS)

    Chang, Ho; Lan, Chou-Wei; Guo, Jia-Bin

    2011-12-01

    This paper studies the influence of addition of 100 nm diameter nickel nano-particles on the friction properties of synthetic grease (Li base, VG100) in pneumatic cylinder. The friction force test of pneumatic cylinder equipment measures the frictional force between seal and cylinder bore in pneumatic cylinders. The lubricants with addition of nickel nano-particles were used for lubricating the contact interface between seal and cylinder bore. The friction force test equipment employ a load cell force sensor to measure the friction force between seals and cylinder bores. Results obtained from experimental tests are compared to determine the friction force between seals and cylinder bore in pneumatic cylinders. The study leads to the conclusion that the addition of nickel nano-particles to synthetic grease results in a decrease in friction force between seals and cylinder bores in pneumatic cylinder. This tribological behavior is closely related to the deposition of nano-particles on the rubbing surfaces

  5. Ultrafast folding kinetics and cooperativity of villin headpiece in single-molecule force spectroscopy.

    PubMed

    Žoldák, Gabriel; Stigler, Johannes; Pelz, Benjamin; Li, Hongbin; Rief, Matthias

    2013-11-01

    In this study we expand the accessible dynamic range of single-molecule force spectroscopy by optical tweezers to the microsecond range by fast sampling. We are able to investigate a single molecule for up to 15 min and with 300-kHz bandwidth as the protein undergoes tens of millions of folding/unfolding transitions. Using equilibrium analysis and autocorrelation analysis of the time traces, the full energetics as well as real-time kinetics of the ultrafast folding of villin headpiece 35 and a stable asparagine 68 alanine/lysine 70 methionine variant can be measured directly. We also performed Brownian dynamics simulations of the response of the bead-DNA system to protein-folding fluctuations. All key features of the force-dependent deflection fluctuations could be reproduced: SD, skewness, and autocorrelation function. Our measurements reveal a difference in folding pathway and cooperativity between wild-type and stable variant of headpiece 35. Autocorrelation force spectroscopy pushes the time resolution of single-molecule force spectroscopy to ∼10 µs thus approaching the timescales accessible for all atom molecular dynamics simulations. PMID:24145407

  6. Quantification of Staphylococcus aureus adhesion forces on various dental restorative materials using atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Merghni, Abderrahmen; Kammoun, Dorra; Hentati, Hajer; Janel, Sébastien; Popoff, Michka; Lafont, Frank; Aouni, Mahjoub; Mastouri, Maha

    2016-08-01

    In the oral cavity dental restorative biomaterials can act as a reservoir for infection with opportunistic Staphylococcus aureus pathogen, which can lead to the occurrence of secondary caries and treatment failures. Our aim was to evaluate the adhesion forces by S. aureus on four dental restorative biomaterials and to correlate this finding to differences in specific surface characteristics. Additionally, the influence of salivary conditioning films in exerted adhesion forces was investigated. The substrate hydrophobicity was measured by goniometer and the surface free energy was calculated using the equilibrium advancing contact angle values of water, formamide, and diiodomethane on the tested surfaces. The surface roughness was determined using atomic force microscope (AFM). Additionally, cell force spectroscopy was achieved to quantify the forces that drive cell-substrate interactions. S. aureus bacterium exerted a considerable adhesion forces on various dental restorative materials, which decreased in the presence of saliva conditioning film. The influence of the surface roughness and free energy in initial adhesion appears to be more important than the effect of hydrophobicity, either in presence or absence of saliva coating. Hence, control of surface properties of dental restorative biomaterials is of crucial importance in preventing the attachment and subsequent the biofilm formation.

  7. Control and Reversal of the Electrophoretic Force on DNA in a Charged Nanopore

    PubMed Central

    Luan, Binquan

    2011-01-01

    Electric field-driven transport of DNA through solid-state nanopores is the key process in nanopore-based DNA sequencing that promises dramatic reduction of genome sequencing costs. A major hurdle in the development of this sequencing method is that DNA transport through the nanopores occurs too quickly for the DNA sequence to be detected. By means of all-atom molecular dynamics simulations, we demonstrate in this communication that velocity of DNA transport through a nanopore can be controlled by the charge state of the nanopore surface. In particular, we show that the charge density of the nanopore surface controls the magnitude and/or direction of the electro-osmotic flow through the nanopore and thereby can significantly reduce or even reverse the effective electrophoretic force on DNA. Our work suggests a physical mechanism to control DNA transport in a nanopore by chemical, electrical or electrochemical modification of the nanopore surface. PMID:21339610

  8. Transformation of the dihedral corrective map for D-amino residues using the CHARMM force field

    NASA Astrophysics Data System (ADS)

    Turpin, Eleanor R.; Hirst, Jonathan D.

    2012-08-01

    Molecular dynamics simulations in explicit solvent were performed on two peptides and two proteins containing D-amino residues, using three implementations of the CHARMM22 all-atom force field: (a) with the standard CMAP corrective term, (b) neglecting the correction entirely and (c) using a transformation of the CMAP grid (φ, ψ) → (-φ, -ψ) for the D-amino residues. The transformed map led to sampling of conformations which are closest to the X-ray crystallographic structures for D-amino residues and the standard CMAP correction destabilises D-amino secondary structure. Thus, the transformation of the CMAP term is needed to simulate proteins and peptides containing D-amino residues correctly.

  9. Air Force construction automation/robotics

    NASA Astrophysics Data System (ADS)

    Nease, Al; Dusseault, Christopher

    1994-01-01

    The Air Force has several unique requirements that are being met through the development of construction robotic technology. The missions associated with these requirements place construction/repair equipment operators in potentially harmful situations. Additionally, force reductions require that human resources be leveraged to the maximum extent possible and that more stringent construction repair requirements push for increased automation. To solve these problems, the U.S. Air Force is undertaking a research and development effort at Tyndall AFB, FL to develop robotic teleoperation, telerobotics, robotic vehicle communications, automated damage assessment, vehicle navigation, mission/vehicle task control architecture, and associated computing environment. The ultimate goal is the fielding of robotic repair capability operating at the level of supervised autonomy. The authors of this paper will discuss current and planned efforts in construction/repair, explosive ordnance disposal, hazardous waste cleanup, fire fighting, and space construction.

  10. EPS forces in Bacillus subtilis biofilms

    NASA Astrophysics Data System (ADS)

    Zhang, Wenbo; Angelini, Thomas; Tsai, Shih-Ming; Nixon, Ryan

    2014-03-01

    Bacteria have evolved to congregate in complex communities known as biofilms. The structure that holds a biofilm together is a matrix called extracellular polymeric substance (EPS). It has been observed in previous studies that EPS up-regulation occurs when the nutrient levels fall below a threshold concentration; this increase in EPS concentration produces an osmotic pressure that forces the colony to spread outward. This osmotic pressure may drive nutrient uptake, but the stresses generated by the EPS matrix has never been measured. Here we present measurements of the forces exerted by a biofilm on its supporting substrate and on its fluid nutrients. In our experiments, we use a technique analogous to traction force microscopy to measure strain in agar nutrient substrates imposed by Bacillus subtilis biofilms. By running additional test to measure the permeability and elastic modulus of the agar, we can estimate the pressure generated by the biofilm.

  11. The Forces at Play in Optical Force Microscopy

    NASA Astrophysics Data System (ADS)

    Brocious, Jordan

    Optical force microscopy is a novel technique where mechanical detection with a cantilevered probe replaces the detection of photons to investigate optically induced processes and states. A theoretical and experimental analysis is performed here of the forces present in optical force microscopy operated in tapping mode, which reveals two dominant optically induced forces, the gradient force and the scattering force. Force-distance curves are reconstructed from experimental amplitude and phase information for glass, gold nanowires and molecular clusters of silicon naphtalocyanine samples. The scattering force is shown to be insensitive to both nano-scale tip-sample distances and sample polarizability and is dependent on the form of the tip. The gradient force demonstrates a z-4 tip-sample distance dependence, localized to a few nanometers, and is strongly dependent on the polarizability of the sample which enables spectroscopic imaging through force detection. The different distance-dependence and polarizability-dependence of the gradient and scattering forces give rise to a complex force-distance curve which determines imaging contrast along with the cantilever set-point, knowledge of which is essential for image interpretation.

  12. 75 FR 81591 - U.S. Air Force Scientific Advisory Board Notice of Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-28

    ... of the Air Force. In addition, the SAB will discuss and reach a consensus on the results of the Air Force Research Laboratory Science and Technology FY11 Review. Pursuant to 5 U.S.C. 552b, as amended,...

  13. Influence of maglev force relaxation on the forces of bulk HTSC subjected to different lateral displacements above the NdFeB guideway

    NASA Astrophysics Data System (ADS)

    Qin, Yujie; Hou, Xiaojing

    2011-02-01

    This paper studied the influence of maglev force relaxation on the force (both levitation and guidance forces) of bulk high-temperature superconductor (HTSC) subjected to different lateral displacements above a NdFeB guideway. Firstly, the maglev forces relaxation property of bulk HTSC above the permanent-magnet guideway (PMG) was studied experimentally, then the levitation and guidance forces were measured by SCML-2 measurement system synchronously at different lateral displacements, some times later(after relaxation), the forces were measured again as the same way. Compared to the two measured results, it was found that the change of the levitation force was larger compared to the case without relaxation, while the change of the guidance force was smaller. In addition, the rate of change of levitation force and guidance force was different for different maximum lateral displacements. This work provided a scientific analysis for the practical application of the bulk HTS.

  14. Atomic Force Microscope

    SciTech Connect

    Day, R.D.; Russell, P.E.

    1988-12-01

    The Atomic Force Microscope (AFM) is a recently developed instrument that has achieved atomic resolution imaging of both conducting and non- conducting surfaces. Because the AFM is in the early stages of development, and because of the difficulty of building the instrument, it is currently in use in fewer than ten laboratories worldwide. It promises to be a valuable tool for obtaining information about engineering surfaces and aiding the .study of precision fabrication processes. This paper gives an overview of AFM technology and presents plans to build an instrument designed to look at engineering surfaces.

  15. Radiative forcing of climate

    NASA Technical Reports Server (NTRS)

    Ramanswamy, V.; Shine, Keith; Leovy, Conway; Wang, Wei-Chyung; Rodhe, Henning; Wuebbles, Donald J.; Ding, M.; Lelieveld, Joseph; Edmonds, Jae A.; Mccormick, M. Patrick

    1991-01-01

    An update of the scientific discussions presented in Chapter 2 of the Intergovernmental Panel on Climate Change (IPCC) report is presented. The update discusses the atmospheric radiative and chemical species of significance for climate change. There are two major objectives of the present update. The first is an extension of the discussion on the Global Warming Potentials (GWP's), including a reevaluation in view of the updates in the lifetimes of the radiatively active species. The second important objective is to underscore major developments in the radiative forcing of climate due to the observed stratospheric ozone losses occurring between 1979 and 1990.

  16. Causal Entropic Forces

    NASA Astrophysics Data System (ADS)

    Wissner-Gross, A. D.; Freer, C. E.

    2013-04-01

    Recent advances in fields ranging from cosmology to computer science have hinted at a possible deep connection between intelligence and entropy maximization, but no formal physical relationship between them has yet been established. Here, we explicitly propose a first step toward such a relationship in the form of a causal generalization of entropic forces that we find can cause two defining behaviors of the human “cognitive niche”—tool use and social cooperation—to spontaneously emerge in simple physical systems. Our results suggest a potentially general thermodynamic model of adaptive behavior as a nonequilibrium process in open systems.

  17. Potential of mean force of association of large hydrophobic particles: toward the nanoscale limit.

    PubMed

    Makowski, Mariusz; Czaplewski, Cezary; Liwo, Adam; Scheraga, Harold A

    2010-01-21

    The potentials of mean force (PMFs) were determined, in both water with the TIP3P water model and in vacuo, for systems involving formation of nonpolar dimers composed of bicyclooctane, adamantane (both an all-atom model and a sphere with the radius of 3.4 A representing adamantane), and fullerene, respectively. A series of umbrella-sampling molecular dynamics simulations with the AMBER force field were carried out for each pair under both environmental conditions. The PMFs were calculated by using the weighted histogram analysis method. The results were compared with our previously determined PMF for neopentane. The shape of the PMFs for dimers of all four nonpolar molecules is characteristic of hydrophobic interactions with contact and solvent-separated minima and desolvation maxima. The positions of all these minima and maxima change with the size of the nonpolar molecule; for larger molecules they shift toward larger distances. Comparison of the PMFs of the bicyclooctane, adamantane, and fullerene dimers in water and in vacuo shows that hydrophobic interactions in each dimer are different from that for the dimer of neopentane. Interactions in the bicyclooctane, adamantane, and fullerene dimers are stronger in vacuo than in water. These dimers cannot be treated as classical, spherical, hydrophobic objects. The solvent contribution to the PMF was also computed by subtracting the PMF determined in vacuo from that in explicit solvent. The solvent contribution to the PMFs of bicyclooctane, adamantane, and fullerene is positive, as opposed to that of neopentane. The water molecules in the first solvation sphere of both adamantane and neopentane dimers are more ordered as compared to bulk water, with their dipole moments pointing away from the surface of the dimers. The average number of hydrogen bonds per water molecule in the first hydration shell of adamantane is smaller compared to that in bulk water, but this shell is thicker for all-atom adamantane than for

  18. Lateral Casimir force beyond the proximity-force approximation.

    PubMed

    Rodrigues, Robson B; Neto, Paulo A Maia; Lambrecht, Astrid; Reynaud, Serge

    2006-03-17

    We argue that the appropriate variable to study a nontrivial geometry dependence of the Casimir force is the lateral component of the Casimir force, which we evaluate between two corrugated metallic plates outside the validity of the proximity-force approximation. The metallic plates are described by the plasma model, with arbitrary values for the plasma wavelength, the plate separation, and the corrugation period, the corrugation amplitude remaining the smallest length scale. Our analysis shows that in realistic experimental situations the proximity-force approximation overestimates the force by up to 30%. PMID:16605712

  19. Uncertainty in NIST Force Measurements

    PubMed Central

    Bartel, Tom

    2005-01-01

    This paper focuses upon the uncertainty of force calibration measurements at the National Institute of Standards and Technology (NIST). The uncertainty of the realization of force for the national deadweight force standards at NIST is discussed, as well as the uncertainties associated with NIST’s voltage-ratio measuring instruments and with the characteristics of transducers being calibrated. The combined uncertainty is related to the uncertainty of dissemination for force transfer standards sent to NIST for calibration. PMID:27308181

  20. Enhancement of electric force by ion-neutral collisions

    SciTech Connect

    Makrinich, G.; Fruchtman, A.

    2009-11-02

    The measured force exerted on an ion flow by an electric field is found to be larger than the electric force that can be exerted if the ions are collisionless. In addition, the increase of the gas pressure is found to result in an increase of the electric force despite a simultaneous decrease of the deposited electric power. Employing a simple model, we argue that these experimental findings result from the electric force being felt by the ions for a longer time, their residence time in the acceleration region is increased due to their slowing-down collisions with neutrals.

  1. Direct Measurement of Forces Between Linear Polysaccharides Xanthan and Schizophyllan

    NASA Astrophysics Data System (ADS)

    Rau, Donald C.; Parsegian, V. Adrian

    1990-09-01

    Direct osmotic stress measurements have been made of forces between helices of xanthan, an industrially important charged polysaccharide. Exponentially decaying hydration forces, much like those already measured between lipid bilayer membranes or DNA double helices, dominate the interactions at close separation. Interactions between uncharged schizophyllans also show the same kind of hydration force seen between xanthans. In addition to the practical possibilities for modifying solution and suspension properties through recognition and control of molecular forces, there is now finally the opportunity for theorists to relate macroscopic properties of a polymer solution to the microscopic properties that underlie them.

  2. Current Induced Forces on Adsorbates at Conducting Carbon Nanotubes

    NASA Technical Reports Server (NTRS)

    Mingo, N.; Yang, Liu; Han, Jie

    2001-01-01

    The problem addressed is force on an impurity due to electric current. In order to determine the size and direction of the force, as well as its dependence on the voltage, LCAO (Linear Combination of Atomic Orbitals) and the Green's Function approach were implemented. The resultant induced mean force was directed outwards in addition to a smaller component in the electron flow direction. At low bias, force is larger for larger radius, and crosses over the opposite trend when increasing the bias. The crossover current is approximately inversely proportional to the radius.

  3. Labyrinth seal forces on a whirling rotor

    NASA Technical Reports Server (NTRS)

    Wright, D. V.

    1983-01-01

    An experimental investigation of air labyrinth seal forces on a subsynchronously whirling model rotor is described and test results are given for diverging, converging, and straight two-strip seals. The effects of pressure drop, back pressure, whirl direction, and whirl frequency are shown. These results provide basic experimental data needed in the development of design methods for predicting and preventing self-excited whirl of turbine rotors and other machines having labyrinth seals. The total dynamic seal forces on the whirling model rotor are measured accurately by means of a novel active damping and stiffness system that is adjusted to obtain neutral whirl stability of the model rotor system. In addition, the whirling pressure pattern in the seal annulus is measured for a few test conditions and the corresponding pressure forces on the rotor are compared with the total measured forces. This comparison shows that either radial and axial pressure gradients in the seal annulus or drag forces on the rotor are significant.

  4. High-Resolution Traction Force Microscopy

    PubMed Central

    Plotnikov, Sergey V.; Sabass, Benedikt; Schwarz, Ulrich S.; Waterman, Clare M.

    2015-01-01

    Cellular forces generated by the actomyosin cytoskeleton and transmitted to the extracellular matrix (ECM) through discrete, integrin-based protein assemblies, that is, focal adhesions, are critical to developmental morphogenesis and tissue homeostasis, as well as disease progression in cancer. However, quantitative mapping of these forces has been difficult since there has been no experimental technique to visualize nanonewton forces at submicrometer spatial resolution. Here, we provide detailed protocols for measuring cellular forces exerted on two-dimensional elastic substrates with a high-resolution traction force microscopy (TFM) method. We describe fabrication of polyacrylamide substrates labeled with multiple colors of fiducial markers, functionalization of the substrates with ECM proteins, setting up the experiment, and imaging procedures. In addition, we provide the theoretical background of traction reconstruction and experimental considerations important to design a high-resolution TFM experiment. We describe the implementation of a new algorithm for processing of images of fiducial markers that are taken below the surface of the substrate, which significantly improves data quality. We demonstrate the application of the algorithm and explain how to choose a regularization parameter for suppression of the measurement error. A brief discussion of different ways to visualize and analyze the results serves to illustrate possible uses of high-resolution TFM in biomedical research. PMID:24974038

  5. Pairing forces in nuclei

    SciTech Connect

    Chasman, R.R.

    1996-12-31

    In this contribution, the author mentions some features of pairing forces that are unique to nuclei and cover some areas of major interest in nuclear structure research, that involve pairing. At the level of most nuclear structure studies, nuclei are treated as consisting of two kinds of fermions (protons and neutrons) in a valence space with rather few levels. These features give rise to unique aspects of pairing forces in nuclei: (1) n-p pairing in T = 0 as well as the usual T = 1 pairing that is characteristic of like fermions; (2) a need to correct pairing calculations for the (1/N) effects that can typically be neglected in superconducting solids. An issue of current concern is the nature of the pairing interaction: several recent studies suggest a need for a density dependent form of the pairing interaction. There is a good deal of feedback between the questions of accurate calculations of pairing interactions and the form and magnitude of the pairing interaction. Finally, the authors discuss some many-body wave functions that are a generalization of the BCS wave function form, and apply them to a calculation of energy level spacings in superdeformed rotational bands.

  6. Force reflecting hand controller

    NASA Technical Reports Server (NTRS)

    Mcaffee, Douglas A. (Inventor); Snow, Edward R. (Inventor); Townsend, William T. (Inventor)

    1993-01-01

    A universal input device for interfacing a human operator with a slave machine such as a robot or the like includes a plurality of serially connected mechanical links extending from a base. A handgrip is connected to the mechanical links distal from the base such that a human operator may grasp the handgrip and control the position thereof relative to the base through the mechanical links. A plurality of rotary joints is arranged to connect the mechanical links together to provide at least three translational degrees of freedom and at least three rotational degrees of freedom of motion of the handgrip relative to the base. A cable and pulley assembly for each joint is connected to a corresponding motor for transmitting forces from the slave machine to the handgrip to provide kinesthetic feedback to the operator and for producing control signals that may be transmitted from the handgrip to the slave machine. The device gives excellent kinesthetic feedback, high-fidelity force/torque feedback, a kinematically simple structure, mechanically decoupled motion in all six degrees of freedom, and zero backlash. The device also has a much larger work envelope, greater stiffness and responsiveness, smaller stowage volume, and better overlap of the human operator's range of motion than previous designs.

  7. Magnetic force microscopy

    PubMed Central

    Passeri, Daniele; Dong, Chunhua; Reggente, Melania; Angeloni, Livia; Barteri, Mario; Scaramuzzo, Francesca A; De Angelis, Francesca; Marinelli, Fiorenzo; Antonelli, Flavia; Rinaldi, Federica; Marianecci, Carlotta; Carafa, Maria; Sorbo, Angela; Sordi, Daniela; Arends, Isabel WCE; Rossi, Marco

    2014-01-01

    Magnetic force microscopy (MFM) is an atomic force microscopy (AFM) based technique in which an AFM tip with a magnetic coating is used to probe local magnetic fields with the typical AFM spatial resolution, thus allowing one to acquire images reflecting the local magnetic properties of the samples at the nanoscale. Being a well established tool for the characterization of magnetic recording media, superconductors and magnetic nanomaterials, MFM is finding constantly increasing application in the study of magnetic properties of materials and systems of biological and biomedical interest. After reviewing these latter applications, three case studies are presented in which MFM is used to characterize: (i) magnetoferritin synthesized using apoferritin as molecular reactor; (ii) magnetic nanoparticles loaded niosomes to be used as nanocarriers for drug delivery; (iii) leukemic cells labeled using folic acid-coated core-shell superparamagnetic nanoparticles in order to exploit the presence of folate receptors on the cell membrane surface. In these examples, MFM data are quantitatively analyzed evidencing the limits of the simple analytical models currently used. Provided that suitable models are used to simulate the MFM response, MFM can be used to evaluate the magnetic momentum of the core of magnetoferritin, the iron entrapment efficiency in single vesicles, or the uptake of magnetic nanoparticles into cells. PMID:25050758

  8. Forces Stabilizing Proteins

    PubMed Central

    Pace, C. Nick; Scholtz, J. Martin; Grimsley, Gerald R.

    2014-01-01

    The goal of this article is to summarize what has been learned about the major forces stabilizing proteins since the late 1980s when site-directed mutagenesis became possible. The following conclusions are derived from experimental studies of hydrophobic and hydrogen bonding variants. 1. Based on studies of 138 hydrophobic interaction variants in 11 proteins, burying a –CH2– group on folding contributes 1.1 ± 0.5 kcal/mol to protein stability. 2. The burial of nonpolar side chains contributes to protein stability in two ways: first, a term that depends on the removal of the side chains from water and, more importantly, the enhanced London dispersion forces that result from the tight packing in the protein interior. 3. Based on studies of 151 hydrogen bonding variants in 15 proteins, forming a hydrogen bond on folding contributes 1.1 ± 0.8 kcal/mol to protein stability. 4. The contribution of hydrogen bonds to protein stability is strongly context dependent. 5. Hydrogen bonds by side chains and peptide groups make similar contributions to protein stability. 6. Polar group burial can make a favorable contribution to protein stability even if the polar group is not hydrogen bonded. 7. Hydrophobic interactions and hydrogen bonds both make large contributions to protein stability. PMID:24846139

  9. Force-Field Parameter Fitter

    Energy Science and Technology Software Center (ESTSC)

    2015-05-27

    ParFit is a flexible and extendable framework and library of classes for fitting force-field parameters to data from high-level ab-initio calculations on the basis of deterministic and stochastic algorithms. Currently, the code is fitting MM3 and Merck force-field parameters but could easily extend to other force-field types.

  10. Electronic Force Gage for Welders

    NASA Technical Reports Server (NTRS)

    Bradley, J. W.; Gates, G.

    1983-01-01

    Welding force monitored in process. Electronic force gage uses strain gage on deformable member. Oscilloscope trace of welding force photographed and compared with standard trace during calibration and troubleshooting of resistance welding equipment. Adaptable to small scale resistance welding in electronics industry.

  11. Gradient and scattering forces in photoinduced force microscopy

    NASA Astrophysics Data System (ADS)

    Jahng, Junghoon; Brocious, Jordan; Fishman, Dmitry A.; Huang, Fei; Li, Xiaowei; Tamma, Venkata Ananth; Wickramasinghe, H. Kumar; Potma, Eric Olaf

    2014-10-01

    A theoretical and experimental analysis of the dominant forces measured in photoinduced force microscopy is presented. It is shown that when operated in the noncontact and soft-contact modes, the microscope is sensitive to the optically induced gradient force (Fg) and the scattering force (Fsc). The reconstructed force-distance curve reveals a tip-dependent scattering force in the 30-60 pN range. Whereas the scattering force is virtually insensitive to the nanoscopic tip-sample distance, the gradient force shows a z-4 dependence and is manifest only for tip-sample distances of a few nm. Measurements on glass, gold nanowires, and molecular clusters of silicon naphtalocyanine confirm that the gradient force is strongly dependent on the polarizability of the sample, enabling spectroscopic imaging through force detection. The nearly constant Fsc and the spatially dependent Fg give rise to a complex force-distance curve, which varies from point to point in the specimen and dictates the image contrast observed for a given set point of the cantilevered tip.

  12. Interfacial force sensor with force-feedback control

    SciTech Connect

    Joyce, S.A.; Houston, J.E.; Smith, B.K.

    1990-01-01

    A new interfacial force microscope capable of measuring the forces between two surfaces over the entire range of surface separations, up to contact, has been developed. The design is centered around a differential capacitance displacement sensor where the common capacitor plate is supported by torsion bars. A force-feedback control system balances the interfacial forces at the sensor, maintaining the common capacitor plate at its rest position. This control eliminates the instability which occurs with the conventional cantilever-based force sensors when the attractive force gradient exceeds the mechanical stiffness of the cantilever. The ability to measure interfacial forces at surface separations smaller than this instability point using the feedback control is demonstrated. 11 refs., 3 figs.

  13. Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors.

    PubMed

    Mosayebi, Majid; Louis, Ard A; Doye, Jonathan P K; Ouldridge, Thomas E

    2015-12-22

    The rupture of double-stranded DNA under stress is a key process in biophysics and nanotechnology. In this article, we consider the shear-induced rupture of short DNA duplexes, a system that has been given new importance by recently designed force sensors and nanotechnological devices. We argue that rupture must be understood as an activated process, where the duplex state is metastable and the strands will separate in a finite time that depends on the duplex length and the force applied. Thus, the critical shearing force required to rupture a duplex depends strongly on the time scale of observation. We use simple models of DNA to show that this approach naturally captures the observed dependence of the force required to rupture a duplex within a given time on duplex length. In particular, this critical force is zero for the shortest duplexes, before rising sharply and then plateauing in the long length limit. The prevailing approach, based on identifying when the presence of each additional base pair within the duplex is thermodynamically unfavorable rather than allowing for metastability, does not predict a time-scale-dependent critical force and does not naturally incorporate a critical force of zero for the shortest duplexes. We demonstrate that our findings have important consequences for the behavior of a new force-sensing nanodevice, which operates in a mixed mode that interpolates between shearing and unzipping. At a fixed time scale and duplex length, the critical force exhibits a sigmoidal dependence on the fraction of the duplex that is subject to shearing. PMID:26575598

  14. Force interactions between magnetite, silica, and bentonite studied with atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Dobryden, I.; Potapova, E.; Holmgren, A.; Weber, H.; Hedlund, J.; Almqvist, N.

    2015-04-01

    Iron ore pellets consist of variety of mineral particles and are an important refined product used in steel manufacturing. Production of high-quality pellets requires good understanding of interactions between different constituents, such as magnetite, gangue residues, bentonite, and additives. Much research has been reported on magnetite, silica, and bentonite surface properties and their effect on pellet strength but more scant with a focus on a fundamental particle-particle interaction. To probe such particle interaction, atomic force microscopy (AFM) using colloidal probe technique has proven to be a suitable tool. In this work, the measurements were performed between magnetite-magnetite, bentonite-magnetite, silica-bentonite, and silica-magnetite particles in 1 mM CaCl2 solution at various pH values. The interaction character, i.e., repulsion or attraction, was determined by measuring and analyzing AFM force curves. The observed quantitative changes in interaction forces were in good agreement with the measured zeta-potentials for the particles at the same experimental conditions. Particle aggregation was studied by measuring the adhesion force. Absolute values of adhesion forces for different systems could not be compared due to the difference in particle size and contact geometry. Therefore, the relative change of adhesion force between pH 6 and 10 was used for comparison. The adhesion force decreased for the magnetite-magnetite and bentonite-silica systems and slightly increased for the magnetite-bentonite system at pH 10 as compared to pH 6, whereas a pronounced decrease in adhesion force was observed in the magnetite-silica system. Thus, the presence of silica particles on the magnetite surface could have a negative impact on the interaction between magnetite and bentonite in balling due to the reduction of the adhesion force.

  15. Influence of impeller shroud forces on turbopump rotor dynamics

    NASA Technical Reports Server (NTRS)

    Williams, Jim P.; Childs, Dara W.

    1989-01-01

    The shrouded-impeller leakage path forces calculated by Childs (1987) have been analyzed to answer two questions. First, because of certain characteristics of the results of Childs, the forces could not be modeled with traditional approaches. Therefore, an approach has been devised to include the forces in conventional rotordynamic analyses. The forces were approximated by traditional stiffness, damping and inertia coefficients with the addition of whirl-frequency-dependent direct and cross-coupled stiffness terms. The forces were found to be well-modeled with this approach. Finally, the effect these forces had on a simple rotor-bearing system was analyzed, and, therefore, they, in addition to seal forces, were applied to a Jeffcott rotor. The traditional methods of dynamic system analysis were modified to incorporate the impeller forces and yielded results for the eigenproblem, frequency response, critical speed, transient response and an iterative technique for finding the frequency of free vibration as well as system stability. All results lead to the conclusion that the forces have little influence on natural frequency but can have appreciable effects on system stability. Specifically, at higher values of fluid swirl at the leakage path entrance, relative stability is reduced. The only unexpected response characteristics that occurred are attributed to the nonlinearity of the model.

  16. Incorporation of additives into polymers

    DOEpatents

    McCleskey, T. Mark; Yates, Matthew Z.

    2003-07-29

    There has been invented a method for incorporating additives into polymers comprising: (a) forming an aqueous or alcohol-based colloidal system of the polymer; (b) emulsifying the colloidal system with a compressed fluid; and (c) contacting the colloidal polymer with the additive in the presence of the compressed fluid. The colloidal polymer can be contacted with the additive by having the additive in the compressed fluid used for emulsification or by adding the additive to the colloidal system before or after emulsification with the compressed fluid. The invention process can be carried out either as a batch process or as a continuous on-line process.

  17. Deciphering the roles of multiple additives in organocatalyzed Michael additions.

    PubMed

    Günler, Z Inci; Companyó, Xavier; Alfonso, Ignacio; Burés, Jordi; Jimeno, Ciril; Pericàs, Miquel A

    2016-05-21

    The synergistic effects of multiple additives (water and acetic acid) on the asymmetric Michael addition of acetone to nitrostyrene catalyzed by primary amine-thioureas (PAT) were precisely determined. Acetic acid facilitates hydrolysis of the imine intermediates, thus leading to catalytic behavior, and minimizes the formation of the double addition side product. In contrast, water slows down the reaction but minimizes catalyst deactivation, eventually leading to higher final yields. PMID:27128165

  18. Updates on Force Limiting Improvements

    NASA Technical Reports Server (NTRS)

    Kolaini, Ali R.; Scharton, Terry

    2013-01-01

    The following conventional force limiting methods currently practiced in deriving force limiting specifications assume one-dimensional translation source and load apparent masses: Simple TDOF model; Semi-empirical force limits; Apparent mass, etc.; Impedance method. Uncorrelated motion of the mounting points for components mounted on panels and correlated, but out-of-phase, motions of the support structures are important and should be considered in deriving force limiting specifications. In this presentation "rock-n-roll" motions of the components supported by panels, which leads to a more realistic force limiting specifications are discussed.

  19. Parallel computation with the force

    NASA Technical Reports Server (NTRS)

    Jordan, H. F.

    1985-01-01

    A methodology, called the force, supports the construction of programs to be executed in parallel by a force of processes. The number of processes in the force is unspecified, but potentially very large. The force idea is embodied in a set of macros which produce multiproceossor FORTRAN code and has been studied on two shared memory multiprocessors of fairly different character. The method has simplified the writing of highly parallel programs within a limited class of parallel algorithms and is being extended to cover a broader class. The individual parallel constructs which comprise the force methodology are discussed. Of central concern are their semantics, implementation on different architectures and performance implications.

  20. Critical Casimir forces between planar and crenellated surfaces

    NASA Astrophysics Data System (ADS)

    Tröndle, M.; Harnau, L.; Dietrich, S.

    2015-06-01

    We study critical Casimir forces between planar walls and geometrically structured substrates within mean-field theory. As substrate structures, crenellated surfaces consisting of periodic arrays of rectangular crenels and merlons are considered. Within the widely used proximity force approximation, both the top surfaces of the merlons and the bottom surfaces of the crenels contribute to the critical Casimir force. However, for such systems the full, numerically determined critical Casimir forces deviate significantly from the pairwise addition formalism underlying the proximity force approximation. A first-order correction to the proximity force approximation is presented in terms of a step contribution arising from the critical Casimir interaction between a planar substrate and the right-angled steps of the merlons consisting of their upper and lower edges as well as their sidewalls.

  1. Anisotropic particles near surfaces: Propulsion force and friction

    NASA Astrophysics Data System (ADS)

    Müller, Boris; Krüger, Matthias

    2016-03-01

    We theoretically study the phenomenon of propulsion through Casimir forces in thermal nonequilibrium. Using fluctuational electrodynamics, we derive a formula for the propulsion force for an arbitrary small object in two scenarios: (i) for the object being isolated, and (ii) for the object being close to a planar surface. In the latter case, the propulsion force (i.e., the force parallel to the surface) increases with decreasing distance, i.e., it couples to the near field. We numerically calculate the lateral force acting on a hot spheroid near a surface and show that it can be as large as the gravitational force, thus being potentially measurable in fly-by experiments. We close by linking our results to well-known relations of linear-response theory in fluctuational electrodynamics: Looking at the friction of the anisotropic object for constant velocity, we identify a correction term that is additional to the typically used approach.

  2. Generalized force model of traffic dynamics

    NASA Astrophysics Data System (ADS)

    Helbing, Dirk; Tilch, Benno

    1998-07-01

    Floating car data of car-following behavior in cities were compared to existing microsimulation models, after their parameters had been calibrated to the experimental data. With these parameter values, additional simulations have been carried out, e.g., of a moving car which approaches a stopped car. It turned out that, in order to manage such kinds of situations without producing accidents, improved traffic models are needed. Good results were obtained with the proposed generalized force model.

  3. Silicon force sensor

    DOEpatents

    Galambos, Paul C.; Crenshaw, Thomas B.; Nishida, Erik E.; Burnett, Damon J.; Lantz, Jeffrey W.

    2016-07-05

    The various technologies presented herein relate to a sensor for measurement of high forces and/or high load shock rate(s), whereby the sensor utilizes silicon as the sensing element. A plate of Si can have a thinned region formed therein on which can be formed a number of traces operating as a Wheatstone bridge. The brittle Si can be incorporated into a layered structure comprising ductile and/or compliant materials. The sensor can have a washer-like configuration which can be incorporated into a nut and bolt configuration, whereby tightening of the nut and bolt can facilitate application of a compressive preload upon the sensor. Upon application of an impact load on the bolt, the compressive load on the sensor can be reduced (e.g., moves towards zero-load), however the magnitude of the preload can be such that the load on the sensor does not translate to tensile stress being applied to the sensor.

  4. [Galileo and centrifugal force].

    PubMed

    Vilain, Christiane

    This work intends to focus on Galileo's study of what is now called "centrifugal force," within the framework of the Second Day of his Dialogo written in 1632, rather than on the previously published commentaries on the topic. Galileo proposes three geometrical demonstrations in order to prove that gravity will always overcome centrifugalforce, and that the potential rotation of the Earth, whatever its speed, cannot in any case project objects beyond it. Each of these demonstrations must consequently contain an error and it has seemed to us that the first one had not been understood up until now. Our analysis offers an opportunity to return to Galileo's geometrical representation of dynamical questions; actually, we get an insight into the sophistication of Galileo's practices more than into his mistakes. Our second point, concerning the historiography of the problem, shows an evolution from anachronic critics to more contextual considerations, in the course of the second half of the twentieth century. PMID:25029818

  5. Force protection: today's reality.

    PubMed

    Torgerson, Ron

    2004-11-11

    Most US infrastructure and major chemical manufacturing facilities as well as their supporting utility systems are inherently vulnerable to a terrorist attack. Force protection is a military and civilian term used to protect personnel and critical facilities and assets against would-be aggressors or terrorists. The war on terrorism is a 200-300-year war. Terrorist attacks on US soil could become as common-place as in the State of Israel. It is very easy to penetrate infrastructure or plants as evidenced by vulnerability assessments performed for states, cities, plants, and military facilities by Versar and others around the country. Chemical, biological, radiological, nuclear, and explosive weapons can be readily used to attack facilities in the US. This paper will explain some of those vulnerabilities, outline the current DoD standard as it relates to vulnerability assessments, and explain how this may be used in commercial applications to deter potential aggressors. PMID:15573418

  6. Force Limit System

    NASA Technical Reports Server (NTRS)

    Pawlik, Ralph; Krause, David; Bremenour, Frank

    2011-01-01

    The Force Limit System (FLS) was developed to protect test specimens from inadvertent overload. The load limit value is fully adjustable by the operator and works independently of the test system control as a mechanical (non-electrical) device. When a test specimen is loaded via an electromechanical or hydraulic test system, a chance of an overload condition exists. An overload applied to a specimen could result in irreparable damage to the specimen and/or fixturing. The FLS restricts the maximum load that an actuator can apply to a test specimen. When testing limited-run test articles or using very expensive fixtures, the use of such a device is highly recommended. Test setups typically use electronic peak protection, which can be the source of overload due to malfunctioning components or the inability to react quickly enough to load spikes. The FLS works independently of the electronic overload protection.

  7. Forced Migration: Refugee Populations

    PubMed Central

    Boyle, Joyceen S.

    2015-01-01

    Undocumented migration is a global phenomenon that manifests in various contexts. This article describes the impact of the movement of large numbers of people in several African countries, producing a unique type of migrant—the refugee. We describe issues that refugee movements create on fragile health care systems, situations that precipitate refugee movements, certain human rights violations that are of particular concern such as gender based violence (GBV) and child soldiers, and lastly, implications for nursing practice and policy. We use examples from several countries in Sub-Saharan Africa, including the Democratic Republic of the Congo, Rwanda, Liberia, Sierra Leone, and Mozambique. Drawing on key documents from the United Nations High Commissioner for Refugees, current literature, as well as the international experience of the authors, this article presents an overview of forced migration and discusses opportunities for nurses to impact research, practice and policy related to refugee health. PMID:25645484

  8. Flow mechanotransduction regulates traction forces, intercellular forces, and adherens junctions

    PubMed Central

    Ting, Lucas H.; Jahn, Jessica R.; Jung, Joon I.; Shuman, Benjamin R.; Feghhi, Shirin; Han, Sangyoon J.; Rodriguez, Marita L.

    2012-01-01

    Endothelial cells respond to fluid shear stress through mechanotransduction responses that affect their cytoskeleton and cell-cell contacts. Here, endothelial cells were grown as monolayers on arrays of microposts and exposed to laminar or disturbed flow to examine the relationship among traction forces, intercellular forces, and cell-cell junctions. Cells under laminar flow had traction forces that were higher than those under static conditions, whereas cells under disturbed flow had lower traction forces. The response in adhesion junction assembly matched closely with changes in traction forces since adherens junctions were larger in size for laminar flow and smaller for disturbed flow. Treating the cells with calyculin-A to increase myosin phosphorylation and traction forces caused an increase in adherens junction size, whereas Y-27362 cause a decrease in their size. Since tugging forces across cell-cell junctions can promote junctional assembly, we developed a novel approach to measure intercellular forces and found that these forces were higher for laminar flow than for static or disturbed flow. The size of adherens junctions and tight junctions matched closely with intercellular forces for these flow conditions. These results indicate that laminar flow can increase cytoskeletal tension while disturbed flow decreases cytoskeletal tension. Consequently, we found that changes in cytoskeletal tension in response to shear flow conditions can affect intercellular tension, which in turn regulates the assembly of cell-cell junctions. PMID:22447948

  9. Normal Force and Drag Force in Magnetorheological Finishing

    SciTech Connect

    Miao, C.; Shafrir, S.N.; Lambropoulos, J.C.; Jacobs, S.D.

    2010-01-13

    The material removal in magnetorheological finishing (MRF) is known to be controlled by shear stress, tau, which equals drag force, Fd, divided by spot area, As. However, it is unclear how the normal force, Fn, affects the material removal in MRF and how the measured ratio of drag force to normal force Fd/Fn, equivalent to coefficient of friction, is related to material removal. This work studies, for the first time for MRF, the normal force and the measured ratio Fd/Fn as a function of material mechanical properties. Experimental data were obtained by taking spots on a variety of materials including optical glasses and hard ceramics with a spot-taking machine (STM). Drag force and normal force were measured with a dual load cell. Drag force decreases linearly with increasing material hardness. In contrast, normal force increases with hardness for glasses, saturating at high hardness values for ceramics. Volumetric removal rate decreases with normal force across all materials. The measured ratio Fd/Fn shows a strong negative linear correlation with material hardness. Hard materials exhibit a low “coefficient of friction”. The volumetric removal rate increases with the measured ratio Fd/Fn which is also correlated with shear stress, indicating that the measured ratio Fd/Fn is a useful measure of material removal in MRF.

  10. Microphotonic Forces from Superfluid Flow

    NASA Astrophysics Data System (ADS)

    McAuslan, D. L.; Harris, G. I.; Baker, C.; Sachkou, Y.; He, X.; Sheridan, E.; Bowen, W. P.

    2016-04-01

    In cavity optomechanics, radiation pressure and photothermal forces are widely utilized to cool and control micromechanical motion, with applications ranging from precision sensing and quantum information to fundamental science. Here, we realize an alternative approach to optical forcing based on superfluid flow and evaporation in response to optical heating. We demonstrate optical forcing of the motion of a cryogenic microtoroidal resonator at a level of 1.46 nN, roughly 1 order of magnitude larger than the radiation pressure force. We use this force to feedback cool the motion of a microtoroid mechanical mode to 137 mK. The photoconvective forces we demonstrate here provide a new tool for high bandwidth control of mechanical motion in cryogenic conditions, while the ability to apply forces remotely, combined with the persistence of flow in superfluids, offers the prospect for new applications.

  11. Force measurements during vibration testing

    SciTech Connect

    Smallwood, D.O.; Coleman, R.G.

    1993-12-31

    Experimental measurements of force into a ``rigid`` test item representing a typical system level vibration test were conducted to evaluate several methods of force measurements. The methods evaluated included: (1) Direct measurement with force gages between the test item and the fixturing; (2) Measurement of the force at the shaker/fixture interface and correcting the force required to drive the fixturing using two methods, (a) mass subtraction and (b) SWAT (sum of weighted accelerations technique), (3) Force deduced from voltage and current needed to drive the test item. All of the methods worked over a limited frequency range of five to a few hundred Hertz. The widest bandwidth was achieved with force at the shaker/fixture interface with SWAT corrections and from the voltage and current measurements.

  12. Future Air Force systems.

    PubMed

    Tremaine, S A

    1986-10-01

    Planning for the future is under way in earnest at the Aeronautical Systems Division (ASD) at Wright-Patterson Air Force Base. It has been statistically established that it takes from 14-16 years from the generation of a new system idea to enter into engineering development. With this unpleasing, but realistic, schedule in mind, ASD has, during the last 3 years, been initiating long-term planning projects that are pre-starts for new system ideas. They are generated from throughout the Air Force and are locally managed and funded. Through this process, which spans from 12-14 months, specific and revolutionary new ideas for the systems of the future are generated. This article addresses more than a dozen specific new ideas in work at ASD today. These ideas range from a need to replace the C-130 type aircraft after the year 2000 to planning a follow-on to the B-18 well into the 21st century. Among other specific projects are investigation into an immortal fighter intended to be free of reliability and maintenance demands for an especially long period of operation, a new training system and advanced trainer to replace the T-38, a transatmospheric vehicle that could operate in the 100,000-500,000 foot flight region (30,480-152,400 m), and a new means of defending against hostile cruise missile launchers and cruise missiles. Other ideas are also addressed. The article concludes with emphasis on systems that can operate hypersonically in and out of the known atmosphere and greater use of airbreathing propulsion systems operating between Mach 3 and Mach 6. PMID:3778403

  13. Research and Development of Small Force Standards at NIM

    NASA Astrophysics Data System (ADS)

    Hu, Gang; Song, Le; Meng, Feng; Zhang, Wei; Zhang, Zhimin; Zhang, Yue; Zheng, Yelong

    With the development and industrialization of micro- and nano- technology, small force measurements are widely applied in many fields such as advanced materials, bio-technology, aerospace and so on. For realizing traceable small forces and founding small force metrology hierarchy in China, NIM has launched a research project on small force metrology in 2011. 2 methods for small force realization at the scale of nano-Newton to micro-Newton are applied: electrical force based method and mass based method. The initial prototype of small force standard, which is based on the electrostatic force realization and adopts a coaxial cylindrical capacitor, has been developed and experimented. 2 kinds of micro force transmission mechanism are applied to the prototype: a parallelogram mechanism with 4 flexure hinges, and a lever-type force measurement system based on an elastic torsion bar. The structure and key units of 2 schemes are described in detail, the experiment results are demonstrated. The system stiffness of torsion bar scheme is smaller than that of flexure hinges scheme. In addition, structure of the initial prototype will be improved, and the environment conditions will be controlled strictly in our further experiments to minimize the creep of our system.

  14. Recent advances in the surface forces apparatus (SFA) technique

    NASA Astrophysics Data System (ADS)

    Israelachvili, J.; Min, Y.; Akbulut, M.; Alig, A.; Carver, G.; Greene, W.; Kristiansen, K.; Meyer, E.; Pesika, N.; Rosenberg, K.; Zeng, H.

    2010-03-01

    The surface forces apparatus (SFA) has been used for many years to measure the physical forces between surfaces, such as van der Waals (including Casimir) and electrostatic forces in vapors and liquids, adhesion and capillary forces, forces due to surface and liquid structure (e.g. solvation and hydration forces), polymer, steric and hydrophobic interactions, bio-specific interactions as well as friction and lubrication forces. Here we describe recent developments in the SFA technique, specifically the SFA 2000, its simplicity of operation and its extension into new areas of measurement of both static and dynamic forces as well as both normal and lateral (shear and friction) forces. The main reason for the greater simplicity of the SFA 2000 is that it operates on one central simple-cantilever spring to generate both coarse and fine motions over a total range of seven orders of magnitude (from millimeters to ångstroms). In addition, the SFA 2000 is more spacious and modulated so that new attachments and extra parts can easily be fitted for performing more extended types of experiments (e.g. extended strain friction experiments and higher rate dynamic experiments) as well as traditionally non-SFA type experiments (e.g. scanning probe microscopy and atomic force microscopy) and for studying different types of systems.

  15. Chin force in violin playing.

    PubMed

    Obata, Satoshi; Kinoshita, Hiroshi

    2012-06-01

    Force generated between the left mandible of violinists and the chinrest of the violin was examined using a force-sensing chinrest developed in this study. A strain-gauge force sensor was built, and it was fixed between the violin's top plate and a chin cup. Fifteen professional/amateur violinists held the violin statically, played musical scales with different sound properties and sounding techniques, as well as an excerpt from a Max Bruch concerto. Peak and mean forces were evaluated for each task. In a separate experiment, lateral movement of the lower teeth due to different levels of voluntary chin force exertion was measured. Static holding forces observed were 15 and 22 N with and without the help of the left hand, respectively. Peak force increased from 16 N at soft dynamics to 20 N at strong dynamics during scales. The force further increased to 29 N with the use of vibrato technique and 35 N during shifts. Tempo and hand position did not affect the force. Playing a Bruch concerto induced a mean peak force of 52 N, ranging from 31 to 82 N among the violinists. The developed force-sensing chinrest could accurately record the generated chin force. Typical chin force to stabilize the violin during ordinary musical performance was less than 30 N, but it could momentarily exceed 50 N when technically demanding musical pieces were performed. The lateral shift of the mandible was fairly small (<0.4 mm) even with high chin-force exertion, possibly due to clenching of the molars. PMID:21952980

  16. Numerical study of the hydrodynamic drag force in atomic force microscopy measurements undertaken in fluids.

    PubMed

    Méndez-Méndez, J V; Alonso-Rasgado, M T; Faria, E Correia; Flores-Johnson, E A; Snook, R D

    2014-11-01

    When atomic force microscopy (AFM) is employed for in vivo study of immersed biological samples, the fluid medium presents additional complexities, not least of which is the hydrodynamic drag force due to viscous friction of the cantilever with the liquid. This force should be considered when interpreting experimental results and any calculated material properties. In this paper, a numerical model is presented to study the influence of the drag force on experimental data obtained from AFM measurements using computational fluid dynamics (CFD) simulation. The model provides quantification of the drag force in AFM measurements of soft specimens in fluids. The numerical predictions were compared with experimental data obtained using AFM with a V-shaped cantilever fitted with a pyramidal tip. Tip velocities ranging from 1.05 to 105 μm/s were employed in water, polyethylene glycol and glycerol with the platform approaching from a distance of 6000 nm. The model was also compared with an existing analytical model. Good agreement was observed between numerical results, experiments and analytical predictions. Accurate predictions were obtained without the need for extrapolation of experimental data. In addition, the model can be employed over the range of tip geometries and velocities typically utilized in AFM measurements. PMID:25080275

  17. Enantioselective Michael Addition of Water

    PubMed Central

    Chen, Bi-Shuang; Resch, Verena; Otten, Linda G; Hanefeld, Ulf

    2015-01-01

    The enantioselective Michael addition using water as both nucleophile and solvent has to date proved beyond the ability of synthetic chemists. Herein, the direct, enantioselective Michael addition of water in water to prepare important β-hydroxy carbonyl compounds using whole cells of Rhodococcus strains is described. Good yields and excellent enantioselectivities were achieved with this method. Deuterium labeling studies demonstrate that a Michael hydratase catalyzes the water addition exclusively with anti-stereochemistry. PMID:25529526

  18. Probing cellular traction forces with magnetic nanowires and microfabricated force sensor arrays

    NASA Astrophysics Data System (ADS)

    Lin, Yi-Chia; Kramer, Corinne M.; Chen, Christopher S.; Reich, Daniel H.

    2012-02-01

    In this paper, the use of magnetic nanowires for the study of cellular response to force is demonstrated. High-aspect ratio Ni rods with diameter 300 nm and lengths up to 20 μm were bound to or internalized by pulmonary artery smooth muscle cells (SMCs) cultured on arrays of flexible micropost force sensors. Forces and torques were applied to the cells by driving the nanowires with AC magnetic fields in the frequency range 0.1-10 Hz, and the changes in cellular contractile forces were recorded with the microposts. These local stimulations yield global force reinforcement of the cells’ traction forces, but this contractile reinforcement can be effectively suppressed upon addition of a calcium channel blocker, ruthenium red, suggesting the role of calcium channels in the mechanical response. The responsiveness of the SMCs to actuation depends on the frequency of the applied stimulation. These results show that the combination of magnetic nanoparticles and micropatterned, flexible substrates can provide new approaches to the study of cellular mechanotransduction.

  19. Gasoline additives, emissions, and performance

    SciTech Connect

    1995-12-31

    The papers included in this publication deal with the influence of fuel, additive, and hardware changes on a variety of vehicle performance characteristics. Advanced techniques for measuring these performance parameters are also described. Contents include: Fleet test evaluation of gasoline additives for intake valve and combustion chamber deposit clean up; A technique for evaluating octane requirement additives in modern engines on dynamometer test stands; A fleet test of two additive technologies comparing their effects on tailpipe emissions; Investigation into the vehicle exhaust emissions of high percentage ethanol blends; Variability in hydrocarbon speciation measurements at low emission (ULEV) levels; and more.

  20. 19. Photographic copy of an asconstructed site plan for additions ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    19. Photographic copy of an as-constructed site plan for additions to North Base: Job No. Muroc A(511), Military Construction, Third District Region, San Bernardino, California; Muroc Bombing Range, Muroc Lake, Calif; Additional Temporary Construction, Materiel Center Flight Test Base, Location Grading & Paving Plan, Sheet No. 1 of 21, March 1943. Reproduced from the holdings of the National Archives, Pacific Southwest Region - Edwards Air Force Base, North Base, North Base Road, Boron, Kern County, CA

  1. 18. Photographic copy of site plan for additions to North ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    18. Photographic copy of site plan for additions to North Base: Job No. Muroc A(511), Military Construction, Third District Region, San Bernardino, California; Muroc Bombing Range, Muroc Lake, Calif; Additional Temporary Construction, Materiel Center Flight Test Base, Location Plan, February 1943. Reproduced from the holdings of the National Archives, Pacific Southwest Region - Edwards Air Force Base, North Base, North Base Road, Boron, Kern County, CA

  2. Variability of a "force signature" during windmill softball pitching and relationship between discrete force variables and pitch velocity.

    PubMed

    Nimphius, Sophia; McGuigan, Michael R; Suchomel, Timothy J; Newton, Robert U

    2016-06-01

    This study assessed reliability of discrete ground reaction force (GRF) variables over multiple pitching trials, investigated the relationships between discrete GRF variables and pitch velocity (PV) and assessed the variability of the "force signature" or continuous force-time curve during the pitching motion of windmill softball pitchers. Intraclass correlation coefficient (ICC) for all discrete variables was high (0.86-0.99) while the coefficient of variance (CV) was low (1.4-5.2%). Two discrete variables were significantly correlated to PV; second vertical peak force (r(5)=0.81, p=0.03) and time between peak forces (r(5)=-0.79; p=0.03). High ICCs and low CVs support the reliability of discrete GRF and PV variables over multiple trials and significant correlations indicate there is a relationship between the ability to produce force and the timing of this force production with PV. The mean of all pitchers' curve-average standard deviation of their continuous force-time curves demonstrated low variability (CV=4.4%) indicating a repeatable and identifiable "force signature" pattern during this motion. As such, the continuous force-time curve in addition to discrete GRF variables should be examined in future research as a potential method to monitor or explain changes in pitching performance. PMID:26999033

  3. Bottlebrush Polymer Additives for Binary Polymer Blends

    NASA Astrophysics Data System (ADS)

    Mah, Hui Zhen; Afzali, Pantea; Phan, Hanh; Qi, Luqing; Pesek, Stacy; Verduzco, Rafael; Stein, Gila

    Bottlebrush polymers are highly branched polymers that have been used in applications such as self-assembling photonics, drug delivery and stimuli-responsive surface coatings. However, they have not been widely studied as compatibilizers for polymer blends. In this study, bottlebrush polymers with poly(styrene-r-methyl methacrylate) side chains were used as additives for thin film blends of polystyrene (PS) and poly (methyl methacrylate) (PMMA). The blends were heated above the glass transition temperature to drive phase separation, and the resulting morphology was characterized with atomic force microscopy and optical microscopy. Outcomes were compared with PS/PMMA blends that contain conventional compatibilizers such as linear random copolymers of poly(styrene-r-methyl methacrylate) and diblock PS-PMMA copolymers. The bottlebrush additive accumulates at the PS/PMMA interface and drives the formation of vesicle-like droplets that assemble into longer chains. The continuity of the chains depends on the blend composition, where a network structure is achieved close to the critical composition. This unusual microstructure was not observed with the other additives, and may be a consequence of preferential wetting of the bottlebrush by the PS phase.

  4. 75 FR 5967 - Procurement List; Additions and Deletions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-05

    ...@AbilityOne.gov . SUPPLEMENTARY INFORMATION: Additions On 12/4/2009 (74 FR 63732) and 12/11/2009 (74 FR...., Santa Ana, CA Deletions On 11/23/2009 (74 FR 61114-61115) and 11/27/2009 (74 FR 62287), the Committee...: Declassification/Demilitarization of Hardware, Robins Air Force Base, GA. NPA: Epilepsy Association of...

  5. 1. Northeast front and southeast side of original section. Addition ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. Northeast front and southeast side of original section. Addition to rear view to west. - Offutt Air Force Base, Looking Glass Airborne Command Post, Aerospace Ground Equipment (AGE) Storage Facility, Far Northwest end of Project Looking Glass Historic District, Bellevue, Sarpy County, NE

  6. Computer Maintenance Operations Center (CMOC), additional computer support equipment ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Computer Maintenance Operations Center (CMOC), additional computer support equipment - Beale Air Force Base, Perimeter Acquisition Vehicle Entry Phased-Array Warning System, Techinical Equipment Building, End of Spencer Paul Road, north of Warren Shingle Road (14th Street), Marysville, Yuba County, CA

  7. Anterior Hip Joint Force Increases with Hip Extension, Decreased Gluteal Force, or Decreased Iliopsoas Force

    PubMed Central

    Lewis, Cara L.; Sahrmann, Shirley A.; Moran, Daniel W.

    2008-01-01

    Abnormal or excessive force on the anterior hip joint may cause anterior hip pain, subtle hip instability and a tear of the acetabular labrum. We propose that both the pattern of muscle force and hip joint position can affect the magnitude of anterior joint force and thus possibly lead to excessive force and injury. The purpose of this study was to determine the effect of hip joint position and of weakness of the gluteal and iliopsoas muscles on anterior hip joint force. We used a musculoskeletal model to estimate hip joint forces during simulated prone hip extension and supine hip flexion under 4 different muscle force conditions and across a range of hip extension and flexion positions. Weakness of specified muscles was simulated by decreasing the modeled maximum force value for the gluteal muscles during hip extension and the iliopsoas muscle during hip flexion. We found that decreased force contribution from the gluteal muscles during hip extension and the iliopsoas muscle during hip flexion resulted in an increase in the anterior hip joint force. The anterior hip joint force was greater when the hip was in extension than when the hip was in flexion. Further studies are warranted to determine if increased utilization of the gluteal muscles during hip extension and of the iliopsoas muscle during hip flexion, and avoidance of hip extension beyond neutral would be beneficial for people with anterior hip pain, subtle hip instability, or an anterior acetabular labral tear. PMID:17707385

  8. The Effect of Increasing Inertia upon Vertical Ground Reaction Forces during Locomotion

    NASA Technical Reports Server (NTRS)

    DeWitt, John K.; Hagan, R. Donald; Cromwell, Ronita L.

    2007-01-01

    The addition of inertia to exercising astronauts could increase ground reaction forces and potentially provide a greater health benefit. However, conflicting results have been reported regarding the adaptations to additional mass (inertia) without additional net weight (gravitational force) during locomotion. We examined the effect of increasing inertia while maintaining net gravitational force on vertical ground reaction forces and kinematics during walking and running. Vertical ground reaction force was measured for ten healthy adults (5 male/5 female) during walking (1.34 m/s) and running (3.13 m/s) using a force-measuring treadmill. Subjects completed locomotion at normal weight and mass, and at 10, 20, 30, and 40% of added inertial force. The added gravitational force was relieved with overhead suspension, so that the net force between the subject and treadmill at rest remained equal to 100% body weight. Peak vertical impact forces and loading rates increased with increased inertia during walking, and decreased during running. As inertia increased, peak vertical propulsive forces decreased during walking and did not change during running. Stride time increased during walking and running, and contact time increased during running. Vertical ground reaction force production and adaptations in gait kinematics were different between walking and running. The increased inertial forces were utilized independently from gravitational forces by the motor control system when determining coordination strategies.

  9. An Integrated Higgs Force Theory

    NASA Astrophysics Data System (ADS)

    Colella, Antonio

    2016-03-01

    An Integrated Higgs force theory (IHFT) was based on 2 key requirement amplifications: a matter particle/Higgs force was one and inseparable; a matter particle/Higgs force bidirectionally condensed/evaporated from/to super force. These were basis of 5 theories: particle creation, baryogenesis, superpartner/quark decays, spontaneous symmetry breaking, and stellar black holes. Our universe's 129 matter/force particles contained 64 supersymmetric Higgs particles; 9 transient matter particles/Higgs forces decayed to 8 permanent matter particles/Higgs forces; mass was given to a matter particle by its Higgs force and gravitons; and sum of 8 Higgs force energies of 8 permanent matter particles was dark energy. An IHFT's essence is the intimate physical relationships between 8 theories. These theories are independent because physicists in one theory worked independently of physicists in the other seven. An IHFT's premise is without sacrificing their integrities, 8 independent existing theories are replaced by 8 interrelated amplified theories. Requirement amplifications provide interfaces between the 8 theories. Intimate relationships between 8 theories including the above 5 and string, Higgs forces, and Super Universe are described. The sorting category selected was F. PARTICLES AND FIELDS (e.g., F1 Higgs Physics, F10 Alternative Beyond the Standard Model Physics, F11 Dark Sector Theories and Searches, and F12 Particle Cosmology).

  10. Theory of Casimir Forces without the Proximity-Force Approximation.

    PubMed

    Lapas, Luciano C; Pérez-Madrid, Agustín; Rubí, J Miguel

    2016-03-18

    We analyze both the attractive and repulsive Casimir-Lifshitz forces recently reported in experimental investigations. By using a kinetic approach, we obtain the Casimir forces from the power absorbed by the materials. We consider collective material excitations through a set of relaxation times distributed in frequency according to a log-normal function. A generalized expression for these forces for arbitrary values of temperature is obtained. We compare our results with experimental measurements and conclude that the model goes beyond the proximity-force approximation. PMID:27035293

  11. Theory of Casimir Forces without the Proximity-Force Approximation

    NASA Astrophysics Data System (ADS)

    Lapas, Luciano C.; Pérez-Madrid, Agustín; Rubí, J. Miguel

    2016-03-01

    We analyze both the attractive and repulsive Casimir-Lifshitz forces recently reported in experimental investigations. By using a kinetic approach, we obtain the Casimir forces from the power absorbed by the materials. We consider collective material excitations through a set of relaxation times distributed in frequency according to a log-normal function. A generalized expression for these forces for arbitrary values of temperature is obtained. We compare our results with experimental measurements and conclude that the model goes beyond the proximity-force approximation.

  12. Automated force controller for amplitude modulation atomic force microscopy.

    PubMed

    Miyagi, Atsushi; Scheuring, Simon

    2016-05-01

    Atomic Force Microscopy (AFM) is widely used in physics, chemistry, and biology to analyze the topography of a sample at nanometer resolution. Controlling precisely the force applied by the AFM tip to the sample is a prerequisite for faithful and reproducible imaging. In amplitude modulation (oscillating) mode AFM, the applied force depends on the free and the setpoint amplitudes of the cantilever oscillation. Therefore, for keeping the applied force constant, not only the setpoint amplitude but also the free amplitude must be kept constant. While the AFM user defines the setpoint amplitude, the free amplitude is typically subject to uncontrollable drift, and hence, unfortunately, the real applied force is permanently drifting during an experiment. This is particularly harmful in biological sciences where increased force destroys the soft biological matter. Here, we have developed a strategy and an electronic circuit that analyzes permanently the free amplitude of oscillation and readjusts the excitation to maintain the free amplitude constant. As a consequence, the real applied force is permanently and automatically controlled with picoNewton precision. With this circuit associated to a high-speed AFM, we illustrate the power of the development through imaging over long-duration and at various forces. The development is applicable for all AFMs and will widen the applicability of AFM to a larger range of samples and to a larger range of (non-specialist) users. Furthermore, from controlled force imaging experiments, the interaction strength between biomolecules can be analyzed. PMID:27250433

  13. The influence of electrostatic forces on the structure and dynamics of molecular ionic liquids

    NASA Astrophysics Data System (ADS)

    Schröder, C.; Steinhauser, O.

    2008-06-01

    The vast majority of molecular dynamics simulations are based on nonpolarizable force fields with fixed partial charges for all atoms. The traditional way to obtain these charges are quantum-mechanical calculations performed prior to simulation. Unfortunately, the set of the partial charges heavily relies on the method and the basis set used. Therefore, investigations of the influence of charge variation on simulation data are necessary in order to validate various charge sets. This paper elucidates the consequences of different charge sets on the structure and dynamics of the ionic liquid: 1-ethyl-3-methyl-imidazolium dicyanoamide. The structural features seem to be more or less independent of the partial charge set pointing to a dominance of shape force as modeled by Lennard-Jones parameters. This can be seen in the radial distribution and orientational correlation functions. The role of electrostatic forces comes in when studying dynamical properties. Here, significant deviations between different charge sets can be observed. Overall, dynamics seems to be governed by viscosity. In fact, all dynamical parameters presented in this work can be converted from one charge set to another by viscosity scaling.

  14. Color Addition and Subtraction Apps

    ERIC Educational Resources Information Center

    Ruiz, Frances; Ruiz, Michael J.

    2015-01-01

    Color addition and subtraction apps in HTML5 have been developed for students as an online hands-on experience so that they can more easily master principles introduced through traditional classroom demonstrations. The evolution of the additive RGB color model is traced through the early IBM color adapters so that students can proceed step by step…

  15. 75 FR 27313 - Proposed Additions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-14

    ... FROM PEOPLE WHO ARE BLIND OR SEVERELY DISABLED PROCUREMENT LIST Proposed Additions AGENCY: Committee for Purchase From People Who Are Blind or Severely Disabled. ACTION: Proposed additions to the... or Severely Disabled, Jefferson Plaza 2, Suite 10800, 1421 Jefferson Davis Highway,...

  16. Assessment of the Transferability of a Protein Force Field for the Simulation of Peptide-Surface Interactions

    PubMed Central

    Vellore, Nadeem A.; Yancey, Jeremy A.; Collier, Galen; Stuart, Steven J.

    2010-01-01

    In order to evaluate the transferability of existing empirical force fields for all-atom molecular simulations of protein adsorption behavior, we have developed and applied a method to calculate the adsorption free energy (ΔGads) of model peptides on functionalized surfaces for comparison with available experimental data. Simulations were conducted using the CHARMM program and force field using a host-guest peptide with the sequence TGTG-X-GTGT (where G and T are glycine and threonine amino acid residues, respectively, with X representing valine, threonine, aspartic acid, phenylalanine or lysine) over nine different functionalized alkanethiol self-assembled monolayer (SAM) surfaces with explicitly represented solvent. ΔGads was calculated using biased-energy replica exchange molecular dynamics to adequately sample the conformational states of the system. The simulation results showed that the CHARMM force-field was able to represent ΔGads within 1 kcal/mol of the experimental values for most systems, while deviations as large as 4 kcal/mol were found for others. In particular, the simulations reveal that CHARMM underestimates the strength of adsorption on the hydrophobic and positively charged amine surfaces. These results provide a means for force field evaluation and modification for the eventual development and validation of an interfacial force field for the accurate simulation of protein adsorption behavior. PMID:20222735

  17. Tunneling magnetic force microscopy

    NASA Technical Reports Server (NTRS)

    Burke, Edward R.; Gomez, Romel D.; Adly, Amr A.; Mayergoyz, Isaak D.

    1993-01-01

    We have developed a powerful new tool for studying the magnetic patterns on magnetic recording media. This was accomplished by modifying a conventional scanning tunneling microscope. The fine-wire probe that is used to image surface topography was replaced with a flexible magnetic probe. Images obtained with these probes reveal both the surface topography and the magnetic structure. We have made a thorough theoretical analysis of the interaction between the probe and the magnetic fields emanating from a typical recorded surface. Quantitative data about the constituent magnetic fields can then be obtained. We have employed these techniques in studies of two of the most important issues of magnetic record: data overwrite and maximizing data-density. These studies have shown: (1) overwritten data can be retrieved under certain conditions; and (2) improvements in data-density will require new magnetic materials. In the course of these studies we have developed new techniques to analyze magnetic fields of recorded media. These studies are both theoretical and experimental and combined with the use of our magnetic force scanning tunneling microscope should lead to further breakthroughs in the field of magnetic recording.

  18. Deep atomic force microscopy

    SciTech Connect

    Barnard, H.; Drake, B.; Randall, C.; Hansma, P. K.

    2013-12-15

    The Atomic Force Microscope (AFM) possesses several desirable imaging features including the ability to produce height profiles as well as two-dimensional images, in fluid or air, at high resolution. AFM has been used to study a vast selection of samples on the scale of angstroms to micrometers. However, current AFMs cannot access samples with vertical topography of the order of 100 μm or greater. Research efforts have produced AFM scanners capable of vertical motion greater than 100 μm, but commercially available probe tip lengths are still typically less than 10 μm high. Even the longest probe tips are below 100 μm and even at this range are problematic. In this paper, we present a method to hand-fabricate “Deep AFM” probes with tips of the order of 100 μm and longer so that AFM can be used to image samples with large scale vertical topography, such as fractured bone samples.

  19. Maximum bow force revisited.

    PubMed

    Mores, Robert

    2016-08-01

    Schelleng [J. Acoust. Soc. Am. 53, 26-41 (1973)], Askenfelt [J. Acoust. Soc. Am. 86, 503-516 (1989)], Schumacher [J. Acoust. Soc. Am. 96, 1985-1998 (1994)], and Schoonderwaldt, Guettler, and Askenfelt [Acta Acust. Acust. 94, 604-622 (2008)] formulated-in different ways-how the maximum bow force relates to bow velocity, bow-bridge distance, string impedance, and friction coefficients. Issues of uncertainty are how to account for friction or for the rotational admittance of the strings. Related measurements at the respective transitions between regimes of Helmholtz motion and non-Helmholtz motion employ a variety of bowing machines and stringed instruments. The related findings include all necessary parameters except the friction coefficients, leaving the underlying models unconfirmed. Here, a bowing pendulum has been constructed which allows precise measurement of relevant bowing parameters, including the friction coefficients. Two cellos are measured across all strings for three different bow-bridge distances. The empirical data suggest that-taking the diverse elements of existing models as options-Schelleng's model combined with Schumacher's velocity term yields the best fit. Furthermore, the pendulum employs a bow driving mechanism with adaptive impedance which discloses that mentioned regimes are stable and transitions between them sometimes require a hysteresis on related parameters. PMID:27586745

  20. Force Limited Vibration Testing Monograph

    NASA Technical Reports Server (NTRS)

    Scharton, Terry D.

    1997-01-01

    The practice of limiting the shaker force in vibration tests was investigated at the NASA Jet Propulsion Laboratory (JPL) in 1990 after the mechanical failure of an aerospace component during a vibration test. Now force limiting is used in almost every major vibration test at JPL and in many vibration tests at NASA Goddard Space Flight Center (GSFC) and at many aerospace contractors. The basic ideas behind force limiting have been in the literature for several decades, but the piezo-electric force transducers necessary to conveniently implement force limiting have been available only in the last decade. In 1993, funding was obtained from the NASA headquarters Office of Chief Engineer to develop and document the technology needed to establish force limited vibration testing as a standard approach available to all NASA centers and aerospace contractors. This monograph is the final report on that effort and discusses the history, theory, and applications of the method in some detail.

  1. Tangential torque effects on the control of grip forces when holding objects with a precision grip.

    PubMed

    Kinoshita, H; Bäckström, L; Flanagan, J R; Johansson, R S

    1997-09-01

    When we manipulate small objects, our fingertips are generally subjected to tangential torques about the axis normal to the grasp surface in addition to linear forces tangential to the grasp surface. Tangential torques can arise because the normal force is distributed across the contact area rather than focused at a point. We investigated the effects of tangential torques and tangential forces on the minimum normal forces required to prevent slips (slip force) and on the normal forces actually employed by subjects to hold an object in a stationary position with the use of the tips of the index finger and thumb. By changing the location of the object's center of gravity in relation to the grasp surface, various levels of tangential torque (0-50 N x mm) were created while the subject counteracted object rotation. Tangential force (0-3.4 N) was varied by changing the weight of the object. The flat grasp surfaces were covered with rayon, suede, or sandpaper, providing differences in friction in relation to the skin. Under zero tangential force, both the employed normal force and the slip force increased in proportion to tangential torque with a slope that reflected the current frictional condition. Likewise, with pure tangential force, these forces increased in proportion to tangential force. The effects of combined tangential torques and tangential forces on the slip force were primarily additive, but there was a significant interaction of these variables. Specifically, the increase in slip force for a given increment in torque decreases as a function of tangential force. A mathematical model was developed that successfully predicted slip force from tangential torque, tangential force, and an estimate of coefficient of static friction in the digit-surface interface. The effects of combined tangential torques and forces on the employed normal force showed the same pattern as the effects on the slip force. The safety margin against frictional slips, measured as the

  2. Entropic force and entanglement system

    SciTech Connect

    Myung, Yun Soo; Kim, Yong-Wan

    2010-05-15

    We introduce the isothermal cavity, static holographic screen, and accelerating surface as holographic screen to study the entropic force in the presence of the Schwarzschild black hole. These may merge to provide a consistent holographic screen to define the entropic force on the stretched horizon near the event horizon. Considering the similarity between the stretched horizon of black hole and the entanglement system, we may define the entropic force in the entanglement system without referring to the source mass.

  3. Interparticle Forces Underlying Nanoparticle Self-Assemblies.

    PubMed

    Luo, Dan; Yan, Cong; Wang, Tie

    2015-12-01

    Studies on the self-assembly of nanoparticles have been a hot topic in nanotechnology for decades and still remain relevant for the present and future due to their tunable collective properties as well as their remarkable applications to a wide range of fields. The novel properties of nanoparticle assemblies arise from their internal interactions and assemblies with the desired architecture key to constructing novel nanodevices. Therefore, a comprehensive understanding of the interparticle forces of nanoparticle self-assemblies is a pre-requisite to the design and control of the assembly processes, so as to fabricate the ideal nanomaterial and nanoproducts. Here, different categories of interparticle forces are classified and discussed according to their origins, behaviors and functions during the assembly processes, and the induced collective properties of the corresponding nanoparticle assemblies. Common interparticle forces, such as van der Waals forces, electrostatic interactions, electromagnetic dipole-dipole interactions, hydrogen bonds, solvophonic interactions, and depletion interactions are discussed in detail. In addition, new categories of assembly principles are summarized and introduced. These are termed template-mediated interactions and shape-complementary interactions. A deep understanding of the interactions inside self-assembled nanoparticles, and a broader perspective for the future synthesis and fabrication of these promising nanomaterials is provided. PMID:26436692

  4. Force fluctuation in a semiflexible loop

    NASA Astrophysics Data System (ADS)

    Waters, James; Kim, Harold; Harold Kim Team

    DNA-binding proteins can regulate genetic expression by holding two sites in close proximity, forming a closed loop. Such complexes may require strong bending of DNA segments on the order of one persistence length or less. Both this elastic bending and the thermal fluctuations of the DNA molecule are necessary to describe the resulting behavior. To explore this problem, we consider a discrete model of a wormlike chain, kept in the fixed extension ensemble. By using a novel method to sample conformations in both position and momentum space, we can obtain a distribution of constraint forces as a function of chain length, extension, and flexibility. Our coarse-grained model allows us to explore the space of these parameters more efficiently than a detailed molecular dynamics approach. We find that increasing contour length decreases average force by relieving bending stress, but that the additional freedom allows fluctuations in the constraint force to increase. This implies that the probability of large forces may go up even as the mean goes down, impacting the lifetime of such bound states in a way unforeseen by purely equilibrium methods.

  5. The Physics Force presents The Physics Circus

    NASA Astrophysics Data System (ADS)

    Dahlberg, E. Dan

    2015-03-01

    The Physics Force of the University of Minnesota is an outreach program developed with the goal to show students and the public Science is Fun, Science is Interesting, and Science is Understandable. The program grew from a rather small effort by three high school physics teachers and two University of Minnesota staff members. In the almost three decades since its humble beginnings of 100 attendees in a year, it has grown to an average attendance of over 36,000 annually. In the last three years alone, about 110,000 Minnesotans have seen a performance of The Physics Circus which is roughly 2% of the population of the state. In addition to the performances in Minnesota, The Force performed two years at Disney's Epcot Center, was featured on Newton's Apple, and made appearances on the very successful German TV science show, the Knoff-Hoff Show. I will begin the talk with some of our motivation to develop The Physics Force arising from the current ``scientific state'' of our society and then provide more information on The Force including both some history and examples taken from our Physics Circus.

  6. Coaxial atomic force microscope tweezers

    NASA Astrophysics Data System (ADS)

    Brown, K. A.; Aguilar, J. A.; Westervelt, R. M.

    2010-03-01

    We demonstrate coaxial atomic force microscope (AFM) tweezers that can trap and place small objects using dielectrophoresis (DEP). An attractive force is generated at the tip of a coaxial AFM probe by applying a radio frequency voltage between the center conductor and a grounded shield; the origin of the force is found to be DEP by measuring the pull-off force versus applied voltage. We show that the coaxial AFM tweezers can perform three-dimensional assembly by picking up a specified silica microsphere, imaging with the microsphere at the end of the tip, and placing it at a target destination.

  7. Sensing mode atomic force microscope

    DOEpatents

    Hough, Paul V.; Wang, Chengpu

    2004-11-16

    An atomic force microscope is described having a cantilever comprising a base and a probe tip on an end opposite the base; a cantilever drive device connected to the base; a magnetic material coupled to the probe tip, such that when an incrementally increasing magnetic field is applied to the magnetic material an incrementally increasing force will be applied to the probe tip; a moveable specimen base; and a controller constructed to obtain a profile height of a specimen at a point based upon a contact between the probe tip and a specimen, and measure an adhesion force between the probe tip and the specimen by, under control of a program, incrementally increasing an amount of a magnetic field until a release force, sufficient to break the contact, is applied. An imaging method for atomic force microscopy involving measuring a specimen profile height and adhesion force at multiple points within an area and concurrently displaying the profile and adhesion force for each of the points is also described. A microscope controller is also described and is constructed to, for a group of points, calculate a specimen height at a point based upon a cantilever deflection, a cantilever base position and a specimen piezo position; calculate an adhesion force between a probe tip and a specimen at the point by causing an incrementally increasing force to be applied to the probe tip until the probe tip separates from a specimen; and move the probe tip to a new point in the group.

  8. Sensing mode atomic force microscope

    DOEpatents

    Hough, Paul V. C.; Wang, Chengpu

    2006-08-22

    An atomic force microscope is described having a cantilever comprising a base and a probe tip on an end opposite the base; a cantilever drive device connected to the base; a magnetic material coupled to the probe tip, such that when an incrementally increasing magnetic field is applied to the magnetic material an incrementally increasing force will be applied to the probe tip; a moveable specimen base; and a controller constructed to obtain a profile height of a specimen at a point based upon a contact between the probe tip and a specimen, and measure an adhesion force between the probe tip and the specimen by, under control of a program, incrementally increasing an amount of a magnetic field until a release force, sufficient to break the contact, is applied. An imaging method for atomic force microscopy involving measuring a specimen profile height and adhesion force at multiple points within an area and concurrently displaying the profile and adhesion force for each of the points is also described. A microscope controller is also described and is constructed to, for a group of points, calculate a specimen height at a point based upon a cantilever deflection, a cantilever base position and a specimen piezo position; calculate an adhesion force between a probe tip and a specimen at the point by causing an incrementally increasing force to be applied to the probe tip until the probe tip separates from a specimen; and move the probe tip to a new point in the group.

  9. Force As A Momentum Current

    SciTech Connect

    Munera, Hector A.

    2010-07-28

    Advantages of a neo-Cartesian approach to classical mechanics are noted. If conservation of linear momentum is the fundamental principle, Newton's three laws become theorems. A minor paradox in static Newtonian mechanics is identified, and solved by reinterpreting force as a current of momentum. Contact force plays the role of a mere midwife in the exchange of momentum; however, force cannot be eliminated from physics because it provides the numerical value for momentum current. In this sense, in a neo-Cartesian formulation of mechanics the concept of force becomes strengthened rather than weakened.

  10. Color Addition and Subtraction Apps

    NASA Astrophysics Data System (ADS)

    Ruiz, Frances; Ruiz, Michael J.

    2015-10-01

    Color addition and subtraction apps in HTML5 have been developed for students as an online hands-on experience so that they can more easily master principles introduced through traditional classroom demonstrations. The evolution of the additive RGB color model is traced through the early IBM color adapters so that students can proceed step by step in understanding mathematical representations of RGB color. Finally, color addition and subtraction are presented for the X11 colors from web design to illustrate yet another real-life application of color mixing.

  11. Adding Value to Force Diagrams: Representing Relative Force Magnitudes

    ERIC Educational Resources Information Center

    Wendel, Paul

    2011-01-01

    Nearly all physics instructors recognize the instructional value of force diagrams, and this journal has published several collections of exercises to improve student skill in this area. Yet some instructors worry that too few students perceive the conceptual and problem-solving utility of force diagrams, and over recent years a rich variety of…

  12. Grip-load force coordination in cerebellar patients.

    PubMed

    Serrien, D J; Wiesendanger, M

    1999-09-01

    The study examined the anticipatory grip force modulations to load force changes during a drawer-opening task. An impact force was induced by a mechanical stop which abruptly arrested movement of the pulling hand. In performing this task, normal subjects generated a typical grip force profile characterized by an initial force impulse related to drawer movement onset, followed by a ramp-like grip force increase prior to the impending load perturbation. Finally, a reactive response was triggered by the impact. In patients with bilateral cerebellar dysfunction, the drawer-opening task was performed with an alternative control strategy. During pulling, grip force was increased to a high (overestimated) default level. The latter suggests that cerebellar patients were unable to adjust and to scale precisely the grip force according to the load force. In addition, the latency between impact and reactive activity was prolonged in the patients, suggesting an impaired cerebellar transmission of the long-latency responses. In conclusion, these data demonstrate the involvement of cerebellar circuits in both proactive and reactive mechanisms in view of predictable load perturbations during manipulative behavior. PMID:10473743

  13. Implication of radiative forcing distribution for energy transport

    NASA Astrophysics Data System (ADS)

    Huang, Yi

    2016-04-01

    Radiative forcing of a homogeneous greenhouse gas can be very inhomogeneous because the forcing is dependent on other atmospheric and surface variables. In the case of doubling CO2, the mean instantaneous forcing at the top of the atmosphere is found to vary geographically and temporally from positive to negative values, with the range being more than three times the magnitude of the global mean value. The vertical temperature change across the atmospheric column (temperature lapse rate) is found to be the best single predictor for explaining forcing variation. In addition, the masking effects of clouds and water vapor also contribute to forcing inhomogeneity. A regression model that predicts forcing from geophysical variables is constructed. This model can explain more than 90% of the variance of the forcing. Applying this model to analyzing the forcing variation in the CMIP5 models, we find that inter-model discrepancy in CO2 forcing caused by model climatology leads to considerable discrepancy in their projected change in poleward energy transport.

  14. Bacterial adhesion force quantification by fluidic force microscopy

    NASA Astrophysics Data System (ADS)

    Potthoff, Eva; Ossola, Dario; Zambelli, Tomaso; Vorholt, Julia A.

    2015-02-01

    Quantification of detachment forces between bacteria and substrates facilitates the understanding of the bacterial adhesion process that affects cell physiology and survival. Here, we present a method that allows for serial, single bacterial cell force spectroscopy by combining the force control of atomic force microscopy with microfluidics. Reversible bacterial cell immobilization under physiological conditions on the pyramidal tip of a microchanneled cantilever is achieved by underpressure. Using the fluidic force microscopy technology (FluidFM), we achieve immobilization forces greater than those of state-of-the-art cell-cantilever binding as demonstrated by the detachment of Escherichia coli from polydopamine with recorded forces between 4 and 8 nN for many cells. The contact time and setpoint dependence of the adhesion forces of E. coli and Streptococcus pyogenes, as well as the sequential detachment of bacteria out of a chain, are shown, revealing distinct force patterns in the detachment curves. This study demonstrates the potential of the FluidFM technology for quantitative bacterial adhesion measurements of cell-substrate and cell-cell interactions that are relevant in biofilms and infection biology.Quantification of detachment forces between bacteria and substrates facilitates the understanding of the bacterial adhesion process that affects cell physiology and survival. Here, we present a method that allows for serial, single bacterial cell force spectroscopy by combining the force control of atomic force microscopy with microfluidics. Reversible bacterial cell immobilization under physiological conditions on the pyramidal tip of a microchanneled cantilever is achieved by underpressure. Using the fluidic force microscopy technology (FluidFM), we achieve immobilization forces greater than those of state-of-the-art cell-cantilever binding as demonstrated by the detachment of Escherichia coli from polydopamine with recorded forces between 4 and 8 nN for many

  15. Atomic Force Microscope Operation

    NASA Technical Reports Server (NTRS)

    2008-01-01

    [figure removed for brevity, see original site] Click on image for animation (large file)

    This animation is a scientific illustration of the operation of NASA's Phoenix Mars Lander's Atomic Force Microscope, or AFM. The AFM is part of Phoenix's Microscopy, Electrochemistry, and Conductivity Analyzer, or MECA.

    The AFM is used to image the smallest Martian particles using a very sharp tip at the end of one of eight beams.

    The beam of the AFM is set into vibration and brought up to the surface of a micromachined silicon substrate. The substrate has etched in it a series of pits, 5 micrometers deep, designed to hold the Martian dust particles.

    The microscope then maps the shape of particles in three dimensions by scanning them with the tip.

    At the end of the animation is a 3D representation of the AFM image of a particle that was part of a sample informally called 'Sorceress.' The sample was delivered to the AFM on the 38th Martian day, or sol, of the mission (July 2, 2008).

    The image shows four round pits, only 5 microns in depth, that were micromachined into the silicon substrate.

    A Martian particle only one micrometer, or one millionth of a meter, across is held in the upper left pit.

    The rounded particle shown at the highest magnification ever seen from another world is a particle of the dust that cloaks Mars. Such dust particles color the Martian sky pink, feed storms that regularly envelop the planet and produce Mars' distinctive red soil.

    The AFM was developed by a Swiss-led consortium, with Imperial College London producing the silicon substrate that holds sampled particles.

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  16. Calculators and Computers: Graphical Addition.

    ERIC Educational Resources Information Center

    Spero, Samuel W.

    1978-01-01

    A computer program is presented that generates problem sets involving sketching graphs of trigonometric functions using graphical addition. The students use calculators to sketch the graphs and a computer solution is used to check it. (MP)

  17. Atomic Force Microscope Mediated Chromatography

    NASA Technical Reports Server (NTRS)

    Anderson, Mark S.

    2013-01-01

    sliding plate system, consisting of two flat surfaces, one of which has a recessed channel. A fluid flow is produced by axially sliding one plate past another, where the fluid has mechanical shear forces imposed at each point along the channel length. The shear-induced flow rates are very reproducible, and do not have pressure or voltage gradient limitations. SDC opens up a new range of enhanced separation kinetics by permitting the sample confinement with submicron dimensions. Small, highly confined liquid is advantageous for chromatographic separation because the separation rate is known to scale according to the square of the confined sample diameter. In addition, because shear-driven flows are not limited by fluid velocity, shear-driven liquid chromatography may provide up to 100,000 plate efficiency.

  18. Polyolefins as additives in plastics

    SciTech Connect

    Deanin, R.D.

    1993-12-31

    Polyolefins are not only major commodity plastics - they are also very useful as additives, both in other polyolefins and also in other types of plastics. This review covers ethylene, propylene, butylene and isobutylene polymers, in blends with each other, and as additives to natural rubber, styrene/butadiene rubber, polystyrene, polyvinyl chloride, polymethyl methacrylate, polyphenylene oxide, polycarbonate, thermoplastic polyesters, polyurethanes, polyamides, and mixed automotive plastics recycling.

  19. Optimisation of industrial production of low-force sensors - adhesive bonding of force-centring ball

    NASA Astrophysics Data System (ADS)

    Maeder, T.; Jacq, C.; Blot, M.; Ryser, P.

    2016-01-01

    This work addresses the issue of attaching the force-centring part (a round ball) to the load cell of a force sensor, a piezoresistive thick-film Wheatstone bridge deposited onto a ceramic cantilever. As the current soldering process requires expensive metallisation steps for both the ball and the cantilever, and subjects the solder pads used for mounting the cantilever to an additional reflow cycle, an alternative adhesive bonding process was developed, allowing both simpler production and the use of other ball materials such as ceramic and glass. The selfcentring action of solder capillary forces was ensured by structuring the adhesive so as to form a mechanical cuvette allowing centring of the ball by gravity. The selected adhesive materials exhibited good printability and bonding, as well as surviving the subsequent soldering and cleaning process steps.

  20. 26 CFR 20.2201-1 - Members of the Armed Forces dying during an induction period.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 26 Internal Revenue 14 2013-04-01 2013-04-01 false Members of the Armed Forces dying during an... Miscellaneous § 20.2201-1 Members of the Armed Forces dying during an induction period. (a) The additional...) (see paragraph (b) of this section) and while in active service as a member of the Armed Forces of...

  1. 26 CFR 20.2201-1 - Members of the Armed Forces dying during an induction period.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 26 Internal Revenue 14 2011-04-01 2010-04-01 true Members of the Armed Forces dying during an... Miscellaneous § 20.2201-1 Members of the Armed Forces dying during an induction period. (a) The additional...) (see paragraph (b) of this section) and while in active service as a member of the Armed Forces of...

  2. 26 CFR 20.2201-1 - Members of the Armed Forces dying during an induction period.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 26 Internal Revenue 14 2010-04-01 2010-04-01 false Members of the Armed Forces dying during an... Miscellaneous § 20.2201-1 Members of the Armed Forces dying during an induction period. (a) The additional...) (see paragraph (b) of this section) and while in active service as a member of the Armed Forces of...

  3. 75 FR 2785 - Naturalization for Certain Persons in the U.S. Armed Forces

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-19

    ... and 329 RIN 1615-AB85 Naturalization for Certain Persons in the U.S. Armed Forces AGENCY: U.S... year the length of time a member of the United States Armed Forces has to serve to qualify for naturalization through service in the Armed Forces. In addition, this rule amends DHS regulations by...

  4. 26 CFR 20.2201-1 - Members of the Armed Forces dying during an induction period.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 26 Internal Revenue 14 2014-04-01 2013-04-01 true Members of the Armed Forces dying during an... Miscellaneous § 20.2201-1 Members of the Armed Forces dying during an induction period. (a) The additional...) (see paragraph (b) of this section) and while in active service as a member of the Armed Forces of...

  5. Exotic nuclei and nuclear forces

    NASA Astrophysics Data System (ADS)

    Otsuka, Takaharu

    2013-01-01

    I overview new aspects of the structure of exotic nuclei as compared to stable nuclei, focusing on several characteristic effects of nuclear forces. The shell structure of nuclei has been proposed by Mayer and Jensen, and has been considered to be kept valid basically for all nuclei, with well-known magic numbers, 2, 8, 20, 28, 50, …. Nuclear forces were shown, very recently, to change this paradigm. It will be presented that the evolution of shell structure occurs in various ways as more neutrons and/or protons are added, and I will present basic points of this shell evolution in terms of the monopole interaction of nuclear forces. I will discuss three types of nuclear forces. The first one is the tensor force. The tensor force is one of the most fundamental nuclear forces, but its first-order effect on the shell structure has been clarified only recently in studies on exotic nuclei. The tensor force can change the spin-orbit splitting depending on the occupation of specific orbits. This results in changes of the shell structure in many nuclei, and consequently some of Mayer-Jensen's magic numbers are lost and new ones emerge, in certain nuclei. This mechanism can be understood in an intuitive way, meaning that the effect is general and robust. The second type of nuclear forces is central force. I will show a general but unknown property of the central force in the shell-model Hamiltonian that can describe nuclear properties in a good agreement with experiment. I will then demonstrate how it can be incorporated into a simple model of the central force, and will discuss how this force works in the shell evolution. Actually, by combining this central force with the tensor force, one can understand and foresee how the same proton-neutron interaction drives the shell evolution, for examples such as Sn/Sb isotopes, N = 20 nuclei and Ni/Cu isotopes. The distribution of single-particle strength is discussed also in comparison to (e,e‧p) experiment on 48Ca. The shell

  6. The Forced Hard Spring Equation

    ERIC Educational Resources Information Center

    Fay, Temple H.

    2006-01-01

    Through numerical investigations, various examples of the Duffing type forced spring equation with epsilon positive, are studied. Since [epsilon] is positive, all solutions to the associated homogeneous equation are periodic and the same is true with the forcing applied. The damped equation exhibits steady state trajectories with the interesting…

  7. Hebrew as a Binding Force.

    ERIC Educational Resources Information Center

    Fischler, Ben-Zion

    1990-01-01

    The role of the Hebrew language as a cohesive force and the history of modern Hebrew instruction are chronicled. It is proposed that despite the scattering of its speakers and periods of use only as a literary or business language, Hebrew has been a binding force for the Jewish people. It was with considerable struggle that Hebrew gained…

  8. Pseudo force acting between bodies

    NASA Astrophysics Data System (ADS)

    Baruah, Abhinav Ray; Deva, Anish; Sarma, Arun

    It has been shown that a non-contact force acts between two macroscopic physical objects held close together, which is not associated with the gravitational and electrostatic force. An experiment was conducted with objects of different mass, material and geometry to find the magnitude and properties of this apparent or pseudo force. The order of magnitude was found to be 10-5 and it remained constant for all types of objects while only the coefficient increased as the distance between the objects reduced. It only started acting at small distances and failed to make a body move if it experienced static friction from any contact surface. The nature of the force was found to be attractive as well as repulsive. Due to gravitation being a solely attractive force, it was eliminated as a possible reason for the pseudo force. The experiment was performed twice, once by grounding the apparatus and then again without grounding. The order of the force remained the same for both cases. As the test objects were held by hand, they were grounded through the human body. Also, none of the objects used were in contact with each other for the duration of this work, preventing any contact electrification. Due to these factors, the force was not considered electrostatic in nature.

  9. How Does Force Affect Motion?

    ERIC Educational Resources Information Center

    Darling, Gerald

    2012-01-01

    Whether playing soccer at recess, walking to lunch, or sitting at their desk, children encounter forces every moment of their lives. The connection between force and motion is absolutely amazing to children, so anyone working with them better be prepared for the battery of tough questions they ask: "What made the ball move that way? Why does a…

  10. Force Generation by Flapping Foils

    NASA Astrophysics Data System (ADS)

    Bandyopadhyay, P. R.; Donnelly, M.

    1996-11-01

    Aquatic animals like fish use flapping caudal fins to produce axial and cross-stream forces. During WW2, German scientists had built and tested an underwater vehicle powered by similar flapping foils. We have examined the forces produced by a pair of flapping foils. We have examined the forced produced by a pair of flapping foils attached to the tail end of a small axisymmetric cylinder. The foils operate in-phase (called waving), or in anti-phase (called clapping). In a low-speed water tunnel, we have undertaken time-dependent measurements of axial and cross-stream forces and moments that are exerted by the vortex shedding process over the entire body. Phase-matched LDV measurements of vorticity-velocity vectors, as well as limited flow visualization of the periodic vortex shedding process have also been carried out. The direction of the induced velocity within a pair of shed vortices determines the nature of the forces produced, viz., thrust or drag or cross-stream forces. The clapping mode produces a widely dispersed symmetric array of vortices which results in axial forces only (thrust and rag). On the other hand, the vortex array is staggered in the waving mode and cross-stream (maneuvering) forces are then generated.

  11. Dielectrophoresis force of colloidal nanoparticles

    NASA Astrophysics Data System (ADS)

    Huang, Hao; Ou-Yang, Daniel

    Dielectrophoresis (DEP) is the motion of a polarizable colloidal particle in a non­uniform electric field. The magnitude of the DEP force is known to be proportional to the gradient of E2. The DEP force also depends on the relative polarizability of the particle to that of the surrounding medium. Due to its ease of use, DEP has been proposed for a variety of applications to manipulate colloidal particles in a microfluidic setting. However, accurate measurements of the DEP force on colloidal nanoparticles are lacking. A new method is proposed to measure accurately the DEP potential force of colloidal nanoparticles by using confocal fluorescence imaging to determine the density distributions of dilute colloidal nanoparticle in a DEP potential force field. The DEP potential field can be calculated from the particle density distributions since the spatial distribution of the particle number density follows the Boltzmann distribution of the DEP potential energy. The validity of the measured DEP force is tested by examining the force as a function of the E field strength and particle size. The classic Maxwell­Wagner­O'Konski is found to be inadequate to fully describe the frequency dependence of the DEP force. NSF 0928299, Emulsion Polymer Institute, Department of Physics of Lehigh University.

  12. ADDITIVITY ASSESSMENT OF TRIHALOMETHANE MIXTURES BY PROPORTIONAL RESPONSE ADDITION

    EPA Science Inventory

    If additivity is known or assumed, the toxicity of a chemical mixture may be predicted from the dose response curves of the individual chemicals comprising the mixture. As single chemical data are abundant and mixture data sparse, mixture risk methods that utilize single chemical...

  13. Atomic Force Microscopy of Biological Membranes

    PubMed Central

    Frederix, Patrick L.T.M.; Bosshart, Patrick D.; Engel, Andreas

    2009-01-01

    Abstract Atomic force microscopy (AFM) is an ideal method to study the surface topography of biological membranes. It allows membranes that are adsorbed to flat solid supports to be raster-scanned in physiological solutions with an atomically sharp tip. Therefore, AFM is capable of observing biological molecular machines at work. In addition, the tip can be tethered to the end of a single membrane protein, and forces acting on the tip upon its retraction indicate barriers that occur during the process of protein unfolding. Here we discuss the fundamental limitations of AFM determined by the properties of cantilevers, present aspects of sample preparation, and review results achieved on reconstituted and native biological membranes. PMID:19167286

  14. Friction forces on atoms after acceleration

    DOE PAGESBeta

    Intravaia, Francesco; Mkrtchian, Vanik E.; Buhmann, Stefan Yoshi; Scheel, Stefan; Dalvit, Diego A. R.; Henkel, Carsten

    2015-05-12

    The aim of this study is to revisit the calculation of atom–surface quantum friction in the quantum field theory formulation put forward by Barton (2010 New J. Phys. 12 113045). We show that the power dissipated into field excitations and the associated friction force depend on how the atom is boosted from being initially at rest to a configuration in which it is moving at constant velocity (v) parallel to the planar interface. In addition, we point out that there is a subtle cancellation between the one-photon and part of the two-photon dissipating power, resulting in a leading order contributionmore » to the frictional power which goes as v4. These results are also confirmed by an alternative calculation of the average radiation force, which scales as v3.« less

  15. Friction forces on atoms after acceleration

    SciTech Connect

    Intravaia, Francesco; Mkrtchian, Vanik E.; Buhmann, Stefan Yoshi; Scheel, Stefan; Dalvit, Diego A. R.; Henkel, Carsten

    2015-05-12

    The aim of this study is to revisit the calculation of atom–surface quantum friction in the quantum field theory formulation put forward by Barton (2010 New J. Phys. 12 113045). We show that the power dissipated into field excitations and the associated friction force depend on how the atom is boosted from being initially at rest to a configuration in which it is moving at constant velocity (v) parallel to the planar interface. In addition, we point out that there is a subtle cancellation between the one-photon and part of the two-photon dissipating power, resulting in a leading order contribution to the frictional power which goes as v4. These results are also confirmed by an alternative calculation of the average radiation force, which scales as v3.

  16. Force-controlled lifting of molecular wires

    NASA Astrophysics Data System (ADS)

    Fournier, N.; Wagner, C.; Weiss, C.; Temirov, R.; Tautz, F. S.

    2011-07-01

    Lifting a single molecular wire off the surface with a combined frequency-modulated atomic force and tunneling microscope it is possible to monitor the evolution of both the wire configuration and the contacts simultaneously with the transport conductance experiment. In particular, critical points where individual bonds to the surface are broken and instabilities where the wire is prone to change its contact configuration can be identified in the force gradient and dissipation responses of the junction. This additional mechanical information can be used to unambiguously determine the conductance of a true molecular wire, that is, of a molecule that is contacted via a pointlike “crocodile clip” to each of the electrodes but is otherwise free.

  17. 76 FR 53419 - Procurement List; Proposed Additions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-26

    ...., Farmville, VA. Service Type/Location: Grounds Maintenance, Air Force Research Laboratory Stockbridge Test... Activity: Dept. of the Air Force, FA8751 AFRL RIKO, Rome, NY. Patricia Briscoe, Deputy Director,...

  18. Detecting the gravitational sensitivity of Paramecium caudatum using magnetic forces

    NASA Astrophysics Data System (ADS)

    Guevorkian, Karine; Valles, James M., Jr.

    2006-03-01

    Under normal conditions, Paramecium cells regulate their swimming speed in response to the pN level mechanical force of gravity. This regulation, known as gravikinesis, is more pronounced when the external force is increased by methods such as centrifugation. Here we present a novel technique that simulates gravity fields using the interactions between strong inhomogeneous magnetic fields and cells. We are able to achieve variable gravities spanning from 10xg to -8xg; where g is earth's gravity. Our experiments show that the swimming speed regulation of Paramecium caudatum to magnetically simulated gravity is a true physiological response. In addition, they reveal a maximum propulsion force for paramecia. This advance establishes a general technique for applying continuously variable forces to cells or cell populations suitable for exploring their force transduction mechanisms.

  19. Sensor for direct measurement of interaction forces in probe microscopy

    NASA Astrophysics Data System (ADS)

    Degertekin, F. L.; Onaran, A. G.; Balantekin, M.; Lee, W.; Hall, N. A.; Quate, C. F.

    2005-11-01

    We introduce a sensor for direct measurement of tip-sample interaction forces in probe microscopy. The sensor uses a micromachined membrane structure built on a transparent substrate with an integrated diffraction grating for optical interferometric detection, and a built-in electrostatic actuator. To demonstrate our concept for this sensor, we measured the force curves between an atomic force microscope (AFM) cantilever tip and a micromachined aluminum sensor membrane built on a quartz substrate. We also measured transient interaction forces exerted on the sensor membrane during each cycle of the vibrating AFM cantilever. These agree well with the temporal response of the sensor to a short force pulse applied by our integrated electrostatic actuator. With the addition of an integrated tip, this structure may be used for scanning probe microscopy with a bandwidth limited by the membrane dynamics.

  20. Recent Investments by NASA's National Force Measurement Technology Capability

    NASA Technical Reports Server (NTRS)

    Commo, Sean A.; Ponder, Jonathan D.

    2016-01-01

    The National Force Measurement Technology Capability (NFMTC) is a nationwide partnership established in 2008 and sponsored by NASA's Aeronautics Evaluation and Test Capabilities (AETC) project to maintain and further develop force measurement capabilities. The NFMTC focuses on force measurement in wind tunnels and provides operational support in addition to conducting balance research. Based on force measurement capability challenges, strategic investments into research tasks are designed to meet the experimental requirements of current and future aerospace research programs and projects. This paper highlights recent and force measurement investments into several areas including recapitalizing the strain-gage balance inventory, developing balance best practices, improving calibration and facility capabilities, and researching potential technologies to advance balance capabilities.

  1. Direct Cytoskeleton Forces Cause Membrane Softening in Red Blood Cells

    PubMed Central

    Rodríguez-García, Ruddi; López-Montero, Iván; Mell, Michael; Egea, Gustavo; Gov, Nir S.; Monroy, Francisco

    2015-01-01

    Erythrocytes are flexible cells specialized in the systemic transport of oxygen in vertebrates. This physiological function is connected to their outstanding ability to deform in passing through narrow capillaries. In recent years, there has been an influx of experimental evidence of enhanced cell-shape fluctuations related to metabolically driven activity of the erythroid membrane skeleton. However, no direct observation of the active cytoskeleton forces has yet been reported to our knowledge. Here, we show experimental evidence of the presence of temporally correlated forces superposed over the thermal fluctuations of the erythrocyte membrane. These forces are ATP-dependent and drive enhanced flickering motions in human erythrocytes. Theoretical analyses provide support for a direct force exerted on the membrane by the cytoskeleton nodes as pulses of well-defined average duration. In addition, such metabolically regulated active forces cause global membrane softening, a mechanical attribute related to the functional erythroid deformability. PMID:26083919

  2. Measurement and analysis of forces in grinding of silicon nitride

    SciTech Connect

    Jahanmir, S.; Hwang, T.; Whitenton, E.P.; Job, L.S.; Evans, C.J.

    1995-12-31

    Using an instrumented surface grinder, the two components of grinding forces (normal and tangential) were measured for different types of silicon nitride ceramics. The influences of grinding parameters, such as down feed and table speed, and grinding fluids on forces were determined. In addition to these measurements, the specific grinding energy defined as the energy per unit volume of removed material was calculated. This parameter and the measured forces were then analyzed to determine possible correlations with mechanical properties of the silicon nitrides. It was found that, in general, the grinding forces and the specific grinding energy increase with the hardness. Both the grinding forces and the specific grinding energy were influenced by the grinding fluid and the grinding parameters. The implication of these results on the mechanisms of material removal in grinding of silicon nitride and the possible tribological effects are discussed.

  3. Entropic forces in Brownian motion

    NASA Astrophysics Data System (ADS)

    Roos, Nico

    2014-12-01

    Interest in the concept of entropic forces has risen considerably since Verlinde proposed in 2011 to interpret the force in Newton's second law and gravity as entropic forces. Brownian motion—the motion of a small particle (pollen) driven by random impulses from the surrounding molecules—may be the first example of a stochastic process in which such forces are expected to emerge. In this article, it is shown that at least two types of entropic force can be identified in three-dimensional Brownian motion. This analysis yields simple derivations of known results of Brownian motion, Hooke's law, and—applying an external (non-radial) force—Curie's law and the Langevin-Debye equation.

  4. Nonadditivity of critical Casimir forces

    NASA Astrophysics Data System (ADS)

    Paladugu, Sathyanarayana; Callegari, Agnese; Tuna, Yazgan; Barth, Lukas; Dietrich, Siegfried; Gambassi, Andrea; Volpe, Giovanni

    2016-04-01

    In soft condensed matter physics, effective interactions often emerge due to the spatial confinement of fluctuating fields. For instance, microscopic particles dissolved in a binary liquid mixture are subject to critical Casimir forces whenever their surfaces confine the thermal fluctuations of the order parameter of the solvent close to its critical demixing point. These forces are theoretically predicted to be nonadditive on the scale set by the bulk correlation length of the fluctuations. Here we provide direct experimental evidence of this fact by reporting the measurement of the associated many-body forces. We consider three colloidal particles in optical traps and observe that the critical Casimir force exerted on one of them by the other two differs from the sum of the forces they exert separately. This three-body effect depends sensitively on the distance from the critical point and on the chemical functionalisation of the colloid surfaces.

  5. Gene regulation by mechanical forces

    NASA Technical Reports Server (NTRS)

    Oluwole, B. O.; Du, W.; Mills, I.; Sumpio, B. E.

    1997-01-01

    Endothelial cells are subjected to various mechanical forces in vivo from the flow of blood across the luminal surface of the blood vessel. The purpose of this review was to examine the data available on how these mechanical forces, in particular cyclic strain, affect the expression and regulation of endothelial cell function. Studies from various investigators using models of cyclic strain in vitro have shown that various vasoactive mediators such as nitric oxide and prostacyclin are induced by the effect of mechanical deformation, and that the expression of these mediators may be regulated at the transcription level by mechanical forces. There also seems to be emerging evidence that endothelial cells may also act as mechanotransducers, whereby the transmission of external forces induces various cytoskeletal changes and second messenger cascades. Furthermore, it seems these forces may act on specific response elements of promoter genes.

  6. Nonadditivity of critical Casimir forces.

    PubMed

    Paladugu, Sathyanarayana; Callegari, Agnese; Tuna, Yazgan; Barth, Lukas; Dietrich, Siegfried; Gambassi, Andrea; Volpe, Giovanni

    2016-01-01

    In soft condensed matter physics, effective interactions often emerge due to the spatial confinement of fluctuating fields. For instance, microscopic particles dissolved in a binary liquid mixture are subject to critical Casimir forces whenever their surfaces confine the thermal fluctuations of the order parameter of the solvent close to its critical demixing point. These forces are theoretically predicted to be nonadditive on the scale set by the bulk correlation length of the fluctuations. Here we provide direct experimental evidence of this fact by reporting the measurement of the associated many-body forces. We consider three colloidal particles in optical traps and observe that the critical Casimir force exerted on one of them by the other two differs from the sum of the forces they exert separately. This three-body effect depends sensitively on the distance from the critical point and on the chemical functionalisation of the colloid surfaces. PMID:27097797

  7. Nonadditivity of critical Casimir forces

    PubMed Central

    Paladugu, Sathyanarayana; Callegari, Agnese; Tuna, Yazgan; Barth, Lukas; Dietrich, Siegfried; Gambassi, Andrea; Volpe, Giovanni

    2016-01-01

    In soft condensed matter physics, effective interactions often emerge due to the spatial confinement of fluctuating fields. For instance, microscopic particles dissolved in a binary liquid mixture are subject to critical Casimir forces whenever their surfaces confine the thermal fluctuations of the order parameter of the solvent close to its critical demixing point. These forces are theoretically predicted to be nonadditive on the scale set by the bulk correlation length of the fluctuations. Here we provide direct experimental evidence of this fact by reporting the measurement of the associated many-body forces. We consider three colloidal particles in optical traps and observe that the critical Casimir force exerted on one of them by the other two differs from the sum of the forces they exert separately. This three-body effect depends sensitively on the distance from the critical point and on the chemical functionalisation of the colloid surfaces. PMID:27097797

  8. Entropic forces exerted on a rough wall by a grafted semiflexible polymer.

    PubMed

    Bayati, Parvin; Ghassab, Leila; Najafi, Ali

    2014-10-01

    We study the entropic force due to a fluctuating semiflexible polymer that is grafted from one end and confined by a rigid and rough wall from the other end. We show how roughness of the wall modifies the entropic force. In addition to the perpendicular force that is present in the case of a flat wall, roughness of the wall adds a lateral component to the force. Both perpendicular and lateral components of the force are examined for different values of amplitude and wavelength of the roughness and at different temperatures. The lateral force is controlled by the local slope of the wall while the perpendicular force is only sensitive to the curvature of the wall. We show that for small compression, the entropic force is increased by increasing the curvature of the confining wall. In addition to the biophysical relevance, the results may also be useful in developing an AFM-based experimental technique for probing the roughness of surfaces. PMID:25315449

  9. [INVITED] Lasers in additive manufacturing

    NASA Astrophysics Data System (ADS)

    Pinkerton, Andrew J.

    2016-04-01

    Additive manufacturing is a topic of considerable ongoing interest, with forecasts predicting it to have major impact on industry in the future. This paper focusses on the current status and potential future development of the technology, with particular reference to the role of lasers within it. It begins by making clear the types and roles of lasers in the different categories of additive manufacturing. This is followed by concise reviews of the economic benefits and disadvantages of the technology, current state of the market and use of additive manufacturing in different industries. Details of these fields are referenced rather than expanded in detail. The paper continues, focusing on current indicators to the future of additive manufacturing. Barriers to its development, trends and opportunities in major industrial sectors, and wider opportunities for its development are covered. Evidence indicates that additive manufacturing may not become the dominant manufacturing technology in all industries, but represents an excellent opportunity for lasers to increase their influence in manufacturing as a whole.

  10. Evaluation of certain food additives.

    PubMed

    2015-01-01

    This report represents the conclusions of a Joint FAO/WHO Expert Committee convened to evaluate the safety of various food additives, including flavouring agents, and to prepare specifications for identity and purity. The first part of the report contains a general discussion of the principles governing the toxicological evaluation of and assessment of dietary exposure to food additives, including flavouring agents. A summary follows of the Committee's evaluations of technical, toxicological and dietary exposure data for eight food additives (Benzoe tonkinensis; carrageenan; citric and fatty acid esters of glycerol; gardenia yellow; lutein esters from Tagetes erecta; octenyl succinic acid-modified gum arabic; octenyl succinic acid-modified starch; paprika extract; and pectin) and eight groups of flavouring agents (aliphatic and alicyclic hydrocarbons; aliphatic and aromatic ethers; ionones and structurally related substances; miscellaneous nitrogen-containing substances; monocyclic and bicyclic secondary alcohols, ketones and related esters; phenol and phenol derivatives; phenyl-substituted aliphatic alcohols and related aldehydes and esters; and sulfur-containing heterocyclic compounds). Specifications for the following food additives were revised: citric acid; gellan gum; polyoxyethylene (20) sorbitan monostearate; potassium aluminium silicate; and Quillaia extract (Type 2). Annexed to the report are tables summarizing the Committee's recommendations for dietary exposures to and toxicological evaluations of all of the food additives and flavouring agents considered at this meeting. PMID:26118220

  11. Kelvin Probe Force Microscopy by Dissipative Electrostatic Force Modulation

    NASA Astrophysics Data System (ADS)

    Miyahara, Yoichi; Topple, Jessica; Schumacher, Zeno; Grutter, Peter

    2015-11-01

    We report an experimental technique for Kelvin probe force microscopy using the dissipation signal of frequency-modulation atomic force microscopy for bias-voltage feedback. It features a simple implementation and faster scanning as it requires no low-frequency modulation. The dissipation is caused by the oscillating electrostatic force that is coherent with the tip oscillation, which is induced by a sinusoidally oscillating voltage applied between the tip and sample. We analyze the effect of the phase of the oscillating force on the frequency shift and dissipation and found that the relative phase of 90° that causes only the dissipation is the most appropriate for Kelvin-probe-force-microscopy measurements. The present technique requires a significantly smaller ac-voltage amplitude by virtue of enhanced force detection due to the resonance enhancement and the use of fundamental flexural-mode oscillation for electrostatic force detection. This feature will be of great importance in the electrical characterizations of technically relevant materials whose electrical properties are influenced by the externally applied electric field as is the case in semiconductor electronic devices.

  12. Manipulating crystallization with molecular additives.

    PubMed

    Shtukenberg, Alexander G; Lee, Stephanie S; Kahr, Bart; Ward, Michael D

    2014-01-01

    Given the importance of organic crystals in a wide range of industrial applications, the chemistry, biology, materials science, and chemical engineering communities have focused considerable attention on developing methods to control crystal structure, size, shape, and orientation. Tailored additives have been used to control crystallization to great effect, presumably by selectively binding to particular crystallographic surfaces and sites. However, substantial knowledge gaps still exist in the fundamental mechanisms that govern the formation and growth of organic crystals in both the absence and presence of additives. In this review, we highlight research discoveries that reveal the role of additives, either introduced by design or present adventitiously, on various stages of formation and growth of organic crystals, including nucleation, dislocation spiral growth mechanisms, growth inhibition, and nonclassical crystal morphologies. The insights from these investigations and others of their kind are likely to guide the development of innovative methods to manipulate crystallization for a wide range of materials and applications. PMID:24579880

  13. Additive Manufacturing of Hybrid Circuits

    NASA Astrophysics Data System (ADS)

    Sarobol, Pylin; Cook, Adam; Clem, Paul G.; Keicher, David; Hirschfeld, Deidre; Hall, Aaron C.; Bell, Nelson S.

    2016-07-01

    There is a rising interest in developing functional electronics using additively manufactured components. Considerations in materials selection and pathways to forming hybrid circuits and devices must demonstrate useful electronic function; must enable integration; and must complement the complex shape, low cost, high volume, and high functionality of structural but generally electronically passive additively manufactured components. This article reviews several emerging technologies being used in industry and research/development to provide integration advantages of fabricating multilayer hybrid circuits or devices. First, we review a maskless, noncontact, direct write (DW) technology that excels in the deposition of metallic colloid inks for electrical interconnects. Second, we review a complementary technology, aerosol deposition (AD), which excels in the deposition of metallic and ceramic powder as consolidated, thick conformal coatings and is additionally patternable through masking. Finally, we show examples of hybrid circuits/devices integrated beyond 2-D planes, using combinations of DW or AD processes and conventional, established processes.

  14. Tougher Addition Polyimides Containing Siloxane

    NASA Technical Reports Server (NTRS)

    St. Clair, T. L.; Maudgal, S.

    1986-01-01

    Laminates show increased impact resistances and other desirable mechanical properties. Bismaleamic acid extended by reaction of diaminosiloxane with maleic anhydride in 1:1 molar ratio, followed by reaction with half this molar ratio of aromatic dianhydride. Bismaleamic acid also extended by reaction of diaminosiloxane with maleic anhydride in 1:2 molar ratio, followed by reaction with half this molar ratio of aromatic diamine (Michael-addition reaction). Impact resistances improved over those of unmodified bismaleimide, showing significant increase in toughness. Aromatic addition polyimides developed as both matrix and adhesive resins for applications on future aircraft and spacecraft.

  15. ForceFit: a code to fit classical force fields to ab-initio potential energy surfaces

    SciTech Connect

    Henson, Neil Jon; Waldher, Benjamin; Kuta, Jadwiga; Clark, Aurora; Clark, Aurora E

    2009-01-01

    The ForceFit program package has been developed for fitting classical force field parameters based upon a force matching algorithm to quantum mechanical gradients of configurations that span the potential energy surface of the system. The program, which runs under Unix and is written in C++, is an easy to use, nonproprietary platform that enables gradient fitting of a wide variety of functional force field forms to quantum mechanical information obtained from an array of common electronic structure codes. All aspects of the fitting process are run from a graphical user interface, from the parsing of quantum mechanical data, assembling of a potential energy surface database, setting the force field and variables to be optimized, choosing a molecular mechanics code for comparison to the reference data, and finally, the initiation of a least squares minimization algorithm. Furthermore, the code is based on a modular templated code design that enables the facile addition of new functionality to the program.

  16. Application of Lorentz force techniques for flow rate measurement

    NASA Astrophysics Data System (ADS)

    Ebert, Reschad Johann; Resagk, Christian

    2014-11-01

    We report on the progress of the Lorentz force velocimetry (LFV): a contactless non-invasive flow velocity measurement technique. This method has been developed and demonstrated for various applications in our institute and in industry. At applications for weakly conducting fluids such as electrolytes with conductivities in the range of 1 - 10 S/m the challenging bottleneck is the detection of the tiny Lorentz forces in the noisy environment of the test channel. For the force measurement a state-of-the-art electromagnetic force compensation balance is used. Due to this device the mass of the Lorentz force generating magnets is limited. For enabling larger magnet systems and for higher force signals we have developed and tested a buoyancy based weight force compensation method which will be presented here. Additionally, results of LFV measurements at non-symmetric fluid profiles will be shown. By that an evaluation of the feasibility of this measurement principle for disturbed fluid profiles that are relevant for developing the LFV for weakly conducting fluids towards industrial applications can be made. Additionally a prospective setup for using the LFV for molten salt flows will be explained.

  17. Technical Note: Estimating Aerosol Effects on Cloud Radiative Forcing

    SciTech Connect

    Ghan, Steven J.

    2013-10-09

    Estimating anthropogenic aerosol effects on the planetary energy balance through the aerosol influence on clouds using the difference in cloud radiative forcing from simulations with and without anthropogenic emissions produces estimates that are positively biased. A more representative method is suggested using the difference in cloud radiative forcing calculated with aerosol radiative effects neglected. The method also yields an aerosol radiative forcing decomposition that includes a term quantifying the impact of changes in surface albedo. The method requires only two additional diagnostic calculations: the whole-sky and clear-sky top-of-atmosphere radiative flux with aerosol radiative effects neglected.

  18. Fluctuation-induced casimir forces in granular fluids.

    PubMed

    Cattuto, C; Brito, R; Marconi, U Marini Bettolo; Nori, F; Soto, R

    2006-05-01

    We numerically investigate the behavior of driven noncohesive granular media and find that two fixed large intruder particles, immersed in a sea of small particles, experience, in addition to a short-range depletion force, a long-range repulsive force. The observed long-range interaction is fluctuation-induced and we propose a mechanism similar to the Casimir effect that generates it: The hydrodynamic fluctuations are geometrically confined between the intruders, producing an unbalanced renormalized pressure. An estimation based on computing the possible Fourier modes explains the repulsive force and is in qualitative agreement with the simulations. PMID:16712336

  19. Polarization force-induced changes in the dust sheath formation

    SciTech Connect

    Mayout, Saliha; Bentabet, Karima; Tribeche, Mouloud

    2015-09-15

    The modifications arising in the dusty plasma sheath structure due to the presence of polarization forces acting on the dust grains are investigated. The corresponding appropriate Bohm criterion for sheath formation is obtained. It is found that the critical Mach number, beyond which the dusty plasma electrostatic sheath sets in, decreases whenever the polarization effects become important. In addition, when the polarization force dominates over the electrical one, the dust plasma sheath cannot set in. This happens whenever the dust grain size exceeds a critical threshold. Moreover, the sheath electrostatic potential-gradient becomes abruptly steep, and the sheath thickness becomes broader as the polarization force effects strengthen.

  20. Promoting Additive Acculturation in Schools.

    ERIC Educational Resources Information Center

    Gibson, Margaret A.

    1995-01-01

    A study focusing on 113 ninth graders of Mexican descent indicates that most students and their parents adhere to a strategy of additive acculturation (incorporating skills of the new culture and language), but that the school curriculum and general school climate devalue Mexican culture. (SLD)