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Sample records for hydrophobic interaction model

  1. Soft matter interactions at the molecular scale: interaction forces and energies between single hydrophobic model peptides.

    Science.gov (United States)

    Stock, Philipp; Utzig, Thomas; Valtiner, Markus

    2017-02-08

    In all realms of soft matter research a fundamental understanding of the structure/property relationships based on molecular interactions is crucial for developing a framework for the targeted design of soft materials. However, a molecular picture is often difficult to ascertain and yet essential for understanding the many different competing interactions at play, including entropies and cooperativities, hydration effects, and the enormous design space of soft matter. Here, we characterized for the first time the interaction between single hydrophobic molecules quantitatively using atomic force microscopy, and demonstrated that single molecular hydrophobic interaction free energies are dominated by the area of the smallest interacting hydrophobe. The interaction free energy amounts to 3-4 kT per hydrophobic unit. Also, we find that the transition state of the hydrophobic interactions is located at 3 Å with respect to the ground state, based on Bell-Evans theory. Our results provide a new path for understanding the nature of hydrophobic interactions at the single molecular scale. Our approach enables us to systematically vary hydrophobic and any other interaction type by utilizing peptide chemistry providing a strategic advancement to unravel molecular surface and soft matter interactions at the single molecular scale.

  2. Reference interaction site model with hydrophobicity induced density inhomogeneity: An analytical theory to compute solvation properties of large hydrophobic solutes in the mixture of polyatomic solvent molecules

    International Nuclear Information System (INIS)

    Cao, Siqin; Sheong, Fu Kit; Huang, Xuhui

    2015-01-01

    Reference interaction site model (RISM) has recently become a popular approach in the study of thermodynamical and structural properties of the solvent around macromolecules. On the other hand, it was widely suggested that there exists water density depletion around large hydrophobic solutes (>1 nm), and this may pose a great challenge to the RISM theory. In this paper, we develop a new analytical theory, the Reference Interaction Site Model with Hydrophobicity induced density Inhomogeneity (RISM-HI), to compute solvent radial distribution function (RDF) around large hydrophobic solute in water as well as its mixture with other polyatomic organic solvents. To achieve this, we have explicitly considered the density inhomogeneity at the solute-solvent interface using the framework of the Yvon-Born-Green hierarchy, and the RISM theory is used to obtain the solute-solvent pair correlation. In order to efficiently solve the relevant equations while maintaining reasonable accuracy, we have also developed a new closure called the D2 closure. With this new theory, the solvent RDFs around a large hydrophobic particle in water and different water-acetonitrile mixtures could be computed, which agree well with the results of the molecular dynamics simulations. Furthermore, we show that our RISM-HI theory can also efficiently compute the solvation free energy of solute with a wide range of hydrophobicity in various water-acetonitrile solvent mixtures with a reasonable accuracy. We anticipate that our theory could be widely applied to compute the thermodynamic and structural properties for the solvation of hydrophobic solute

  3. Thermodynamic Molecular Switch in Sequence-Specific Hydrophobic Interaction: Two Computational Models Compared

    Directory of Open Access Journals (Sweden)

    Paul Chun

    2003-01-01

    Full Text Available We have shown in our published work the existence of a thermodynamic switch in biological systems wherein a change of sign in ΔCp°(Treaction leads to a true negative minimum in the Gibbs free energy change of reaction, and hence, a maximum in the related Keq. We have examined 35 pair-wise, sequence-specific hydrophobic interactions over the temperature range of 273–333 K, based on data reported by Nemethy and Scheraga in 1962. A closer look at a single example, the pair-wise hydrophobic interaction of leucine-isoleucine, will demonstrate the significant differences when the data are analyzed using the Nemethy-Scheraga model or treated by the Planck-Benzinger methodology which we have developed. The change in inherent chemical bond energy at 0 K, ΔH°(T0 is 7.53 kcal mol-1 compared with 2.4 kcal mol-1, while ‹ts› is 365 K as compared with 355 K, for the Nemethy-Scheraga and Planck-Benzinger model, respectively. At ‹tm›, the thermal agitation energy is about five times greater than ΔH°(T0 in the Planck-Benzinger model, that is 465 K compared to 497 K in the Nemethy-Scheraga model. The results imply that the negative Gibbs free energy minimum at a well-defined ‹ts›, where TΔS° = 0 at about 355 K, has its origin in the sequence-specific hydrophobic interactions, which are highly dependent on details of molecular structure. The Nemethy-Scheraga model shows no evidence of the thermodynamic molecular switch that we have found to be a universal feature of biological interactions. The Planck-Benzinger method is the best known for evaluating the innate temperature-invariant enthalpy, ΔH°(T0, and provides for better understanding of the heat of reaction for biological molecules.

  4. Driving force for hydrophobic interaction at different length scales.

    Science.gov (United States)

    Zangi, Ronen

    2011-03-17

    We study by molecular dynamics simulations the driving force for the hydrophobic interaction between graphene sheets of different sizes down to the atomic scale. Similar to the prediction by Lum, Chandler, and Weeks for hard-sphere solvation [J. Phys. Chem. B 1999, 103, 4570-4577], we find the driving force to be length-scale dependent, despite the fact that our model systems do not exhibit dewetting. For small hydrophobic solutes, the association is purely entropic, while enthalpy favors dissociation. The latter is demonstrated to arise from the enhancement of hydrogen bonding between the water molecules around small hydrophobes. On the other hand, the attraction between large graphene sheets is dominated by enthalpy which mainly originates from direct solute-solute interactions. The crossover length is found to be inside the range of 0.3-1.5 nm(2) of the surface area of the hydrophobe that is eliminated in the association process. In the large-scale regime, different thermodynamic properties are scalable with this change of surface area. In particular, upon dimerization, a total and a water-induced stabilization of approximately 65 and 12 kJ/mol/nm(2) are obtained, respectively, and on average around one hydrogen bond is gained per 1 nm(2) of graphene sheet association. Furthermore, the potential of mean force between the sheets is also scalable except for interplate distances smaller than 0.64 nm which corresponds to the region around the barrier for removing the last layer of water. It turns out that, as the surface area increases, the relative height of the barrier for association decreases and the range of attraction increases. It is also shown that, around small hydrophobic solutes, the lifetime of the hydrogen bonds is longer than in the bulk, while around large hydrophobes it is the same. Nevertheless, the rearrangement of the hydrogen-bond network for both length-scale regimes is slower than in bulk water. © 2011 American Chemical Society

  5. Inverse colloidal crystal membranes for hydrophobic interaction membrane chromatography.

    Science.gov (United States)

    Vu, Anh T; Wang, Xinying; Wickramasinghe, S Ranil; Yu, Bing; Yuan, Hua; Cong, Hailin; Luo, Yongli; Tang, Jianguo

    2015-08-01

    Hydrophobic interaction membrane chromatography has gained interest due to its excellent performance in the purification of humanized monoclonal antibodies. The membrane material used in hydrophobic interaction membrane chromatography has typically been commercially available polyvinylidene fluoride. In this contribution, newly developed inverse colloidal crystal membranes that have uniform pores, high porosity and, therefore, high surface area for protein binding are used as hydrophobic interaction membrane chromatography membranes for humanized monoclonal antibody immunoglobulin G purification. The capacity of the inverse colloidal crystal membranes developed here is up to ten times greater than commercially available polyvinylidene fluoride membranes with a similar pore size. This work highlights the importance of developing uniform pore size high porosity membranes in order to maximize the capacity of hydrophobic interaction membrane chromatography. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Analysis of hydrophobic interactions of antagonists with the beta2-adrenergic receptor.

    Science.gov (United States)

    Novoseletsky, V N; Pyrkov, T V; Efremov, R G

    2010-01-01

    The adrenergic receptors mediate a wide variety of physiological responses, including vasodilatation and vasoconstriction, heart rate modulation, and others. Beta-adrenergic antagonists ('beta-blockers') thus constitute a widely used class of drugs in cardiovascular medicine as well as in management of anxiety, migraine, and glaucoma. The importance of the hydrophobic effect has been evidenced for a wide range of beta-blocker properties. To better understand the role of the hydrophobic effect in recognition of beta-blockers by their receptor, we carried out a molecular docking study combined with an original approach to estimate receptor-ligand hydrophobic interactions. The proposed method is based on automatic detection of molecular fragments in ligands and the analysis of their interactions with receptors separately. A series of beta-blockers, based on phenylethanolamines and phenoxypropanolamines, were docked to the beta2-adrenoceptor binding site in the crystal structure. Hydrophobic complementarity between the ligand and the receptor was calculated using the PLATINUM web-server (http://model.nmr.ru/platinum). Based on the analysis of the hydrophobic match for molecular fragments of beta-blockers, we have developed a new scoring function which efficiently predicts dissociation constant (pKd) with strong correlations (r(2) approximately 0.8) with experimental data.

  7. Modelling oral up-take of hydrophobic and super-hydrophobic chemicals in fish.

    Science.gov (United States)

    Larisch, Wolfgang; Goss, Kai-Uwe

    2018-01-24

    We have extended a recently published toxicokinetic model for fish (TK-fish) towards the oral up-take of contaminants. Validation with hydrophobic chemicals revealed that diffusive transport through aqueous boundary layers in the gastro-intestinal tract and in the blood is the limiting process. This process can only be modelled correctly if facilitated transport by albumin or bile micelles through these boundary layers is accounted for. In a case study we have investigated the up-take of a super hydrophobic chemical, Dechlorane Plus. Our results suggest that there is no indication of a hydrophobicity or size cut-off in the bioconcentration of this chemical. Based on an extremely high, but mechanistically sound facilitation factor we received model results in good agreement with experimental values from the literature. The results also indicate that established experimental procedures for BCF determination cannot cover the very slow up-take and clearance kinetics that are to be expected for such a chemical.

  8. Dewetting and Hydrophobic Interaction in Physical and Biological Systems

    Science.gov (United States)

    Berne, Bruce J.; Weeks, John D.; Zhou, Ruhong

    2013-01-01

    Hydrophobicity manifests itself differently on large and small length scales. This review focuses on large length scale hydrophobicity, particularly on dewetting at single hydrophobic surfaces and drying in regions bounded on two or more sides by hydrophobic surfaces. We review applicable theories, simulations and experiments pertaining to large scale hydrophobicity in physical and biomoleclar systems and clarify some of the critical issues pertaining to this subject. Given space constraints, we could not review all of the significant and interesting work in this very active field. PMID:18928403

  9. Hydrophobically modified polyelectrolytes : synthesis, properties and interactions with surfactants

    NARCIS (Netherlands)

    Nieuwkerk, A.C.

    1998-01-01

    Hydrophobically modified polyelectrolytes can form micelle-like aggregates, so-called microdomains, in aqueous solution. The hydrophobic side chains constitute the apolar inner part of these microdomains and the hydrophilic groups on the polyelectrolyte backbone are at the surface of the

  10. Hydrophobic ampersand hydrophilic: Theoretical models of solvation for molecular biophysics

    International Nuclear Information System (INIS)

    Pratt, L.R.; Tawa, G.J.; Hummer, G.; Garcia, A.E.; Corcelli, S.A.

    1996-01-01

    Molecular statistical thermodynamic models of hydration for chemistry and biophysics have advanced abruptly in recent years. With liquid water as solvent, salvation phenomena are classified as either hydrophobic or hydrophilic effects. Recent progress in treatment of hydrophilic effects have been motivated by continuum dielectric models interpreted as a modelistic implementation of second order perturbation theory. New results testing that perturbation theory of hydrophilic effects are presented and discussed. Recent progress in treatment of hydrophobic effects has been achieved by applying information theory to discover models of packing effects in dense liquids. The simplest models to which those ideas lead are presented and discussed

  11. Optimization of linear and branched alkane interactions with water to simulate hydrophobic hydration

    Science.gov (United States)

    Ashbaugh, Henry S.; Liu, Lixin; Surampudi, Lalitanand N.

    2011-08-01

    Previous studies of simple gas hydration have demonstrated that the accuracy of molecular simulations at capturing the thermodynamic signatures of hydrophobic hydration is linked both to the fidelity of the water model at replicating the experimental liquid density at ambient pressure and an accounting of polarization interactions between the solute and water. We extend those studies to examine alkane hydration using the transferable potentials for phase equilibria united-atom model for linear and branched alkanes, developed to reproduce alkane phase behavior, and the TIP4P/2005 model for water, which provides one of the best descriptions of liquid water for the available fixed-point charge models. Alkane site/water oxygen Lennard-Jones cross interactions were optimized to reproduce the experimental alkane hydration free energies over a range of temperatures. The optimized model reproduces the hydration free energies of the fitted alkanes with a root mean square difference between simulation and experiment of 0.06 kcal/mol over a wide temperature range, compared to 0.44 kcal/mol for the parent model. The optimized model accurately reproduces the temperature dependence of hydrophobic hydration, as characterized by the hydration enthalpies, entropies, and heat capacities, as well as the pressure response, as characterized by partial molar volumes.

  12. Preferential hydrophobic interactions are responsible for a preference of D-amino acids in the aminoacylation of 5'-AMP with hydrophobic amino acids

    Science.gov (United States)

    Lacey, J. C. Jr; Wickramasinghe, N. S.; Sabatini, R. S.

    1992-01-01

    We have studied the chemistry of aminoacyl AMP to model reactions at the 3' terminus of aminoacyl tRNA for the purpose of understanding the origin of protein synthesis. The present studies relate to the D, L preference in the esterification of 5'-AMP. All N-acetyl amino acids we studied showed faster reaction of the D-isomer, with a generally decreasing preference for D-isomer as the hydrophobicity of the amino acid decreased. The beta-branched amino acids, Ile and Val, showed an extreme preference for D-isomer. Ac-Leu, the gamma-branched amino acid, showed a slightly low D/L ratio relative to its hydrophobicity. The molecular basis for these preferences for D-isomer is understandable in the light of our previous studies and seems to be due to preferential hydrophobic interaction of the D-isomer with adenine. The preference for hydrophobic D-amino acids can be decreased by addition of an organic solvent to the reaction medium. Conversely, peptidylation with Ac-PhePhe shows a preference for the LL isomer over the DD isomer.

  13. Premicellar interaction of PEO-PPO-PEO triblock copolymers with partially hydrophobic alcohols: NMR study

    Czech Academy of Sciences Publication Activity Database

    Kříž, Jaroslav; Dybal, Jiří

    2013-01-01

    Roč. 51, č. 5 (2013), s. 275-282 ISSN 0749-1581 R&D Projects: GA ČR GAP205/11/1657; GA ČR GA203/09/1478 Institutional support: RVO:61389013 Keywords : pluronics * hydrophobic interaction * hydrophobic alcohols Subject RIV: CD - Macromolecular Chemistry Impact factor: 1.559, year: 2013

  14. Molecular-scale hydrophobic interactions between hard-sphere reference solutes are attractive and endothermic.

    Science.gov (United States)

    Chaudhari, Mangesh I; Holleran, Sinead A; Ashbaugh, Henry S; Pratt, Lawrence R

    2013-12-17

    The osmotic second virial coefficients, B2, for atomic-sized hard spheres in water are attractive (B2 attractive with increasing temperature (ΔB2/ΔT attractive and endothermic at moderate temperatures. Hydrophobic interactions between atomic-sized hard spheres in water are more attractive than predicted by the available statistical mechanical theory. These results constitute an initial step toward detailed molecular theory of additional intermolecular interaction features, specifically, attractive interactions associated with hydrophobic solutes.

  15. Different assembly of type IV collagen on hydrophilic and hydrophobic substrata alters endothelial cells interaction

    Directory of Open Access Journals (Sweden)

    NM Coelho

    2010-06-01

    Full Text Available Considering the structural role of type IV collagen (Col IV in the assembly of the basement membrane (BM and the perspective of mimicking its organization for vascular tissue engineering purposes, we studied the adsorption pattern of this protein on model hydrophilic (clean glass and hydrophobic trichloro(octadecylsilane (ODS surfaces known to strongly affect the behavior of other matrix proteins. The amount of fluorescently labeled Col IV was quantified showing saturation of the surface for concentration of the adsorbing solution of about 50μg/ml, but with approximately twice more adsorbed protein on ODS. AFM studies revealed a fine – nearly single molecular size – network arrangement of Col IV on hydrophilic glass, which turns into a prominent and growing polygonal network consisting of molecular aggregates on hydrophobic ODS. The protein layer forms within minutes in a concentration-dependent manner. We further found that human umbilical vein endothelial cells (HUVEC attach less efficiently to the aggregated Col IV (on ODS, as judged by the significantly altered cell spreading, focal adhesions formation and the development of actin cytoskeleton. Conversely, the immunofluorescence studies for integrins revealed that the fine Col IV network formed on hydrophilic substrata is better recognized by the cells via both α1 and α2 heterodimers which support cellular interaction, apart from these on hydrophobic ODS where almost no clustering of integrins was observed.

  16. Characterization of Hydrophobic Interactions of Polymers with Water and Phospholipid Membranes Using Molecular Dynamics Simulations

    Science.gov (United States)

    Drenscko, Mihaela

    Polymers and lipid membranes are both essential soft materials. The structure and hydrophobicity/hydrophilicity of polymers, as well as the solvent they are embedded in, ultimately determines their size and shape. Understating the variation of shape of the polymer as well as its interactions with model biological membranes can assist in understanding the biocompatibility of the polymer itself. Computer simulations, in particular molecular dynamics, can aid in characterization of the interaction of polymers with solvent, as well as polymers with model membranes. In this thesis, molecular dynamics serve to describe polymer interactions with a solvent (water) and with a lipid membrane. To begin with, we characterize the hydrophobic collapse of single polystyrene chains in water using molecular dynamics simulations. Specifically, we calculate the potential of mean force for the collapse of a single polystyrene chain in water using metadynamics, comparing the results between all atomistic with coarse-grained molecular simulation. We next explore the scaling behavior of the collapsed globular shape at the minimum energy configuration, characterized by the radius of gyration, as a function of chain length. The exponent is close to one third, consistent with that predicted for a polymer chain in bad solvent. We also explore the scaling behavior of the Solvent Accessible Surface Area (SASA) as a function of chain length, finding a similar exponent for both all-atomistic and coarse-grained simulations. Furthermore, calculation of the local water density as a function of chain length near the minimum energy configuration suggests that intermediate chain lengths are more likely to form dewetted states, as compared to shorter or longer chain lengths. Next, in order to investigate the molecular interactions between single hydrophobic polymer chains and lipids in biological membranes and at lipid membrane/solvent interface, we perform a series of molecular dynamics simulations of

  17. Hydrophobic interaction chromatography in dual salt system increases protein binding capacity.

    Science.gov (United States)

    Senczuk, Anna M; Klinke, Ralph; Arakawa, Tsutomu; Vedantham, Ganesh; Yigzaw, Yinges

    2009-08-01

    Hydrophobic interaction chromatography (HIC) uses weakly hydrophobic resins and requires a salting-out salt to promote protein-resin interaction. The salting-out effects increase with protein and salt concentration. Dynamic binding capacity (DBC) is dependent on the binding constant, as well as on the flow characteristics during sample loading. DBC increases with the salt concentration but decreases with increasing flow rate. Dynamic and operational binding capacity have a major raw material cost/processing time impact on commercial scale production of monoclonal antibodies. In order to maximize DBC the highest salt concentration without causing precipitation is used. We report here a novel method to maintain protein solubility while increasing the DBC by using a combination of two salting-out salts (referred to as dual salt). In a series of experiments, we explored the dynamic capacity of a HIC resin (TosoBioscience Butyl 650M) with combinations of salts. Using a model antibody, we developed a system allowing us to increase the dynamic capacity up to twofold using the dual salt system over traditional, single salt system. We also investigated the application of this novel approach to several other proteins and salt combinations, and noted a similar protein solubility and DBC increase. The observed increase in DBC in the dual salt system was maintained at different linear flow rates and did not impact selectivity.

  18. Automated Hydrophobic Interaction Chromatography Column Selection for Use in Protein Purification

    Science.gov (United States)

    Murphy, Patrick J. M.; Stone, Orrin J.; Anderson, Michelle E.

    2011-01-01

    In contrast to other chromatographic methods for purifying proteins (e.g. gel filtration, affinity, and ion exchange), hydrophobic interaction chromatography (HIC) commonly requires experimental determination (referred to as screening or "scouting") in order to select the most suitable chromatographic medium for purifying a given protein 1. The method presented here describes an automated approach to scouting for an optimal HIC media to be used in protein purification. HIC separates proteins and other biomolecules from a crude lysate based on differences in hydrophobicity. Similar to affinity chromatography (AC) and ion exchange chromatography (IEX), HIC is capable of concentrating the protein of interest as it progresses through the chromatographic process. Proteins best suited for purification by HIC include those with hydrophobic surface regions and able to withstand exposure to salt concentrations in excess of 2 M ammonium sulfate ((NH4)2SO4). HIC is often chosen as a purification method for proteins lacking an affinity tag, and thus unsuitable for AC, and when IEX fails to provide adequate purification. Hydrophobic moieties on the protein surface temporarily bind to a nonpolar ligand coupled to an inert, immobile matrix. The interaction between protein and ligand are highly dependent on the salt concentration of the buffer flowing through the chromatography column, with high ionic concentrations strengthening the protein-ligand interaction and making the protein immobile (i.e. bound inside the column) 2. As salt concentrations decrease, the protein-ligand interaction dissipates, the protein again becomes mobile and elutes from the column. Several HIC media are commercially available in pre-packed columns, each containing one of several hydrophobic ligands (e.g. S-butyl, butyl, octyl, and phenyl) cross-linked at varying densities to agarose beads of a specific diameter 3. Automated column scouting allows for an efficient approach for determining which HIC media

  19. 3DRISM-HI-D2MSA: an improved analytic theory to compute solvent structure around hydrophobic solutes with proper treatment of solute–solvent electrostatic interactions

    Science.gov (United States)

    Cao, Siqin; Zhu, Lizhe; Huang, Xuhui

    2018-04-01

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

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

    KAUST Repository

    Cao, Siqin

    2017-12-22

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

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

    KAUST Repository

    Cao, Siqin; Zhu, Lizhe; Huang, Xuhui

    2017-01-01

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

  2. Gradient elution behavior of proteins in hydrophobic interaction chromatography with U-shaped retention factor curves.

    Science.gov (United States)

    Creasy, Arch; Lomino, Joseph; Barker, Gregory; Khetan, Anurag; Carta, Giorgio

    2018-04-27

    Protein retention in hydrophobic interaction chromatography is described by the solvophobic theory as a function of the kosmostropic salt concentration. In general, an increase in salt concentration drives protein partitioning to the hydrophobic surface while a decrease reduces it. In some cases, however, protein retention also increases at low salt concentrations resulting in a U-shaped retention factor curve. During gradient elution the salt concentration is gradually decreased from a high value thereby reducing the retention factor and increasing the protein chromatographic velocity. For these conditions, a steep gradient can overtake the protein in the column, causing it to rebind. Two dynamic models, one based on the local equilibrium theory and the other based on the linear driving force approximation, are presented. We show that the normalized gradient slope determines whether the protein elutes in the gradient, partially elutes, or is trapped in the column. Experimental results are presented for two different monoclonal antibodies and for lysozyme on Capto Phenyl (High Sub) resin. One of the mAbs and lysozyme exhibit U-shaped retention factor curves and for each, we determine the critical gradient slope beyond which 100% recovery is no longer possible. Elution with a reverse gradient is also demonstrated at low salt concentrations for these proteins. Understanding this behavior has implications in the design of gradient elution since the gradient slope impacts protein recovery. Copyright © 2018 Elsevier B.V. All rights reserved.

  3. The role of hydrophobic interactions in positioning of peripheral proteins in membranes

    Directory of Open Access Journals (Sweden)

    Lomize Mikhail A

    2007-06-01

    Full Text Available Abstract Background Three-dimensional (3D structures of numerous peripheral membrane proteins have been determined. Biological activity, stability, and conformations of these proteins depend on their spatial positions with respect to the lipid bilayer. However, these positions are usually undetermined. Results We report the first large-scale computational study of monotopic/peripheral proteins with known 3D structures. The optimal translational and rotational positions of 476 proteins are determined by minimizing energy of protein transfer from water to the lipid bilayer, which is approximated by a hydrocarbon slab with a decadiene-like polarity and interfacial regions characterized by water-permeation profiles. Predicted membrane-binding sites, protein tilt angles and membrane penetration depths are consistent with spin-labeling, chemical modification, fluorescence, NMR, mutagenesis, and other experimental studies of 53 peripheral proteins and peptides. Experimental membrane binding affinities of peripheral proteins were reproduced in cases that did not involve a helix-coil transition, specific binding of lipids, or a predominantly electrostatic association. Coordinates of all examined peripheral proteins and peptides with the calculated hydrophobic membrane boundaries, subcellular localization, topology, structural classification, and experimental references are available through the Orientations of Proteins in Membranes (OPM database. Conclusion Positions of diverse peripheral proteins and peptides in the lipid bilayer can be accurately predicted using their 3D structures that represent a proper membrane-bound conformation and oligomeric state, and have membrane binding elements present. The success of the implicit solvation model suggests that hydrophobic interactions are usually sufficient to determine the spatial position of a protein in the membrane, even when electrostatic interactions or specific binding of lipids are substantial. Our

  4. Hydrophobic Interaction Chromatography for Bottom-Up Proteomics Analysis of Single Proteins and Protein Complexes.

    Science.gov (United States)

    Rackiewicz, Michal; Große-Hovest, Ludger; Alpert, Andrew J; Zarei, Mostafa; Dengjel, Jörn

    2017-06-02

    Hydrophobic interaction chromatography (HIC) is a robust standard analytical method to purify proteins while preserving their biological activity. It is widely used to study post-translational modifications of proteins and drug-protein interactions. In the current manuscript we employed HIC to separate proteins, followed by bottom-up LC-MS/MS experiments. We used this approach to fractionate antibody species followed by comprehensive peptide mapping as well as to study protein complexes in human cells. HIC-reversed-phase chromatography (RPC)-mass spectrometry (MS) is a powerful alternative to fractionate proteins for bottom-up proteomics experiments making use of their distinct hydrophobic properties.

  5. Hydrophobic interactions between polymethacrylic acid and sodium laureth sulfate in aqueous solutions

    Science.gov (United States)

    Yaremko, Z. M.; Fedushinskaya, L. B.; Burka, O. A.; Soltys, M. N.

    2014-09-01

    The role of hydrophobic interaction in the development of associative processes is demonstrated, based on the concentration dependences of the viscosity and pH of binary solutions of polymethacrylic acid as an anionic polyelectrolyte and sodium laureth sulfate as an anionic surfactant. It is found that the inflection point on the dependence of the difference between the pH values of binary solutions of polymethacrylic acid and sodium laureth sulfate on the polyelectrolyte concentration is a criterion for determining the predominant contribution from hydrophobic interaction, as is the inflection point on the dependence of pH of individual solutions of polymethacrylic acid on the polyelectrolyte concentration.

  6. Immobilization of molecular cobalt electrocatalyst by hydrophobic interaction with hematite photoanode for highly stable oxygen evolution

    KAUST Repository

    Joya, Khurram

    2015-07-15

    A unique modification of a hematite photoanode with perfluorinated Co-phthalocyanine (CoFPc) by strong binding associated with hydrophobic interaction is demonstrated. The resultant molecular electrocatalyst – hematite photoanode hybrid material showed significant onset shift and high stability for photoelectrochemical oxidation evolution reaction (OER).

  7. Immobilization of molecular cobalt electrocatalyst by hydrophobic interaction with hematite photoanode for highly stable oxygen evolution

    KAUST Repository

    Joya, Khurram; Morlanes, Natalia; Maloney, Edward; Rodionov, Valentin; Takanabe, Kazuhiro

    2015-01-01

    A unique modification of a hematite photoanode with perfluorinated Co-phthalocyanine (CoFPc) by strong binding associated with hydrophobic interaction is demonstrated. The resultant molecular electrocatalyst – hematite photoanode hybrid material showed significant onset shift and high stability for photoelectrochemical oxidation evolution reaction (OER).

  8. Modeling, investigation and formulation of hydrophobic coatings for potential self-cleaning applications

    Science.gov (United States)

    Rios, Pablo Fabian

    Self-cleaning surfaces have received a great deal of attention, both in research and commercial applications. Transparent and non-transparent self-cleaning surfaces are highly desired. The Lotus flower is a symbol of purity in Asian cultures, even when rising from muddy waters it stays clean and untouched by dirt. The Lotus leaf "self-cleaning" surface is hydrophobic and rough, showing a two-layer morphology. While hydrophobicity produces a high contact angle, surface morphology reduces the adhesion of dirt and water to the surface, thus water drops slide easily across the leaf carrying the dirt particles with them. Nature example in the Lotus-effect and extensive scientific research on related fields have rooted wide acceptance that high hydrophobicity can be obtained only by a proper combination of surface chemistry and roughness. Most researchers relate hydrophobicity to a high contact angle. However, the contact angle is not the only parameter that defines liquid-solid interactions. An additional parameter, the sliding angle, related to the adhesion between the liquid drop and the solid surface is also important in cases where liquid sliding is involved, such as self-cleaning applications. In this work, it is postulated that wetting which is related to the contact angle, and interfacial adhesion, which is related to the sliding angle, are interdependent phenomena and have to be considered simultaneously. A variety of models that relate the sliding angle to forces developed along the contact line between a liquid drop and a solid surface have been proposed in the literature. A new model is proposed here that quantifies the drop sliding phenomenon, based also on the interfacial adhesion across the contact area of the liquid/solid interface. The effects of roughness and chemical composition on the contact and sliding angles of hydrophobic smooth and rough surfaces were studied theoretically and experimentally. The validity of the proposed model was investigated

  9. Design and synthesis of an amphiphilic graft hydrogel having a hydrophobic domain formed by multiple interactions

    Energy Technology Data Exchange (ETDEWEB)

    Nitta, Kyohei [Department of Life and Functional Material Science, Graduate School of Natural Science, Konan University, 8-9-1 Okamoto, Higashinada, Kobe 658-8501 (Japan); Japan Society for the Promotion of Science (DC1), Ichibancho, Chiyoda, Tokyo 102-8471 (Japan); Kimoto, Atsushi [Department of Chemistry of Functional Molecules, Faculty of Science and Engineering, Konan University, 8-9-1 Okamoto, Higashinada, Kobe 658-8501 (Japan); Watanabe, Junji, E-mail: junjiknd@konan-u.ac.jp [Department of Chemistry of Functional Molecules, Faculty of Science and Engineering, Konan University, 8-9-1 Okamoto, Higashinada, Kobe 658-8501 (Japan)

    2016-11-01

    A novel hydrogel having hydrophobic oligo segments and hydrophilic poly(acrylamidoglycolic acid) (PAGA) as pH responsive polymer segments was designed and synthesized to be used as a soft biomaterial. Poly(trimethylene carbonate) (PTMC) as the side chain, for which the degrees of polymerization were 9, 19, and 49, and the composition ratios were 1, 5, and 10 mol%, was used as the oligo segment in the hydrogel. The swelling ratio of the hydrogel was investigated under various changes in conditions such as pH, temperature, and hydrogen bonding upon urea addition. Under pH 2–11 conditions, the graft gel reversibly swelled and shrank due to the effect of PAGA main chain. The interior morphology and skin layer of the hydrogel was observed by a scanning electron microscope. The hydrogel composed of PAGA as the hydrophilic polymer backbone had a sponge-like structure, with a pore size of approximately 100 μm. On the other hand, upon increasing the ratio of trimethylene carbonate (TMC) units in the hydrogel, the pores became smaller or disappeared. Moreover, thickness of the skin layer significantly increased with the swelling ratio depended on the incorporation ratios of the PTMC macromonomer. Molecular incorporation in the hydrogel was evaluated using a dye as a model drug molecule. These features would play an important role in drug loading. Increasing the ratio of TMC units favored the adsorption of the dye and activation of the incorporation behavior. - Highlights: • Hydrogen bonding and hydrophobic interaction are dominant factor for forming hydrogels. • Hydrogel properties were tuned by changing in graft length and macromonomer content in feed. • The resulting graft gel could encapsulate and retain organic dye in the hydrogel. • Poly(trimethylene carbonate) segment in the hydrogel was dominant unit for hydrogel.

  10. Design and synthesis of an amphiphilic graft hydrogel having a hydrophobic domain formed by multiple interactions

    International Nuclear Information System (INIS)

    Nitta, Kyohei; Kimoto, Atsushi; Watanabe, Junji

    2016-01-01

    A novel hydrogel having hydrophobic oligo segments and hydrophilic poly(acrylamidoglycolic acid) (PAGA) as pH responsive polymer segments was designed and synthesized to be used as a soft biomaterial. Poly(trimethylene carbonate) (PTMC) as the side chain, for which the degrees of polymerization were 9, 19, and 49, and the composition ratios were 1, 5, and 10 mol%, was used as the oligo segment in the hydrogel. The swelling ratio of the hydrogel was investigated under various changes in conditions such as pH, temperature, and hydrogen bonding upon urea addition. Under pH 2–11 conditions, the graft gel reversibly swelled and shrank due to the effect of PAGA main chain. The interior morphology and skin layer of the hydrogel was observed by a scanning electron microscope. The hydrogel composed of PAGA as the hydrophilic polymer backbone had a sponge-like structure, with a pore size of approximately 100 μm. On the other hand, upon increasing the ratio of trimethylene carbonate (TMC) units in the hydrogel, the pores became smaller or disappeared. Moreover, thickness of the skin layer significantly increased with the swelling ratio depended on the incorporation ratios of the PTMC macromonomer. Molecular incorporation in the hydrogel was evaluated using a dye as a model drug molecule. These features would play an important role in drug loading. Increasing the ratio of TMC units favored the adsorption of the dye and activation of the incorporation behavior. - Highlights: • Hydrogen bonding and hydrophobic interaction are dominant factor for forming hydrogels. • Hydrogel properties were tuned by changing in graft length and macromonomer content in feed. • The resulting graft gel could encapsulate and retain organic dye in the hydrogel. • Poly(trimethylene carbonate) segment in the hydrogel was dominant unit for hydrogel.

  11. Molecular Theory and the Effects of Solute Attractive Forces on Hydrophobic Interactions.

    Science.gov (United States)

    Chaudhari, Mangesh I; Rempe, Susan B; Asthagiri, D; Tan, L; Pratt, L R

    2016-03-03

    The role of solute attractive forces on hydrophobic interactions is studied by coordinated development of theory and simulation results for Ar atoms in water. We present a concise derivation of the local molecular field (LMF) theory for the effects of solute attractive forces on hydrophobic interactions, a derivation that clarifies the close relation of LMF theory to the EXP approximation applied to this problem long ago. The simulation results show that change from purely repulsive atomic solute interactions to include realistic attractive interactions diminishes the strength of hydrophobic bonds. For the Ar-Ar rdfs considered pointwise, the numerical results for the effects of solute attractive forces on hydrophobic interactions are opposite in sign and larger in magnitude than predicted by LMF theory. That comparison is discussed from the point of view of quasichemical theory, and it is suggested that the first reason for this difference is the incomplete evaluation within LMF theory of the hydration energy of the Ar pair. With a recent suggestion for the system-size extrapolation of the required correlation function integrals, the Ar-Ar rdfs permit evaluation of osmotic second virial coefficients B2. Those B2's also show that incorporation of attractive interactions leads to more positive (repulsive) values. With attractive interactions in play, B2 can change from positive to negative values with increasing temperatures. This is consistent with the puzzling suggestions of decades ago that B2 ≈ 0 for intermediate cases of temperature or solute size. In all cases here, B2 becomes more attractive with increasing temperature.

  12. Specific ion effects on the hydrophobic interaction of benzene self-assembled monolayers

    DEFF Research Database (Denmark)

    Dobberschütz, Sören; Pedersen, Morten Rimmen; Hassenkam, Tue

    2015-01-01

    The interaction of aromatic compounds with various ions in aqueous solutions plays a role in a number of fields, as diverse as protein folding and enhanced oil recovery, among others. Therefore, we have investigated the effect of the four electrolytes, KCl, NaCl, MgCl2 and CaCl2, on the hydrophobic...... interaction of benzene self-assembled monolayers. Using the jump to contact phenomenon of an atomic force microscope (AFM) tip as an indicator of attractive forces between the surfaces of a sample and the tip, we discovered lower frequencies in the snap in as well as narrower distributions for the snap...

  13. Isolation of soy bean protein P34 from oil bodies using hydrophobic interaction chromatography

    OpenAIRE

    Sewekow, E.; Keßler, L.; Seidel-Morgenstern, A.; Rothkoetter, H.

    2008-01-01

    Abstract Background Soybeans play a prominent role in allergologic research due to the high incidence of allergic reactions. For detailed studies on specific proteins it is necessary to have access to a large amount of pure substance. Results In this contribution, a method for purifying soybean (Glycine max) protein P34 (also called Gly m Bd 30 K or Gly m 1) using hydrophobic interaction chromatography is presented. After screening experiments using 1 mL HiTrap columns, Butyl Sepharose 4 FF w...

  14. Purification of tracer for somatomedin C radioimmunoassay by hydrophobic interaction chromatography

    Energy Technology Data Exchange (ETDEWEB)

    Baxter, R.C.; Brown, A.S.

    1982-03-01

    A tracer for use in the somatomedin C radiommunoassay by hydrophobic interaction chromatography was purified. Material showing greatest immunoreactivity binds to Octyl Sepharose CL-4B (Pharmacia) in a buffer mixture consisting of 130 mL of acetonitrile and 870 mL of 0.1 mol/L NH/sub 4/HCO/sub 3/, pH 7.8, but is eluted by increasing the acetonitrile content to 180 mL/L. As compared with tracer purified by binding to specific antiserum in liquid phase, precipitating the complex with second antibody, and then dissociating by gel chromatography at acid pH, this tracer shows equal immunoreactivity against specific somatomedin C antiserum. Either preparation allows excellent discrimination between extracts of normal, acromegalic, and hypopituitary plasma samples; thus either is suitable for use in the somatomedin C radioimmunoassay. Tracer purification by hydrophobic interaction chromatography is rapid and inexpensive. It may be useful in preparing highly immunoreactive tracers for other peptide radioimmunoassays.

  15. MICROBIAL CELL-SURFACE HYDROPHOBICITY - THE INVOLVEMENT OF ELECTROSTATIC INTERACTIONS IN MICROBIAL ADHESION TO HYDROCARBONS (MATH)

    NARCIS (Netherlands)

    GEERTSEMADOORNBUSCH, GI; VANDERMEI, HC; BUSSCHER, HJ

    Microbial adhesion to hydrocarbons (MATH) is the most commonly used method to determine microbial cell surface hydrophobicity. Since, however, the assay is based on adhesion, it is questionable whether the results reflect only the cell surface hydrophobicity or an interplay of hydrophobicity and

  16. The interaction between fluid flow and ultra-hydrophobic surface in mini channel

    Directory of Open Access Journals (Sweden)

    Jasikova Darina

    2017-01-01

    Full Text Available Interaction of liquid with ultra-hydrophobic surface is accompanied by creation of layer of air. The effect of the air film has a potential of use in industry in many applications. The quality of the surface is influenced by matrix roughness, the character of physical or chemical cover. There was developed a method for analysis of the liquid flow and the air film using the lighting in volume, visualization with CCD camera and long distance microscope, and optical filters. There were prepared four stainless steel samples of inner channel of dimensions (80 × 8 × 8 mm and initial surface roughness Ra 0.33, Ra 1.0, Ra 2.0, and Ra 2.2. The inner channel was treated with plasma and commercial hydrophobic coating Greblon (WEILBURGER Coatings GmbH. There was realized study focused on the liquid flow velocity profile close to the air film. There are present results for laminar, transient and turbulent flows. The study also estimated the air film thickness depending on the Re number. The knowledge of the air film behaviour helps applied suitable degree of processing and cover for the target application.

  17. Robust cross-links in molluscan adhesive gels: testing for contributions from hydrophobic and electrostatic interactions.

    Science.gov (United States)

    Smith, A M; Robinson, T M; Salt, M D; Hamilton, K S; Silvia, B E; Blasiak, R

    2009-02-01

    The cross-linking interactions that provide cohesive strength to molluscan adhesive gels were investigated. Metal-based interactions have been shown to play an important role in the glue of the slug Arion subfuscus (Draparnaud), but other types of interactions may also contribute to the glue's strength and their role has not been investigated. This study shows that treatments that normally disrupt hydrophobic or electrostatic interactions have little to no effect on the slug glue. High salt concentrations and non-ionic detergent do not affect the solubility of the proteins in the glue or the ability of the glue proteins to stiffen gels. In contrast, metal chelation markedly disrupts the gel. Experiments with gel filtration chromatography identify a 40 kDa protein that is a central component of the cross-links in the glue. This 40 kDa protein forms robust macromolecular aggregations that are stable even in the presence of high concentrations of salt, non-ionic detergent, urea or metal chelators. Metal chelation during glue secretion, however, may block some of these cross-links. Such robust, non-specific interactions in an aqueous environment are highly unusual for hydrogels and reflect an intriguing cross-linking mechanism.

  18. Hydrophobizing coatings for cultural heritage. A detailed study of resin/stone surface interaction

    Science.gov (United States)

    Fermo, P.; Cappelletti, G.; Cozzi, N.; Padeletti, G.; Kaciulis, S.; Brucale, M.; Merlini, M.

    2014-07-01

    Conservation of historical buildings is an important issue and the environmental conditions seriously affect the monument's stones. The protection of cultural heritage buildings and monuments by surface treatment with polymers is a common practice due to their ability to form a protective layer on the monument's surface as well as to control the transport of different fluids from the surface to the monument's interior. In this work, three different substrates were used: Carrara marble, Botticino limestone, and Angera stone. A commercially available Si-based resin (Alpha®SI30) was used as protective agent to improve the hydrophobicity features of the different tested materials. The surface properties of the coating and the relative interaction with the adopted stones were studied using different techniques such as contact angle measurements, electron microscope coupled with an energy dispersive spectrometer, X-ray photoelectron spectroscopy, atomic force microscopy, and attenuated total reflection infrared spectroscopy.

  19. Interaction between human BAP31 and respiratory syncytial virus small hydrophobic (SH) protein

    International Nuclear Information System (INIS)

    Li, Yan; Jain, Neeraj; Limpanawat, Suweeraya; To, Janet; Quistgaard, Esben M.; Nordlund, Par; Thanabalu, Thirumaran; Torres, Jaume

    2015-01-01

    The small hydrophobic (SH) protein is a short channel-forming polypeptide encoded by the human respiratory syncytial virus (hRSV). Deletion of SH protein leads to the viral attenuation in mice and primates, and delayed apoptosis in infected cells. We have used a membrane-based yeast two-hybrid system (MbY2H) and a library from human lung cDNA to detect proteins that bind SH protein. This led to the identification of a membrane protein, B-cell associated protein 31 (BAP31). Transfected SH protein co-localizes with transfected BAP31 in cells, and pulls down endogenous BAP31. Titration of purified C-terminal endodomain of BAP31 against isotopically labeled SH protein in detergent micelles suggests direct interaction between the two proteins. Given the key role of BAP31 in protein trafficking and its critical involvement in pro- and anti-apoptotic pathways, this novel interaction may constitute a potential drug target. - Highlights: • A yeast two-hybrid system (MbY2H) detected BAP31 as a binder of RSV SH protein. • Transfected SH and BAP31 co-localize in lung epithelial cells. • Endogenous BAP31 is pulled down by RSV SH protein. • BAP31 endodomain interacts with the N-terminal α-helix of SH protein in micelles. • This interaction is proposed to be a potential drug target

  20. Interaction between human BAP31 and respiratory syncytial virus small hydrophobic (SH) protein

    Energy Technology Data Exchange (ETDEWEB)

    Li, Yan; Jain, Neeraj; Limpanawat, Suweeraya; To, Janet [School of Biological Sciences, Nanyang Technological University, 637551 (Singapore); Quistgaard, Esben M. [Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm (Sweden); Nordlund, Par [School of Biological Sciences, Nanyang Technological University, 637551 (Singapore); Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm (Sweden); Thanabalu, Thirumaran [School of Biological Sciences, Nanyang Technological University, 637551 (Singapore); Torres, Jaume, E-mail: jtorres@ntu.edu.sg [School of Biological Sciences, Nanyang Technological University, 637551 (Singapore)

    2015-08-15

    The small hydrophobic (SH) protein is a short channel-forming polypeptide encoded by the human respiratory syncytial virus (hRSV). Deletion of SH protein leads to the viral attenuation in mice and primates, and delayed apoptosis in infected cells. We have used a membrane-based yeast two-hybrid system (MbY2H) and a library from human lung cDNA to detect proteins that bind SH protein. This led to the identification of a membrane protein, B-cell associated protein 31 (BAP31). Transfected SH protein co-localizes with transfected BAP31 in cells, and pulls down endogenous BAP31. Titration of purified C-terminal endodomain of BAP31 against isotopically labeled SH protein in detergent micelles suggests direct interaction between the two proteins. Given the key role of BAP31 in protein trafficking and its critical involvement in pro- and anti-apoptotic pathways, this novel interaction may constitute a potential drug target. - Highlights: • A yeast two-hybrid system (MbY2H) detected BAP31 as a binder of RSV SH protein. • Transfected SH and BAP31 co-localize in lung epithelial cells. • Endogenous BAP31 is pulled down by RSV SH protein. • BAP31 endodomain interacts with the N-terminal α-helix of SH protein in micelles. • This interaction is proposed to be a potential drug target.

  1. Molecular-Level Thermodynamic Switch Controls Chemical Equilibrium in Sequence-Specific Hydrophobic Interaction of 35 Dipeptide Pairs

    OpenAIRE

    Chun, Paul W.

    2003-01-01

    Applying the Planck-Benzinger methodology, the sequence-specific hydrophobic interactions of 35 dipeptide pairs were examined over a temperature range of 273–333 K, based on data reported by Nemethy and Scheraga in 1962. The hydrophobic interaction in these sequence-specific dipeptide pairs is highly similar in its thermodynamic behavior to that of other biological systems. The results imply that the negative Gibbs free energy change minimum at a well-defined stable temperature, 〈Ts〉, where t...

  2. Influence of mixed electrolytes and pH on adsorption of bovine serum albumin in hydrophobic interaction chromatography.

    Science.gov (United States)

    Hackemann, Eva; Hasse, Hans

    2017-10-27

    Using salt mixtures instead of single salts can be beneficial for hydrophobic interaction chromatography (HIC). The effect of electrolytes on the adsorption of proteins, however, depends on the pH. Little is known on that dependence for mixed electrolytes. Therefore, the effect of the pH on protein adsorption from aqueous solutions containing mixed salts is systematically studied in the present work for a model system: the adsorption of bovine serum albumin (BSA) on the mildly hydrophobic resin Toyopearl PPG-600M. The pH is adjusted to 4.0, 4.7 or 7.0 using 25mM sodium phosphate or sodium citrate buffer. Binary and ternary salt mixtures of sodium chloride, ammonium chloride, sodium sulfate and ammonium sulfate as well as the pure salts are used at overall ionic strengths between 1500 and 4200mM. The temperature is always 25°C. The influence of the mixed electrolytes on the adsorption behavior of BSA changes completely with varying pH. Positive as well as negative cooperative effects of the mixed electrolytes are observed. The results are analyzed using a mathematical model which was recently introduced by our group. In that model the influence of the electrolytes is described by a Taylor series expansion in the individual ion molarities. After suitable parametrization using a subset of the data determined in the present work, the model successfully predicts the influence of mixed electrolytes on the protein adsorption. Furthermore, results for BSA from the present study are compared to literature data for lysozyme, which are available for the same adsorbent, temperature and salts. By calculating the ratio of the loading of the adsorbent for both proteins particularly favorable separation conditions can be selected. Hence, a model-based optimization of solvents for protein separation is possible. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Polymer-surfactant interactions studied by titration microcalorimetry : Influence of polymer hydrophobicity, electrostatic forces, and surfactant aggregational state

    NARCIS (Netherlands)

    Kevelam, J; van Breemen, J.F.L.; Blokzijl, W.; Engberts, J.B.F.N.

    1996-01-01

    Isothermal titration microcalorimetry has been applied to investigate the interactions between hydrophobically-modified water-soluble polymers and surfactants. The following polymers were used in this study: poly(sodium acrylate-co-n-alkyl methacrylate) (A), where n-alkyl = C9H19, C12H25, and C18H37

  4. The H2A-H2B dimeric kinetic intermediate is stabilized by widespread hydrophobic burial with few fully native interactions.

    Science.gov (United States)

    Guyett, Paul J; Gloss, Lisa M

    2012-01-20

    The H2A-H2B histone heterodimer folds via monomeric and dimeric kinetic intermediates. Within ∼5 ms, the H2A and H2B polypeptides associate in a nearly diffusion limited reaction to form a dimeric ensemble, denoted I₂ and I₂*, the latter being a subpopulation characterized by a higher content of nonnative structure (NNS). The I₂ ensemble folds to the native heterodimer, N₂, through an observable, first-order kinetic phase. To determine the regions of structure in the I₂ ensemble, we characterized 26 Ala mutants of buried hydrophobic residues, spanning the three helices of the canonical histone folds of H2A and H2B and the H2B C-terminal helix. All but one targeted residue contributed significantly to the stability of I₂, the transition state and N₂; however, only residues in the hydrophobic core of the dimer interface perturbed the I₂* population. Destabilization of I₂* correlated with slower folding rates, implying that NNS is not a kinetic trap but rather accelerates folding. The pattern of Φ values indicated that residues forming intramolecular interactions in the peripheral helices contributed similar stability to I₂ and N₂, but residues involved in intermolecular interactions in the hydrophobic core are only partially folded in I₂. These findings suggest a dimerize-then-rearrange model. Residues throughout the histone fold contribute to the stability of I₂, but after the rapid dimerization reaction, the hydrophobic core of the dimer interface has few fully native interactions. In the transition state leading to N₂, more native-like interactions are developed and nonnative interactions are rearranged. Copyright © 2011 Elsevier Ltd. All rights reserved.

  5. Reconciling the understanding of 'hydrophobicity' with physics-based models of proteins.

    Science.gov (United States)

    Harris, Robert C; Pettitt, B Montgomery

    2016-03-02

    The idea that a 'hydrophobic energy' drives protein folding, aggregation, and binding by favoring the sequestration of bulky residues from water into the protein interior is widespread. The solvation free energies (ΔGsolv) of small nonpolar solutes increase with surface area (A), and the free energies of creating macroscopic cavities in water increase linearly with A. These observations seem to imply that there is a hydrophobic component (ΔGhyd) of ΔGsolv that increases linearly with A, and this assumption is widely used in implicit solvent models. However, some explicit-solvent molecular dynamics studies appear to contradict these ideas. For example, one definition (ΔG(LJ)) of ΔGhyd is that it is the free energy of turning on the Lennard-Jones (LJ) interactions between the solute and solvent. However, ΔG(LJ) decreases with A for alanine and glycine peptides. Here we argue that these apparent contradictions can be reconciled by defining ΔGhyd to be a near hard core insertion energy (ΔGrep), as in the partitioning proposed by Weeks, Chandler, and Andersen. However, recent results have shown that ΔGrep is not a simple function of geometric properties of the molecule, such as A and the molecular volume, and that the free energy of turning on the attractive part of the LJ potential cannot be computed from first-order perturbation theory for proteins. The theories that have been developed from these assumptions to predict ΔGhyd are therefore inadequate for proteins.

  6. Interactions between nano-TiO{sub 2} and the oral cavity: Impact of nanomaterial surface hydrophilicity/hydrophobicity

    Energy Technology Data Exchange (ETDEWEB)

    Teubl, Birgit J.; Schimpel, Christa [Institute of Pharmaceutical Sciences, Department of Pharmaceutical Technology, University of Graz, 8010 (Austria); Leitinger, Gerd [Institute of Cell Biology, Histology and Embryology, Research Unit Electron Microscopic Techniques, Medical University of Graz, 8010 (Austria); Center for Medical Research, Medical University of Graz, 8010 (Austria); BioTechMed, Graz 8010 (Austria); Bauer, Bettina [Institute of Pharmaceutical Sciences, Department of Pharmaceutical Technology, University of Graz, 8010 (Austria); Fröhlich, Eleonore [Center for Medical Research, Medical University of Graz, 8010 (Austria); BioTechMed, Graz 8010 (Austria); Zimmer, Andreas [Institute of Pharmaceutical Sciences, Department of Pharmaceutical Technology, University of Graz, 8010 (Austria); BioTechMed, Graz 8010 (Austria); Roblegg, Eva, E-mail: eva.roblegg@uni-graz.at [Institute of Pharmaceutical Sciences, Department of Pharmaceutical Technology, University of Graz, 8010 (Austria); BioTechMed, Graz 8010 (Austria)

    2015-04-09

    Highlights: • Hydrophilic as well as hydrophobic TiO{sub 2} NPs agglomerated under oral physiological conditions. • Particles penetrated the upper and lower buccal epithelium, independent on the degree of hydrophilicity. • Most of the hydrophobic particles were found in vesicular structures, while hydrophilic particles were freely distributed in the cytoplasm. • Hydrophilic particles had a higher potential to trigger toxic effects (e.g., ROS) than hydrophobic particles. - Abstract: Titanium dioxide (TiO{sub 2}) nanoparticles are available in a variety of oral applications, such as food additives and cosmetic products. Thus, questions about their potential impact on the oro-gastrointestinal route rise. The oral cavity represents the first portal of entry and is known to rapidly interact with nanoparticles. Surface charge and size contribute actively to the particle–cell interactions, but the influence of surface hydrophilicity/hydrophobicity has never been shown before. This study addresses the biological impact of hydrophilic (NM 103, rutile, 20 nm) and hydrophobic (NM 104, rutile, 20 nm) TiO{sub 2} particles within the buccal mucosa. Particle characterization was addressed with dynamic light scattering and laser diffraction. Despite a high agglomeration tendency, 10% of the particles/agglomerates were present in the nanosized range and penetrated into the mucosa, independent of the surface properties. However, significant differences were observed in intracellular particle localization. NM 104 particles were found freely distributed in the cytoplasm, whereas their hydrophobic counterparts were engulfed in vesicular structures. Although cell viability/membrane integrity was not affected negatively, screening assays demonstrated that NM 104 particles showed a higher potential to decrease the physiological mitochondrial membrane potential than NM 103, resulting in a pronounced generation of reactive oxygen species.

  7. Interactions between nano-TiO2 and the oral cavity: Impact of nanomaterial surface hydrophilicity/hydrophobicity

    International Nuclear Information System (INIS)

    Teubl, Birgit J.; Schimpel, Christa; Leitinger, Gerd; Bauer, Bettina; Fröhlich, Eleonore; Zimmer, Andreas; Roblegg, Eva

    2015-01-01

    Highlights: • Hydrophilic as well as hydrophobic TiO 2 NPs agglomerated under oral physiological conditions. • Particles penetrated the upper and lower buccal epithelium, independent on the degree of hydrophilicity. • Most of the hydrophobic particles were found in vesicular structures, while hydrophilic particles were freely distributed in the cytoplasm. • Hydrophilic particles had a higher potential to trigger toxic effects (e.g., ROS) than hydrophobic particles. - Abstract: Titanium dioxide (TiO 2 ) nanoparticles are available in a variety of oral applications, such as food additives and cosmetic products. Thus, questions about their potential impact on the oro-gastrointestinal route rise. The oral cavity represents the first portal of entry and is known to rapidly interact with nanoparticles. Surface charge and size contribute actively to the particle–cell interactions, but the influence of surface hydrophilicity/hydrophobicity has never been shown before. This study addresses the biological impact of hydrophilic (NM 103, rutile, 20 nm) and hydrophobic (NM 104, rutile, 20 nm) TiO 2 particles within the buccal mucosa. Particle characterization was addressed with dynamic light scattering and laser diffraction. Despite a high agglomeration tendency, 10% of the particles/agglomerates were present in the nanosized range and penetrated into the mucosa, independent of the surface properties. However, significant differences were observed in intracellular particle localization. NM 104 particles were found freely distributed in the cytoplasm, whereas their hydrophobic counterparts were engulfed in vesicular structures. Although cell viability/membrane integrity was not affected negatively, screening assays demonstrated that NM 104 particles showed a higher potential to decrease the physiological mitochondrial membrane potential than NM 103, resulting in a pronounced generation of reactive oxygen species

  8. Preparation and purification of Flavobacterium heparinum chondroitinases AC and B by hydrophobic interaction chromatography

    Directory of Open Access Journals (Sweden)

    Aguiar J.A.K.

    1999-01-01

    Full Text Available Flavobacterium heparinum is a soil bacterium that produces several mucopolysaccharidases such as heparinase, heparitinases I and II, and chondroitinases AC, B, C and ABC. The purpose of the present study was to optimize the preparation of F. heparinum chondroitinases, which are very useful tools for the identification and structural characterization of chondroitin and dermatan sulfates. We observed that during the routine procedure for cell disruption (ultrasound, 100 kHz, 5 min some of the chondroitinase B activity was lost. Using milder conditions (2 min, most of the chondroitinase B and AC protein was solubilized and the enzyme activities were preserved. Tryptic soy broth without glucose was the best culture medium both for bacterial growth and enzyme induction. Chondroitinases AC and B were separated from each other and also from glucuronidases and sulfatases by hydrophobic interaction chromatography on HP Phenyl-Sepharose. A rapid method for screening of the column fractions was also developed based on the metachromatic shift of the color of dimethylmethylene blue.

  9. Isolation of soybean protein P34 from oil bodies using hydrophobic interaction chromatography

    Directory of Open Access Journals (Sweden)

    Seidel-Morgenstern Andreas

    2008-03-01

    Full Text Available Abstract Background Soybeans play a prominent role in allergologic research due to the high incidence of allergic reactions. For detailed studies on specific proteins it is necessary to have access to a large amount of pure substance. Results In this contribution, a method for purifying soybean (Glycine max protein P34 (also called Gly m Bd 30 K or Gly m 1 using hydrophobic interaction chromatography is presented. After screening experiments using 1 mL HiTrap columns, Butyl Sepharose 4 FF was selected for further systematic investigations. With this stationary phase, suitable operation conditions for two-step gradient elution using ammonium sulphate were determined experimentally. The separation conditions obtained in a small column could be scaled up successfully to column volumes of 7.5 and 75 mL, allowing for high product purities of almost 100% with a yield of 27% for the chromatographic separation step. Conditions could be simplified further using a onestep gradient, which gave comparable purification in a shorter process time. The identity of the purified protein was verified using in-gel digestion and mass spectrometry as well as immunological techniques. Conclusion With the technique presented it is possible to produce, within a short timeframe, pure P34, suitable for further studies where an example antigen is needed.

  10. Computational models for structure-hydrophobicity relationships of 4-carboxyl-2,6-dinitrophenyl azo hydroxynaphthalenes.

    Science.gov (United States)

    Idowu, Olakunle S; Adegoke, Olajire A; Idowu, Abiola; Olaniyi, Ajibola A

    2007-01-01

    Some phenyl azo hydroxynaphthalene dyes (e.g., sunset yellow) are certified as approved colorants for food, cosmetics, and drug formulations. The hydrophobicity of 4 newly synthesized azo dyes of the phenyl azo hydroxynaphthalene class was investigated, as a training set, with the goal of developing models for quantitative structure-property relationships (QSPR). Retention behavior of the molecules reversed-phase thin-layer chromatography (RPTLC) was investigated using liquid paraffin-coated silica gel as the stationary phase. Mobile phases consisted of aqueous mixtures of methanol, acetone, and dimethylformamide (DMF). Basic hydrophobicity parameter (Rmw), specific hydrophobic surface area (S), and isocratic chromatographic hydrophobicity index (phio) were computed from the chromatographic data. The hydrophobicity index (Rm) decreased linearly with increasing concentration of organic modifiers. Extrapolated Rmw values obtained by using DMF and acetone differ significantly from the value obtained by using methanol as organic modifier [P dyes and may also play useful roles in computer-assisted molecular discovery of nontoxic azo dyes.

  11. Structure dependent hydrophobic and hydrophilic interactions between nickel(II) Schiff base complexes and serum albumins: Spectroscopic and docking studies

    Energy Technology Data Exchange (ETDEWEB)

    Koley Seth, Banabithi; Ray, Aurkie; Banerjee, Mousumi; Bhattacharyya, Teerna [Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064 (India); Bhattacharyya, Dhananjay [Computational Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064 (India); Basu, Samita, E-mail: samita.basu@saha.ac.in [Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064 (India)

    2016-03-15

    A systematic and comparative binding study between serum-albumins (SA) and a series of monomeric nickel(II)-Schiff-base-complexes (NSCs), which might be imperative to investigate the function of SA behind nickel allergy, has been carried out through docking and different spectroscopic techniques. The initial docking studies indicate structure-dependent selective hydrophobic and hydrophilic interactions. The pyridine and phenyl containing NSCs, which are more aromatic, show better π–π staking compared to pyrrole one. Again all the NSCs bind with BSA though amino acid residues of IB domain affecting local environment of the Trp-134 surrounded by both hydrophobic and hydrophilic residues instead of the hydrophobically buried Trp-212. In HSA the hydophobically buried Trp-214 is influenced by NSCs. The experimental results nicely support the docking outcomes. The changes in Gibbs free energy, binding affinity and the nature of hydrophilic/hydrophobic interactions of NSC–SA systems indicate greater accessibility of N{sub 2}O{sub 2} donor set complex compared to N{sub 4} one towards SA. Quantum chemical structure optimizations support the better planarity of NSC with N{sub 2}O{sub 2} which provides better binding. Therefore the structural variation of N{sub 2}O{sub 2} donor set complexes becomes much more useful compared to N{sub 4} one to search out the most compatible NSC towards SAs.

  12. The role of hydrophobic interactions for the formation of gas hydrates

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, R.H.; Wang, J.; Eriksson, J.C. [Virginia Polytech Inst. and State Univ., Blacksburg, VA (United States). Center for Advanced Separation Technologies; Sum, A.K. [Colorado School of Mines, Golden, CO (United States). Dept. of Chemical Engineering

    2008-07-01

    The process of hydrate formation remains largely unexplained due to a lack of evidence for the water molecules around the hydrophobic solute such as methane, and the nucleation process leading to the clustering that induces hydrate growth. However, the water structure is known to play a major role in the mechanism for hydrate nucleation. This paper presented evidence that hydrophobic solutes promote the structuring of water. Water molecules at room temperature tend to form ice structures around the hydrocarbon chains of surfactant molecules dissolved in water. An atomic force microscope (AFM) was used in this study to measure the surface forces between thiolated gold surfaces. The purpose was to better understand the structure of the thin films of water between hydrophobic surfaces. The water molecules tended to reorganize themselves to form ordered structures, which may be related to the nucleation of hydrates. The entropy reduction associated with the ice structure can be considered as the net driving force for self-assembly. Recent studies have revealed that long-range attractive forces exist between hydrophobic surfaces, which are likely to result from structuring of the water molecules in the vicinity of the hydrophobic surfaces. Similarly, the hydrophobic nature of most gas hydrate formers may induce ordering of water molecules in the vicinity of dissolved solutes. It was concluded that the results of this study may be used to develop a new mechanism for the formation of gas hydrates, including methane. 20 refs., 2 figs.

  13. PC-SAFT modeling of CO2 solubilities in hydrophobic deep eutectic solvents

    NARCIS (Netherlands)

    Dietz, C.H.J.T.; van Osch, D.J.G.P.; Kroon, M.C.; Sadowski, G.; van Sint Annaland, M.; Gallucci, F.; Zubeir, L.F.; Held, C.

    2017-01-01

    The PC-SAFT 'pseudo-pure' approach was used for the modeling of CO2 solubilities in various hydrophobic deep eutectic solvents (DESs) for the first time. Only liquid density data were used to obtain the segment number, the temperature-independent segment diameter and the dispersion-energy parameter,

  14. Diels-Alder reactions in water : Enforced hydrophobic interaction and hydrogen bonding

    NARCIS (Netherlands)

    Engberts, Jan B.F.N.

    1995-01-01

    Second-order rate constants have been measured for the Diels-Alder (DA) reactions of cyclopentadiene with dienophiles of varying hydrophobicity and hydrogen-bond acceptor capacity in water, in a series of organic solvents and in alcohol-water mixtures. The intramolecular DA reaction of

  15. DIELS-ALDER REACTIONS IN WATER - ENFORCED HYDROPHOBIC INTERACTION AND HYDROGEN-BONDING

    NARCIS (Netherlands)

    Engberts, J.B.F.N.

    Second-order rate constants have been measured for the Diels-Alder (DA) reactions of cyclopentadiene with dienophiles of varying hydrophobicity and hydrogen-bond acceptor capacity in water, in a series of organic solvents and in alcohol-water mixtures. The intramolecular DA reaction of

  16. Interactions between nano-TiO2 and the oral cavity: impact of nanomaterial surface hydrophilicity/hydrophobicity.

    Science.gov (United States)

    Teubl, Birgit J; Schimpel, Christa; Leitinger, Gerd; Bauer, Bettina; Fröhlich, Eleonore; Zimmer, Andreas; Roblegg, Eva

    2015-04-09

    Titanium dioxide (TiO2) nanoparticles are available in a variety of oral applications, such as food additives and cosmetic products. Thus, questions about their potential impact on the oro-gastrointestinal route rise. The oral cavity represents the first portal of entry and is known to rapidly interact with nanoparticles. Surface charge and size contribute actively to the particle-cell interactions, but the influence of surface hydrophilicity/hydrophobicity has never been shown before. This study addresses the biological impact of hydrophilic (NM 103, rutile, 20 nm) and hydrophobic (NM 104, rutile, 20 nm) TiO2 particles within the buccal mucosa. Particle characterization was addressed with dynamic light scattering and laser diffraction. Despite a high agglomeration tendency, 10% of the particles/agglomerates were present in the nanosized range and penetrated into the mucosa, independent of the surface properties. However, significant differences were observed in intracellular particle localization. NM 104 particles were found freely distributed in the cytoplasm, whereas their hydrophobic counterparts were engulfed in vesicular structures. Although cell viability/membrane integrity was not affected negatively, screening assays demonstrated that NM 104 particles showed a higher potential to decrease the physiological mitochondrial membrane potential than NM 103, resulting in a pronounced generation of reactive oxygen species. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. The introduction of hydrogen bond and hydrophobicity effects into the rotational isomeric states model for conformational analysis of unfolded peptides

    Science.gov (United States)

    Engin, Ozge; Sayar, Mehmet; Erman, Burak

    2009-03-01

    Relative contributions of local and non-local interactions to the unfolded conformations of peptides are examined by using the rotational isomeric states model which is a Markov model based on pairwise interactions of torsion angles. The isomeric states of a residue are well described by the Ramachandran map of backbone torsion angles. The statistical weight matrices for the states are determined by molecular dynamics simulations applied to monopeptides and dipeptides. Conformational properties of tripeptides formed from combinations of alanine, valine, tyrosine and tryptophan are investigated based on the Markov model. Comparison with molecular dynamics simulation results on these tripeptides identifies the sequence-distant long-range interactions that are missing in the Markov model. These are essentially the hydrogen bond and hydrophobic interactions that are obtained between the first and the third residue of a tripeptide. A systematic correction is proposed for incorporating these long-range interactions into the rotational isomeric states model. Preliminary results suggest that the Markov assumption can be improved significantly by renormalizing the statistical weight matrices to include the effects of the long-range correlations.

  18. The introduction of hydrogen bond and hydrophobicity effects into the rotational isomeric states model for conformational analysis of unfolded peptides

    International Nuclear Information System (INIS)

    Engin, Ozge; Sayar, Mehmet; Erman, Burak

    2009-01-01

    Relative contributions of local and non-local interactions to the unfolded conformations of peptides are examined by using the rotational isomeric states model which is a Markov model based on pairwise interactions of torsion angles. The isomeric states of a residue are well described by the Ramachandran map of backbone torsion angles. The statistical weight matrices for the states are determined by molecular dynamics simulations applied to monopeptides and dipeptides. Conformational properties of tripeptides formed from combinations of alanine, valine, tyrosine and tryptophan are investigated based on the Markov model. Comparison with molecular dynamics simulation results on these tripeptides identifies the sequence-distant long-range interactions that are missing in the Markov model. These are essentially the hydrogen bond and hydrophobic interactions that are obtained between the first and the third residue of a tripeptide. A systematic correction is proposed for incorporating these long-range interactions into the rotational isomeric states model. Preliminary results suggest that the Markov assumption can be improved significantly by renormalizing the statistical weight matrices to include the effects of the long-range correlations

  19. Preparation of a novel dual-function strong cation exchange/hydrophobic interaction chromatography stationary phase for protein separation.

    Science.gov (United States)

    Zhao, Kailou; Yang, Li; Wang, Xuejiao; Bai, Quan; Yang, Fan; Wang, Fei

    2012-08-30

    We have explored a novel dual-function stationary phase which combines both strong cation exchange (SCX) and hydrophobic interaction chromatography (HIC) characteristics. The novel dual-function stationary phase is based on porous and spherical silica gel functionalized with ligand containing sulfonic and benzyl groups capable of electrostatic and hydrophobic interaction functionalities, which displays HIC character in a high salt concentration, and IEC character in a low salt concentration in mobile phase employed. As a result, it can be employed to separate proteins with SCX and HIC modes, respectively. The resolution and selectivity of the dual-function stationary phase were evaluated under both HIC and SCX modes with standard proteins and can be comparable to that of conventional IEC and HIC columns. More than 96% of mass and bioactivity recoveries of proteins can be achieved in both HIC and SCX modes, respectively. The results indicated that the novel dual-function column could replace two individual SCX and HIC columns for protein separation. Mixed retention mechanism of proteins on this dual-function column based on stoichiometric displacement theory (SDT) in LC was investigated to find the optimal balance of the magnitude of electrostatic and hydrophobic interactions between protein and the ligand on the silica surface in order to obtain high resolution and selectivity for protein separation. In addition, the effects of the hydrophobicity of the ligand of the dual-function packings and pH of the mobile phase used on protein separation were also investigated in detail. The results show that the ligand with suitable hydrophobicity to match the electrostatic interaction is very important to prepare the dual-function stationary phase, and a better resolution and selectivity can be obtained at pH 6.5 in SCX mode. Therefore, the dual-function column can replace two individual SCX and HIC columns for protein separation and be used to set up two-dimensional liquid

  20. Hydrophobic interaction between contiguous residues in the S6 transmembrane segment acts as a stimuli integration node in the BK channel

    Science.gov (United States)

    Carrasquel-Ursulaez, Willy; Contreras, Gustavo F.; Sepúlveda, Romina V.; Aguayo, Daniel; González-Nilo, Fernando

    2015-01-01

    Large-conductance Ca2+- and voltage-activated K+ channel (BK) open probability is enhanced by depolarization, increasing Ca2+ concentration, or both. These stimuli activate modular voltage and Ca2+ sensors that are allosterically coupled to channel gating. Here, we report a point mutation of a phenylalanine (F380A) in the S6 transmembrane helix that, in the absence of internal Ca2+, profoundly hinders channel opening while showing only minor effects on the voltage sensor active–resting equilibrium. Interpretation of these results using an allosteric model suggests that the F380A mutation greatly increases the free energy difference between open and closed states and uncouples Ca2+ binding from voltage sensor activation and voltage sensor activation from channel opening. However, the presence of a bulky and more hydrophobic amino acid in the F380 position (F380W) increases the intrinsic open–closed equilibrium, weakening the coupling between both sensors with the pore domain. Based on these functional experiments and molecular dynamics simulations, we propose that F380 interacts with another S6 hydrophobic residue (L377) in contiguous subunits. This pair forms a hydrophobic ring important in determining the open–closed equilibrium and, like an integration node, participates in the communication between sensors and between the sensors and pore. Moreover, because of its effects on open probabilities, the F380A mutant can be used for detailed voltage sensor experiments in the presence of permeant cations. PMID:25548136

  1. Lecithin hydrophobicity modulates the process of cholesterol crystal nucleation and growth in supersaturated model bile systems.

    OpenAIRE

    Ochi, H; Tazuma, S; Kajiyama, G

    1996-01-01

    The present study was performed to determine whether the degree of lecithin hydrophobicity regulates bile metastability and, therefore, affects the process of cholesterol crystallization. Supersaturated model bile (MB) solutions were prepared with an identical composition on a molar basis (taurocholate/lecithin/cholesterol, 73:19.5:7.5; total lipid concentration 9 g/dl) except for the lecithin species; egg yolk phosphatidylcholine, soybean phosphatidylcholine, 1-palmitoyl-2-linoleoyl-sn-phosp...

  2. Size influences the effect of hydrophobic nanoparticles on lung surfactant model systems.

    Science.gov (United States)

    Dwivedi, Mridula V; Harishchandra, Rakesh Kumar; Koshkina, Olga; Maskos, Michael; Galla, Hans-Joachim

    2014-01-07

    The alveolar lung surfactant (LS) is a complex lipid protein mixture that forms an interfacial monolayer reducing the surface tension to near zero values and thus preventing the lungs from collapse. Due to the expanding field of nanotechnology and the corresponding unavoidable exposure of human beings from the air, it is crucial to study the potential effects of nanoparticles (NPs) on the structural organization of the lung surfactant system. In the present study, we investigated both, the domain structure in pure DPPC monolayers as well as in lung surfactant model systems. In the pure lipid system we found that two different sized hydrophobic polymeric nanoparticles with diameter of ~12 nm and ~136 nm have contrasting effect on the functional and structural behavior. The small nanoparticles inserted into fluid domains at the LE-LC phase transition are not visibly disturbing the phase transition but disrupting the domain morphology of the LE phase. The large nanoparticles led to an expanded isotherm and to a significant decrease in the line tension and thus to a drastic disruption of the domain structures at a much lower number of nanoparticles with respect to the lipid. The surface activity of the model LS films again showed drastic variations due to presence of different sized NPs illustrated by the film balance isotherms and the atomic force microscopy. AFM revealed laterally profuse multilayer protrusion formation on compression but only in the presence of 136 nm sized nanoparticles. Moreover we investigated the vesicle insertion process into a preformed monolayer. A severe inhibition was observed only in the presence of ~136 nm NPs compared to minor effects in the presence of ~12 nm NPs. Our study clearly shows that the size of the nanoparticles made of the same material determines the interaction with biological membranes. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  3. Semi-Automated Hydrophobic Interaction Chromatography Column Scouting Used in the Two-Step Purification of Recombinant Green Fluorescent Protein

    Science.gov (United States)

    Murphy, Patrick J. M.

    2014-01-01

    Background Hydrophobic interaction chromatography (HIC) most commonly requires experimental determination (i.e., scouting) in order to select an optimal chromatographic medium for purifying a given target protein. Neither a two-step purification of untagged green fluorescent protein (GFP) from crude bacterial lysate using sequential HIC and size exclusion chromatography (SEC), nor HIC column scouting elution profiles of GFP, have been previously reported. Methods and Results Bacterial lysate expressing recombinant GFP was sequentially adsorbed to commercially available HIC columns containing butyl, octyl, and phenyl-based HIC ligands coupled to matrices of varying bead size. The lysate was fractionated using a linear ammonium phosphate salt gradient at constant pH. Collected HIC eluate fractions containing retained GFP were then pooled and further purified using high-resolution preparative SEC. Significant differences in presumptive GFP elution profiles were observed using in-line absorption spectrophotometry (A395) and post-run fluorimetry. SDS-PAGE and western blot demonstrated that fluorometric detection was the more accurate indicator of GFP elution in both HIC and SEC purification steps. Comparison of composite HIC column scouting data indicated that a phenyl ligand coupled to a 34 µm matrix produced the highest degree of target protein capture and separation. Conclusions Conducting two-step protein purification using the preferred HIC medium followed by SEC resulted in a final, concentrated product with >98% protein purity. In-line absorbance spectrophotometry was not as precise of an indicator of GFP elution as post-run fluorimetry. These findings demonstrate the importance of utilizing a combination of detection methods when evaluating purification strategies. GFP is a well-characterized model protein, used heavily in educational settings and by researchers with limited protein purification experience, and the data and strategies presented here may aid in

  4. Thz Spectroscopy and DFT Modeling of Intermolecular Vibrations in Hydrophobic Amino Acids

    Science.gov (United States)

    Williams, michael R. C.; Aschaffenburg, Daniel J.; Schmuttenmaer, Charles A.

    2013-06-01

    Vibrations that involve intermolecular displacements occur in molecular crystals at frequencies in the 0.5-5 THz range (˜15-165 cm^{-1}), and these motions are direct indicators of the interaction potential between the molecules. The intermolecular potential energy surface of crystalline hydrophobic amino acids is inherently interesting simply because of the wide variety of forces (electrostatic, dipole-dipole, hydrogen-bonding, van der Waals) that are present. Furthermore, an understanding of these particular interactions is immediately relevant to important topics like protein conformation and pharmaceutical polymorphism. We measured the low-frequency absorption spectra of several polycrystalline hydrophobic amino acids using THz time-domain spectroscopy, and in addition we carried out DFT calculations using periodic boundary conditions and an exchange-correlation functional that accounts for van der Waals dispersion forces. We chose to investigate a series of similar amino acids with closely analogous unit cells (leucine, isoleucine, and allo-isoleucine, in racemic or pseudo-racemic mixtures). This allows us to consider trends in the vibrational spectra as a function of small changes in molecular arrangement and/or crystal geometry. In this way, we gain confidence that peak assignments are not based on serendipitous similarities between calculated and observed features.

  5. Key aromatic/hydrophobic amino acids controlling a cross-amyloid peptide interaction versus amyloid self-assembly.

    Science.gov (United States)

    Bakou, Maria; Hille, Kathleen; Kracklauer, Michael; Spanopoulou, Anna; Frost, Christina V; Malideli, Eleni; Yan, Li-Mei; Caporale, Andrea; Zacharias, Martin; Kapurniotu, Aphrodite

    2017-09-01

    The interaction of the intrinsically disordered polypeptide islet amyloid polypeptide (IAPP), which is associated with type 2 diabetes (T2D), with the Alzheimer's disease amyloid-β (Aβ) peptide modulates their self-assembly into amyloid fibrils and may link the pathogeneses of these two cell-degenerative diseases. However, the molecular determinants of this interaction remain elusive. Using a systematic alanine scan approach, fluorescence spectroscopy, and other biophysical methods, including heterocomplex pulldown assays, far-UV CD spectroscopy, the thioflavin T binding assay, transmission EM, and molecular dynamics simulations, here we identified single aromatic/hydrophobic residues within the amyloid core IAPP region as hot spots or key residues of its cross-interaction with Aβ40(42) peptide. Importantly, we also find that none of these residues in isolation plays a key role in IAPP self-assembly, whereas simultaneous substitution of four aromatic/hydrophobic residues with Ala dramatically impairs both IAPP self-assembly and hetero-assembly with Aβ40(42). Furthermore, our experiments yielded several novel IAPP analogs, whose sequences are highly similar to that of IAPP but have distinct amyloid self- or cross-interaction potentials. The identified similarities and major differences controlling IAPP cross-peptide interaction with Aβ40(42) versus its amyloid self-assembly offer a molecular basis for understanding the underlying mechanisms. We propose that these insights will aid in designing intervention strategies and novel IAPP analogs for the management of type 2 diabetes, Alzheimer's disease, or other diseases related to IAPP dysfunction or cross-amyloid interactions. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  6. Interaction between a hydrophobic rigid face and a flexible alkyl tail: Thermodynamics of self-assembling of sodium cholate and SDS

    International Nuclear Information System (INIS)

    Bai, Guangyue; Sheng, Jianhui; Wang, Yujie; Wu, Hui; Zhao, Yang; Zhuo, Kelei; Bastos, Margarida

    2016-01-01

    Highlights: • Critical concentrations and enthalpy changes for stepwise aggregation are obtained by ITC. • ITC allowed the thermodynamic characterization for NaCA/SDS self-assembling. • Steroid face-to-alkyl chain hydrophobic interaction tends to be saturated at molar ratio 1:1.5. • Alkyl-steroid interaction favors micellization of NaCA/SDS and the mixture shows nonideal behavior. • Intermolecular interaction and excess enthalpies were discussed according to Rubingh’s model. - Abstract: The thermodynamics of molecular self-assembling of an anionic biosurfactant, sodium cholate (NaCA) and its mixtures with sodium dodecyl sulfate (SDS) in aqueous solution have been investigated by isothermal titration calorimetry (ITC), along with fluorescence and conductivity measurements. Different critical concentrations were obtained by these three techniques – critical pre-micelle concentration (cmc_p_r_e) and critical micelle concentration (cmc) for pure NaCA, and critical micelle concentrations (cmc_m_i_x) for the mixed systems with differently initial SDS concentrations. Importantly, ITC allowed us to directly measure the enthalpy changes of pre-micelle formation (ΔH_p_r_e_m_i_c = (−0.28 ± 0.02) kJ·mol"−"1) and of micelle formation (ΔH_m_i_c = (−1.76 ± 0.05) kJ·mol"−"1) for pure NaCA as well as the enthalpies for micellization for the mixed systems NaCA/SDS. The non-ideality of the mixed surfactant solution was evaluated in terms of interaction parameters and excess enthalpies that were calculated in the light of Clint’s and Rubingh’s models. It was found that there is an obvious synergistic effect in the NaCA/SDS mixed system. From all these results we can ascribe the strong interaction between the same charge surfactants NaCA and SDS to the structural difference in their hydrophobic moieties. In fact, the flexible alkyl chains of SDS and the non-planar hydrophobic β-faces of NaCA tend to have a more compact packing than pure NaCA.

  7. The Non-Specific Binding of Fluorescent-Labeled MiRNAs on Cell Surface by Hydrophobic Interaction.

    Science.gov (United States)

    Lu, Ting; Lin, Zongwei; Ren, Jianwei; Yao, Peng; Wang, Xiaowei; Wang, Zhe; Zhang, Qunye

    2016-01-01

    MicroRNAs are small noncoding RNAs about 22 nt long that play key roles in almost all biological processes and diseases. The fluorescent labeling and lipofection are two common methods for changing the levels and locating the position of cellular miRNAs. Despite many studies about the mechanism of DNA/RNA lipofection, little is known about the characteristics, mechanisms and specificity of lipofection of fluorescent-labeled miRNAs. Therefore, miRNAs labeled with different fluorescent dyes were transfected into adherent and suspension cells using lipofection reagent. Then, the non-specific binding and its mechanism were investigated by flow cytometer and laser confocal microscopy. The results showed that miRNAs labeled with Cy5 (cyanine fluorescent dye) could firmly bind to the surface of adherent cells (Hela) and suspended cells (K562) even without lipofection reagent. The binding of miRNAs labeled with FAM (carboxyl fluorescein) to K562 cells was obvious, but it was not significant in Hela cells. After lipofectamine reagent was added, most of the fluorescently labeled miRNAs binding to the surface of Hela cells were transfected into intra-cell because of the high transfection efficiency, however, most of them were still binding to the surface of K562 cells. Moreover, the high-salt buffer which could destroy the electrostatic interactions did not affect the above-mentioned non-specific binding, but the organic solvent which could destroy the hydrophobic interactions eliminated it. These results implied that the fluorescent-labeled miRNAs could non-specifically bind to the cell surface by hydrophobic interaction. It would lead to significant errors in the estimation of transfection efficiency only according to the cellular fluorescence intensity. Therefore, other methods to evaluate the transfection efficiency and more appropriate fluorescent dyes should be used according to the cell types for the accuracy of results.

  8. The Non-Specific Binding of Fluorescent-Labeled MiRNAs on Cell Surface by Hydrophobic Interaction.

    Directory of Open Access Journals (Sweden)

    Ting Lu

    Full Text Available MicroRNAs are small noncoding RNAs about 22 nt long that play key roles in almost all biological processes and diseases. The fluorescent labeling and lipofection are two common methods for changing the levels and locating the position of cellular miRNAs. Despite many studies about the mechanism of DNA/RNA lipofection, little is known about the characteristics, mechanisms and specificity of lipofection of fluorescent-labeled miRNAs.Therefore, miRNAs labeled with different fluorescent dyes were transfected into adherent and suspension cells using lipofection reagent. Then, the non-specific binding and its mechanism were investigated by flow cytometer and laser confocal microscopy. The results showed that miRNAs labeled with Cy5 (cyanine fluorescent dye could firmly bind to the surface of adherent cells (Hela and suspended cells (K562 even without lipofection reagent. The binding of miRNAs labeled with FAM (carboxyl fluorescein to K562 cells was obvious, but it was not significant in Hela cells. After lipofectamine reagent was added, most of the fluorescently labeled miRNAs binding to the surface of Hela cells were transfected into intra-cell because of the high transfection efficiency, however, most of them were still binding to the surface of K562 cells. Moreover, the high-salt buffer which could destroy the electrostatic interactions did not affect the above-mentioned non-specific binding, but the organic solvent which could destroy the hydrophobic interactions eliminated it.These results implied that the fluorescent-labeled miRNAs could non-specifically bind to the cell surface by hydrophobic interaction. It would lead to significant errors in the estimation of transfection efficiency only according to the cellular fluorescence intensity. Therefore, other methods to evaluate the transfection efficiency and more appropriate fluorescent dyes should be used according to the cell types for the accuracy of results.

  9. Epitope mapping of imidazolium cations in ionic liquid-protein interactions unveils the balance between hydrophobicity and electrostatics towards protein destabilisation.

    Science.gov (United States)

    Silva, Micael; Figueiredo, Angelo Miguel; Cabrita, Eurico J

    2014-11-14

    We investigated imidazolium-based ionic liquid (IL) interactions with human serum albumin (HSA) to discern the level of cation interactions towards protein stability. STD-NMR spectroscopy was used to observe the imidazolium IL protons involved in direct binding and to identify the interactions responsible for changes in Tm as accessed by differential scanning calorimetry (DSC). Cations influence protein stability less than anions but still significantly. It was found that longer alkyl side chains of imidazolium-based ILs (more hydrophobic) are associated with a higher destabilisation effect on HSA than short-alkyl groups (less hydrophobic). The reason for such destabilisation lies on the increased surface contact area of the cation with the protein, particularly on the hydrophobic contacts promoted by the terminus of the alkyl chain. The relevance of the hydrophobic contacts is clearly demonstrated by the introduction of a polar moiety in the alkyl chain: a methoxy or alcohol group. Such structural modification reduces the degree of hydrophobic contacts with HSA explaining the lesser extent of protein destabilisation when compared to longer alkyl side chain groups: above [C2mim](+). Competition STD-NMR experiments using [C2mim](+), [C4mim](+) and [C2OHmim](+) also validate the importance of the hydrophobic interactions. The combined effect of cation and anion interactions was explored using (35)Cl NMR. Such experiments show that the nature of the cation has no influence on the anion-protein contacts, still the nature of the anion modulates the cation-protein interaction. Herein we propose that more destabilising anions are likely to be a result of a partial contribution from the cation as a direct consequence of the different levels of interaction (cation-anion pair and cation-protein).

  10. Low-order modelling of a drop on a highly-hydrophobic substrate: statics and dynamics

    Science.gov (United States)

    Wray, Alexander W.; Matar, Omar K.; Davis, Stephen H.

    2017-11-01

    We analyse the behaviour of droplets resting on highly-hydrophobic substrates. This problem is of practical interest due to its appearance in many physical contexts involving the spreading, wetting, and dewetting of fluids on solid substrates. In mathematical terms, it exhibits an interesting challenge as the interface is multi-valued as a function of the natural Cartesian co-ordinates, presenting a stumbling block to typical low-order modelling techniques. Nonetheless, we show that in the static case, the interfacial shape is governed by the Young-Laplace equation, which may be solved explicitly in terms of elliptic functions. We present simple low-order expressions that faithfully reproduce the shapes. We then consider the dynamic case, showing that the predictions of our low-order model compare favourably with those obtained from direct numerical simulations. We also examine the characteristic flow regimes of interest. EPSRC, UK, MEMPHIS program Grant (EP/K003976/1), RAEng Research Chair (OKM).

  11. Rational design of viscosity reducing mutants of a monoclonal antibody: hydrophobic versus electrostatic inter-molecular interactions.

    Science.gov (United States)

    Nichols, Pilarin; Li, Li; Kumar, Sandeep; Buck, Patrick M; Singh, Satish K; Goswami, Sumit; Balthazor, Bryan; Conley, Tami R; Sek, David; Allen, Martin J

    2015-01-01

    High viscosity of monoclonal antibody formulations at concentrations ≥100 mg/mL can impede their development as products suitable for subcutaneous delivery. The effects of hydrophobic and electrostatic intermolecular interactions on the solution behavior of MAB 1, which becomes unacceptably viscous at high concentrations, was studied by testing 5 single point mutants. The mutations were designed to reduce viscosity by disrupting either an aggregation prone region (APR), which also participates in 2 hydrophobic surface patches, or a negatively charged surface patch in the variable region. The disruption of an APR that lies at the interface of light and heavy chain variable domains, VH and VL, via L45K mutation destabilized MAB 1 and abolished antigen binding. However, mutation at the preceding residue (V44K), which also lies in the same APR, increased apparent solubility and reduced viscosity of MAB 1 without sacrificing antigen binding or thermal stability. Neutralizing the negatively charged surface patch (E59Y) also increased apparent solubility and reduced viscosity of MAB 1, but charge reversal at the same position (E59K/R) caused destabilization, decreased solubility and led to difficulties in sample manipulation that precluded their viscosity measurements at high concentrations. Both V44K and E59Y mutations showed similar increase in apparent solubility. However, the viscosity profile of E59Y was considerably better than that of the V44K, providing evidence that inter-molecular interactions in MAB 1 are electrostatically driven. In conclusion, neutralizing negatively charged surface patches may be more beneficial toward reducing viscosity of highly concentrated antibody solutions than charge reversal or aggregation prone motif disruption.

  12. Nuclear import of cutaneous beta genus HPV8 E7 oncoprotein is mediated by hydrophobic interactions between its zinc-binding domain and FG nucleoporins

    Energy Technology Data Exchange (ETDEWEB)

    Onder, Zeynep; Moroianu, Junona, E-mail: moroianu@bc.edu

    2014-01-20

    We have previously discovered and characterized the nuclear import pathways for the E7 oncoproteins of mucosal alpha genus HPVs, type 16 and 11. Here we investigated the nuclear import of cutaneous beta genus HPV8 E7 protein using confocal microscopy after transfections of HeLa cells with EGFP-8E7 and mutant plasmids and nuclear import assays in digitonin-permeabilized HeLa cells. We determined that HPV8 E7 contains a nuclear localization signal (NLS) within its zinc-binding domain that mediates its nuclear import. Furthermore, we discovered that a mostly hydrophobic patch {sub 65}LRLFV{sub 69} within the zinc-binding domain is essential for the nuclear import and localization of HPV8 E7 via hydrophobic interactions with the FG nucleoporins Nup62 and Nup153. Substitution of the hydrophobic residues within the {sub 65}LRLFV{sub 69} patch to alanines, and not R66A mutation, disrupt the interactions between the 8E7 zinc-binding domain and Nup62 and Nup153 and consequently inhibit nuclear import of HPV8 E7. - Highlights: • HPV8 E7 has a cNLS within its zinc-binding domain that mediates its nuclear import. • Discovery of a hydrophobic patch that is critical for the nuclear import of HPV8 E7. • HPV8 E7 nuclear import is mediated by hydrophobic interactions with FG-Nups, Nup62 and Nup153.

  13. Surface modification of hydrophobic polymers for improvement of endothelial cell-surface interactions

    NARCIS (Netherlands)

    Dekker, A.; Dekker, A.; Reitsma, K.; Beugeling, T.; Beugeling, T.; Bantjes, A.; Bantjes, A.; Feijen, Jan; Kirkpatrick, C.J.; van Aken, W.G.

    1992-01-01

    The aim of this study is to improve the interaction of endothelial cells with polymers used in vascular prostheses. Polytetrafluoroethylene (PTFE; Teflon) films were treated by means of nitrogen and oxygen plasmas. Depending on the plasma exposure time, modified PTFE surfaces showed water-contact

  14. Hydration of krypton and consideration of clathrate models of hydrophobic effects from the perspective of quasi-chemical theory.

    Science.gov (United States)

    Ashbaugh, Henry S; Asthagiri, D; Pratt, Lawrence R; Rempe, Susan B

    2003-09-01

    Ab initio molecular dynamics (AIMD) results on a krypton-water liquid solution are presented and compared to recent XAFS results for the radial hydration structure for a Kr atom in liquid water solution. Though these AIMD calculations have important limitations of scale, the comparisons with the liquid solution results are satisfactory and significantly different from the radial distributions extracted from the data on the solid Kr/H(2)O clathrate hydrate phase. The calculations also produce the coordination number distribution that can be examined for metastable coordination structures suggesting possibilities for clathrate-like organization; none are seen in these results. Clathrate pictures of hydrophobic hydration are discussed, as is the quasi-chemical theory that should provide a basis for clathrate pictures. Outer shell contributions are discussed and estimated; they are positive and larger than the positive experimental hydration free energy of Kr(aq), implying that inner shell contributions must be negative and of comparable size. Clathrate-like inner shell hydration structures on a Kr atom solute are obtained for some, but not all, of the coordination number cases observed in the simulation. The structures found have a delicate stability. Inner shell coordination structures extracted from the simulation of the liquid, and then subjected to quantum chemical optimization, always decomposed. Interactions with the outer shell material are decisive in stabilizing coordination structures observed in liquid solution and in clathrate phases. The primitive quasi-chemical estimate that uses a dielectric model for the influence of the outer shell material on the inner shell equilibria gives a contribution to hydration free energy that is positive and larger than the experimental hydration free energy. The 'what are we to tell students' question about hydrophobic hydration, often answered with structural clathrate pictures, is then considered; we propose an

  15. Using the hydrophobic subtraction model to choose orthogonal columns for online comprehensive two-dimensional liquid chromatography

    DEFF Research Database (Denmark)

    Græsbøll, Rune; Nielsen, Nikoline Juul; Christensen, Jan H.

    2014-01-01

    A method for choosing orthogonal columns for a specific sample set in on-line comprehensive two-dimensional liquid chromatography (LC×LC) was developed on the basis of the hydrophobic subtraction model. The method takes into account the properties of the sample analytes by estimating new F...... neutral and 4 acidic oxygenated polycyclic aromatic compounds (PACs) and 3 nitrogen-containing PAC bases was measured isocratically on 12 columns. The isocratic runs were used to determine the hydrophobic subtraction model analyte parameters, and these were used to estimate new F-weights and predict...

  16. A model system to mimic environmentally active surface film roughness and hydrophobicity.

    Science.gov (United States)

    Grant, Jacob S; Shaw, Scott K

    2017-10-01

    This work presents the development and initial assessment of a laboratory platform to allow quantitative studies on model urban films. The platform consists of stearic acid and eicosane mixtures that are solution deposited from hexanes onto smooth, solid substrates. We show that this model has distinctive capabilities to better mimic a naturally occurring film's morphology and hydrophobicity, two important parameters that have not previously been incorporated into model film systems. The physical and chemical properties of the model films are assessed using a variety of analytical instruments. The film thickness and roughness are probed via atomic force microscopy while the film composition, wettability, and water uptake are analyzed by Fourier transform infrared spectroscopy, contact angle goniometry, and quartz crystal microbalance, respectively. Simulated environmental maturation is achieved by exposing the film to regulated amounts of UV/ozone. Ultimately, oxidation of the film is monitored by the analytical techniques mentioned above and proceeds as expected to produce a utile model film system. Including variable roughness and tunable surface coverage results in several key advantages over prior model systems, and will more accurately represent native urban film behavior. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Effect of zinc insertion and hydrophobicity on the membrane interactions and PDT activity of porphyrin photosensitizers.

    Science.gov (United States)

    Pavani, Christiane; Uchoa, Adjaci F; Oliveira, Carla S; Iamamoto, Yassuko; Baptista, Maurício S

    2009-02-01

    A series of photosensitizers (PS), which are meso-substituted tetra-cationic porphyrins, was synthesized in order to study the role of amphiphilicity and zinc insertion in photodynamic therapy (PDT) efficacy. Several properties of the PS were evaluated and compared within the series including photophysical properties (absorption spectra, fluorescence quantum yield Phif, and singlet oxygen quantum yield PhiDelta), uptake by vesicles, mitochondria and HeLa cells, dark and phototoxicity in HeLa cells. The photophysical properties of all compounds are quite similar (Phifinteraction of the zinc-substituted porphyrins is attributed to a complexing effect with phosphate groups of the phospholipids. Zinc insertion was also shown to decrease the interaction with isolated mitochondria and with the mitochondria of HeLa cells, an effect that has been explained by the particular characteristics of the mitochondrial internal membrane. Phototoxicity was shown to increase proportionally with membrane binding efficiency, which is attributed to favorable membrane interactions which allow more efficient membrane photooxidation. For this series of compounds, photodynamic efficiency is directly proportional to the membrane binding and cell uptake, but it is not totally related to mitochondrial targeting.

  18. Rice Starch Particle Interactions at Air/Aqueous Interfaces—Effect of Particle Hydrophobicity and Solution Ionic Strength

    Science.gov (United States)

    McNamee, Cathy E.; Sato, Yu; Wiege, Berthold; Furikado, Ippei; Marefati, Ali; Nylander, Tommy; Kappl, Michael; Rayner, Marilyn

    2018-01-01

    Starch particles modified by esterification with dicarboxylic acids to give octenyl succinic anhydride (OSA) starch is an approved food additive that can be used to stabilize oil in water emulsions used in foods and drinks. However, the effects of the OSA modification of the starch particle on the interfacial interactions are not fully understood. Here, we directly measured the packing of films of rice starch granules, i.e., the natural particle found inside the plant, at air/aqueous interfaces, and the interaction forces in that system as a function of the particle hydrophobicity and ionic strength, in order to gain insight on how starch particles can stabilize emulsions. This was achieved by using a combined Langmuir trough and optical microscope system, and the Monolayer Interaction Particle Apparatus. Native rice starch particles were seen to form large aggregates at air/water interfaces, causing films with large voids to be formed at the interface. The OSA modification of the rice starches particles decreased this aggregation. Increasing the degree of modification improved the particle packing within the film of particles at the air/water interface, due to the introduction of inter-particle electrostatic interactions within the film. The introduction of salt to the water phase caused the particles to aggregate and form holes within the film, due to the screening of the charged groups on the starch particles by the salt. The presence of these holes in the film decreased the stiffness of the films. The effect of the OSA modification was concluded to decrease the aggregation of the particles at an air/water interface. The presence of salts, however, caused the particles to aggregate, thereby reducing the strength of the interfacial film. PMID:29868551

  19. Topological characterization of antireflective and hydrophobic rough surfaces: are random process theory and fractal modeling applicable?

    Science.gov (United States)

    Borri, Claudia; Paggi, Marco

    2015-02-01

    The random process theory (RPT) has been widely applied to predict the joint probability distribution functions (PDFs) of asperity heights and curvatures of rough surfaces. A check of the predictions of RPT against the actual statistics of numerically generated random fractal surfaces and of real rough surfaces has been only partially undertaken. The present experimental and numerical study provides a deep critical comparison on this matter, providing some insight into the capabilities and limitations in applying RPT and fractal modeling to antireflective and hydrophobic rough surfaces, two important types of textured surfaces. A multi-resolution experimental campaign using a confocal profilometer with different lenses is carried out and a comprehensive software for the statistical description of rough surfaces is developed. It is found that the topology of the analyzed textured surfaces cannot be fully described according to RPT and fractal modeling. The following complexities emerge: (i) the presence of cut-offs or bi-fractality in the power-law power-spectral density (PSD) functions; (ii) a more pronounced shift of the PSD by changing resolution as compared to what was expected from fractal modeling; (iii) inaccuracy of the RPT in describing the joint PDFs of asperity heights and curvatures of textured surfaces; (iv) lack of resolution-invariance of joint PDFs of textured surfaces in case of special surface treatments, not accounted for by fractal modeling.

  20. Desorption modeling of hydrophobic organic chemicals from plastic sheets using experimentally determined diffusion coefficients in plastics.

    Science.gov (United States)

    Lee, Hwang; Byun, Da-Eun; Kim, Ju Min; Kwon, Jung-Hwan

    2018-01-01

    To evaluate rate of migration from plastic debris, desorption of model hydrophobic organic chemicals (HOCs) from polyethylene (PE)/polypropylene (PP) films to water was measured using PE/PP films homogeneously loaded with the HOCs. The HOCs fractions remaining in the PE/PP films were compared with those predicted using a model characterized by the mass transfer Biot number. The experimental data agreed with the model simulation, indicating that HOCs desorption from plastic particles can generally be described by the model. For hexachlorocyclohexanes with lower plastic-water partition coefficients, desorption was dominated by diffusion in the plastic film, whereas desorption of chlorinated benzenes with higher partition coefficients was determined by diffusion in the aqueous boundary layer. Evaluation of the fraction of HOCs remaining in plastic films with respect to film thickness and desorption time showed that the partition coefficient between plastic and water is the most important parameter influencing the desorption half-life. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Sorption kinetics and microbial biodegradation activity of hydrophobic chemicals in sewage sludge: Model and measurements based on free concentrations

    NARCIS (Netherlands)

    Artola-Garicano, E.; Borkent, I.; Damen, K.; Jager, T.; Vaes, W.H.J.

    2003-01-01

    In the current study, a new method is introduced with which the rate-limiting factor of biodegradation processes of hydrophobic chemicals in organic and aqueous systems can be determined. The novelty of this approach lies in the combination of a free concentration-based kinetic model with

  2. Model Checking Feature Interactions

    DEFF Research Database (Denmark)

    Le Guilly, Thibaut; Olsen, Petur; Pedersen, Thomas

    2015-01-01

    This paper presents an offline approach to analyzing feature interactions in embedded systems. The approach consists of a systematic process to gather the necessary information about system components and their models. The model is first specified in terms of predicates, before being refined to t...... to timed automata. The consistency of the model is verified at different development stages, and the correct linkage between the predicates and their semantic model is checked. The approach is illustrated on a use case from home automation....

  3. Hydrophobic interaction between the SH2 domain and the kinase domain is required for the activation of Csk.

    Science.gov (United States)

    Mikkola, Esa T; Gahmberg, Carl G

    2010-06-18

    The protein tyrosine kinase C-terminal Src kinase (Csk) is activated by the engagement of its Src homology (SH) 2 domain. However, the molecular mechanism required for this is not completely understood. The crystal structure of the active Csk indicates that Csk could be activated by contact between the SH2 domain and the beta3-alphaC loop in the N-terminal lobe of the kinase domain. To study the importance of this interaction for the SH2-domain-mediated activation of Csk, we mutated the amino acid residues forming the contacts between the SH2 domain and the beta3-alphaC loop. The mutation of the beta3-alphaC loop Ala228 to glycine and of the SH2 domain Tyr116, Tyr133, Leu138, and Leu149 to alanine resulted in the inability of the SH2 domain ligand to activate Csk. Furthermore, the overexpressed Csk mutants A228G, Y133A/Y116A, L138A, and L149A were unable to efficiently inactivate endogenous Src in human embryonic kidney 293 cells. The results suggest that the SH2-domain-mediated activation of Csk is dependent on the binding of the beta3-alphaC loop Ala228 to the hydrophobic pocket formed by the side chains of Tyr116, Tyr133, Leu138, and Leu149 on the surface of the SH2 domain. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

  4. A control on hydrophobic and hydrophilic interactions between HEWL and metal Schiff-base complexes comprising of different metal ions and ligands

    Energy Technology Data Exchange (ETDEWEB)

    Koley Seth, Banabithi; Ray, Aurkie; Basu, Samita, E-mail: samita.basu@saha.ac.in

    2015-05-15

    The structural effects of different copper(II) and nickel(II) Schiff base complexes on hen egg white lysozyme (HEWL) have been investigated through steady state and time resolved absorption and fluorescence, and circular dichroism spectroscopy. The Schiff base ligands with N{sub 4} donor atoms show both hydrophobic and hydrophilic interactions, however hydrophilic interaction prevails with ligands having N{sub 2}O{sub 2} donor atoms. Variation of metal ions from Cu{sup 2+} to Ni{sup 2+} with each type of Schiff base ligand increases the probability of hydrophilic over hydrophobic interactions, which supports their significance in regulating the binding affinity between HEWL and metal complexes. On photo-excitation the complexes comprising of Cu{sup 2+} ion instead of Ni{sup 2+} ion and ligands with N{sub 4} donor system rather than N{sub 2}O{sub 2} donor system, increases the probability of intersystem crossing to populate the corresponding triplet state as observed from laser flash photolysis study. The better binding affinity of nickel complexes with different selectivities compared to copper complexes towards HEWL emphasizes the potentiality of less explored nickel complexes in drug–protein interactions. - Highlights: • Ni{sup II} and Cu{sup II} -Schiff base complexes bind hen egg white lysozyme spontaneously. • Both hydrophobic and hydrophilic interactions are effective for N{sub 4} ligands. • For N{sub 2}O{sub 2} ligands the hydrophilic is predominant over hydrophobic interaction. • Binding affinity and selectivity of Ni{sup II}-complexes are better than Cu{sup II}-complexes. • Replacement of Cu{sup 2+} by Ni{sup 2+} in a ligand enhances chance of hydrophilic interaction.

  5. Predicting hot spots in protein interfaces based on protrusion index, pseudo hydrophobicity and electron-ion interaction pseudopotential features

    Science.gov (United States)

    Xia, Junfeng; Yue, Zhenyu; Di, Yunqiang; Zhu, Xiaolei; Zheng, Chun-Hou

    2016-01-01

    The identification of hot spots, a small subset of protein interfaces that accounts for the majority of binding free energy, is becoming more important for the research of drug design and cancer development. Based on our previous methods (APIS and KFC2), here we proposed a novel hot spot prediction method. For each hot spot residue, we firstly constructed a wide variety of 108 sequence, structural, and neighborhood features to characterize potential hot spot residues, including conventional ones and new one (pseudo hydrophobicity) exploited in this study. We then selected 3 top-ranking features that contribute the most in the classification by a two-step feature selection process consisting of minimal-redundancy-maximal-relevance algorithm and an exhaustive search method. We used support vector machines to build our final prediction model. When testing our model on an independent test set, our method showed the highest F1-score of 0.70 and MCC of 0.46 comparing with the existing state-of-the-art hot spot prediction methods. Our results indicate that these features are more effective than the conventional features considered previously, and that the combination of our and traditional features may support the creation of a discriminative feature set for efficient prediction of hot spots in protein interfaces. PMID:26934646

  6. The interacting boson model

    International Nuclear Information System (INIS)

    Iachello, F.; Arima, A.

    1987-01-01

    The book gives an account of some of the properties of the interacting boson model. The model was introduced in 1974 to describe in a unified way the collective properties of nuclei. The book presents the mathematical techniques used to analyse the structure of the model. The mathematical framework of the model is discussed in detail. The book also contains all the formulae that have been developed throughout the years to account for collective properties of nuclei. These formulae can be used by experimentalists to compare their data with the predictions of the model. (U.K.)

  7. The Role of Hydrophobicity and Surface Receptors at Hyphae of Lyophyllum sp. Strain Karsten in the Interaction with Burkholderia terrae BS001 – Implications for Interactions in Soil

    Science.gov (United States)

    Vila, Taissa; Nazir, Rashid; Rozental, Sonia; dos Santos, Giulia M. P.; Calixto, Renata O. R.; Barreto-Bergter, Eliana; Wick, Lukas Y.; van Elsas, Jan Dirk

    2016-01-01

    The soil bacterium Burkholderia terrae strain BS001 can interact with varying soil fungi, using mechanisms that range from the utilization of carbon/energy sources such as glycerol to the ability to reach novel territories in soil via co-migration with growing fungal mycelia. Here, we investigate the intrinsic properties of the B. terrae BS001 interaction with the basidiomycetous soil fungus Lyophyllum sp. strain Karsten. In some experiments, the ascomycetous Trichoderma asperellum 302 was also used. The hyphae of Lyophyllum sp. strain Karsten were largely hydrophilic on water-containing media versus hydrophobic when aerial, as evidenced by contact angle analyses (CA). Co-migration of B. terrae strain BS001 cells with the hyphae of the two fungi occurred preferentially along the - presumably hydrophilic - soil-dwelling hyphae, whereas aerial hyphae did not allow efficient migration, due to reduced thickness of their surrounding mucous films. Moreover, the cell numbers over the length of the hyphae in soil showed an uneven distribution, i.e., the CFU numbers increased from minima at the inoculation point to maximal numbers in the middle of the extended hyphae, then decreasing toward the terminal side. Microscopic analyses of the strain BS001 associations with the Lyophyllum sp. strain Karsten hyphae in the microcosms confirmed the presence of B. terrae BS001 cells on the mucous matter that was present at the hyphal surfaces of the fungi used. Cell agglomerates were found to accumulate at defined sites on the hyphal surfaces, which were coined ‘fungal-interactive’ hot spots. Evidence was further obtained for the contention that receptors for a physical bacterium-fungus interaction occur at the Lyophyllum sp. strain Karsten hyphal surface, in which the specific glycosphingolipid ceramide monohexoside (CMH) plays an important role. Thus, bacterial adherence may be mediated by heterogeneously distributed fungal-specific receptors, implying the CMH moieties. This

  8. Protein-induced bilayer Perturbations: Lipid ordering and hydrophobic coupling

    DEFF Research Database (Denmark)

    Petersen, Frederic Nicolas Rønne; Laursen, Ib; Bohr, Henrik

    2009-01-01

    The host lipid bilayer is increasingly being recognized as an important non-specific regulator of membrane protein function. Despite considerable progress the interplay between hydrophobic coupling and lipid ordering is still elusive. We use electron spin resonance (ESR) to study the interaction...... between the model protein gramicidin and lipid bilayers of varying thickness. The free energy of the interaction is up to −6 kJ/mol; thus not strongly favored over lipid–lipid interactions. Incorporation of gramicidin results in increased order parameters with increased protein concentration...... and hydrophobic mismatch. Our findings also show that at high protein:lipid ratios the lipids are motionally restricted but not completely immobilized. Both exchange on and off rate values for the lipid ↔ gramicidin interaction are lowest at optimal hydrophobic matching. Hydrophobic mismatch of few Å results...

  9. Control activity of yeast geranylgeranyl diphosphate synthase from dimer interface through H-bonds and hydrophobic interaction.

    Science.gov (United States)

    Chang, Chih-Kang; Teng, Kuo-Hsun; Lin, Sheng-Wei; Chang, Tao-Hsin; Liang, Po-Huang

    2013-04-23

    Previously we showed that yeast geranylgeranyl diphosphate synthase (GGPPS) becomes an inactive monomer when the first N-terminal helix involved in dimerization is deleted. This raises questions regarding why dimerization is required for GGPPS activity and which amino acids in the dimer interface are essential for dimerization-mediated activity. According to the GGPPS crystal structure, three amino acids (N101, N104, and Y105) located in the helix F of one subunit are near the active site of the other subunit. As presented here, when these residues were replaced individually with Ala caused insignificant activity changes, N101A/Y105A and N101A/N104A but not N104A/Y105A showed remarkably decreased k(cat) values (200-250-fold). The triple mutant N101A/N104A/Y105A displayed no detectable activity, although dimer was retained in these mutants. Because N101 and Y105 form H-bonds with H139 and R140 in the other subunit, respectively, we generated H139A/R140A double mutant and found it was inactive and became monomeric. Therefore, the multiple mutations apparently influence the integrity of the catalytic site due to the missing H-bonding network. Moreover, Met111, also on the highly conserved helix F, was necessary for dimer formation and enzyme activity. When Met111 was replaced with Glu, the negative-charged repulsion converted half of the dimer into a monomer. In conclusion, the H-bonds mainly through N101 for maintaining substrate binding stability and the hydrophobic interaction of M111 in dimer interface are essential for activity of yeast GGPPS.

  10. Modeling of Hydrophobic Surfaces by the Stokes Problem With the Stick–Slip Boundary Conditions

    Czech Academy of Sciences Publication Activity Database

    Kučera, R.; Šátek, V.; Haslinger, Jaroslav; Fialová, S.; Pochylý, F.

    2017-01-01

    Roč. 139, č. 1 (2017), č. článku 011202. ISSN 0098-2202 Institutional support: RVO:68145535 Keywords : algebra * boundary conditions * hydrophobicity * Lagrange multipliers * Navier Stokes equations Subject RIV: BA - General Mathematics OBOR OECD: Applied mathematics Impact factor: 1.437, year: 2016 http://fluidsengineering.asmedigitalcollection.asme.org/article.aspx?articleid=2536532

  11. Feasibility study of silica sol as the carrier of a hydrophobic drug in aqueous solution using enrofloxacin as the model

    International Nuclear Information System (INIS)

    Song Meirong; Song Junling; Ning Aimin; Cui Baoan; Cui Shumin; Zhou Yaobing; An Wankai; Dong Xuesong; Zhang Gege

    2010-01-01

    The aim of this study was to determine the feasibility of using silica sol to carry a hydrophobic drug in aqueous solution. Enrofloxacin, which was selected as the model drug because it is a broad-spectrum antibiotic drug with poor solubility in water, was adsorbed onto silica sol in aqueous solution during cooling from 60 deg. C to room temperature. The drug-loaded silica sol was characterized by transmission electron microscopy, Fourier transform infrared spectrum, thermal gravimetric analysis and ultraviolet-visible light spectroscopy. The results showed that enrofloxacin was adsorbed by silica sol without degradation at a loading of 15.23 wt.%. In contrast to the rapid release from pure enrofloxacin, the drug-loaded silica sol showed a slower release over a longer time. Kinetics analysis suggested the drug release from silica sol was mainly a diffusion-controlled process. Therefore, silica sol can be used to carry a hydrophobic drug in aqueous solution for controlled drug delivery.

  12. Nuclear import of high risk HPV16 E7 oncoprotein is mediated by its zinc-binding domain via hydrophobic interactions with Nup62

    Energy Technology Data Exchange (ETDEWEB)

    Eberhard, Jeremy; Onder, Zeynep; Moroianu, Junona, E-mail: moroianu@bc.edu

    2013-11-15

    We previously discovered that nuclear import of high risk HPV16 E7 is mediated by a cNLS located within the zinc-binding domain via a pathway that is independent of karyopherins/importins (Angeline et al., 2003; Knapp et al., 2009). In this study we continued our characterization of the cNLS and nuclear import pathway of HPV16 E7. We find that an intact zinc-binding domain is essential for the cNLS function in mediating nuclear import of HPV16 E7. Mutagenesis of cysteine residues to alanine in each of the two CysXXCys motifs involved in zinc-binding changes the nuclear localization of the EGFP-16E7 and 2xEGFP-16E7 mutants. We further discover that a patch of hydrophobic residues, {sub 65}LRLCV{sub 69}, within the zinc-binding domain of HPV16 E7 mediates its nuclear import via hydrophobic interactions with the FG domain of the central channel nucleoporin Nup62. - Highlights: • An intact zinc-binding domain is essential for the nuclear localization of HPV16 E7. • Identification of a hydrophobic patch that is critical for the nuclear import of HPV16 E7. • HPV16 E7 interacts via its zinc-binding domain with the FG domain of Nup62.

  13. Hydrophobic Interactions Are a Key to MDM2 Inhibition by Polyphenols as Revealed by Molecular Dynamics Simulations and MM/PBSA Free Energy Calculations.

    Directory of Open Access Journals (Sweden)

    Sharad Verma

    Full Text Available p53, a tumor suppressor protein, has been proven to regulate the cell cycle, apoptosis, and DNA repair to prevent malignant transformation. MDM2 regulates activity of p53 and inhibits its binding to DNA. In the present study, we elucidated the MDM2 inhibition potential of polyphenols (Apigenin, Fisetin, Galangin and Luteolin by MD simulation and MM/PBSA free energy calculations. All polyphenols bind to hydrophobic groove of MDM2 and the binding was found to be stable throughout MD simulation. Luteolin showed the highest negative binding free energy value of -173.80 kJ/mol followed by Fisetin with value of -172.25 kJ/mol. It was found by free energy calculations, that hydrophobic interactions (vdW energy have major contribution in binding free energy.

  14. New insights into the interactions between cork chemical components and pesticides. The contribution of π-π interactions, hydrogen bonding and hydrophobic effect.

    Science.gov (United States)

    Olivella, M À; Bazzicalupi, C; Bianchi, A; Fiol, N; Villaescusa, I

    2015-01-01

    The role of chemical components of cork in the sorption of several pesticides has been investigated. For this purpose raw cork and three cork extracted fractions (i.e. cork free of aliphatic extractives, cork free of all extractives and cork free of all extractives and suberin) were used as sorbent of three ionic pesticides (propazine, 2,4-dichlorophenoxy acetic acid (2,4-D) and alachlor) and five non-ionic pesticides (chlorpyrifos, isoproturon, metamitron, methomyl and oxamyl) with a logKow within the range -0.47 to 4.92. The effect of cations on the ionic pesticides, propazine and 2,4-D sorption was also analyzed. Results indicated that the highest yields were obtained for chlorpyrifos and alachlor sorption onto raw cork (>55%). After removal of aliphatic extractives sorption of all pesticides increased that ranged from 3% for propazine to 31% for alachlor. In contrast, removal of phenolic extractives caused a sorption decrease. Low sorption yields were obtained for hydrophobic pesticides such as metamitron, oxamyl and methomyl (cork fractions and extremely low when using raw cork (cork toward aromatic pesticides. Results presented in this paper gain insights into the cork affinities for pesticides and the interactions involved in the sorption process and also enables to envisage sorption affinity of cork for other organic pollutants. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. Water on a Hydrophobic surface

    Science.gov (United States)

    Scruggs, Ryan; Zhu, Mengjue; Poynor, Adele

    2012-02-01

    Hydrophobicity, meaning literally fear of water, is exhibited on the surfaces of non-stick cooking pans and water resistant clothing, on the leaves of the lotus plan, or even during the protein folding process in our bodies. Hydrophobicity is directly measured by determining a contact angle between water and an objects surface. Associated with a hydrophobic surface is the depletion layer, a low density region approximately 0.2 nm thick. We study this region by comparing data found in lab using surface plasmon resonance techniques to theoretical calculations. Experiments use gold slides coated in ODT and Mercapto solutions to model both hydrophobic and hydrophilic surfaces respectively.

  16. Interaction of the Yersinia pestis type III regulatory proteins LcrG and LcrV occurs at a hydrophobic interface

    Directory of Open Access Journals (Sweden)

    Nilles Matthew L

    2002-06-01

    Full Text Available Abstract Background Secretion of anti-host proteins by Yersinia pestis via a type III mechanism is not constitutive. The process is tightly regulated and secretion occurs only after an appropriate signal is received. The interaction of LcrG and LcrV has been demonstrated to play a pivotal role in secretion control. Previous work has shown that when LcrG is incapable of interacting with LcrV, secretion of anti-host proteins is prevented. Therefore, an understanding of how LcrG interacts with LcrV is required to evaluate how this interaction regulates the type III secretion system of Y. pestis. Additionally, information about structure-function relationships within LcrG is necessary to fully understand the role of this key regulatory protein. Results In this study we demonstrate that the N-terminus of LcrG is required for interaction with LcrV. The interaction likely occurs within a predicted amphipathic coiled-coil domain within LcrG. Our results demonstrate that the hydrophobic face of the putative helix is required for LcrV interaction. Additionally, we demonstrate that the LcrG homolog, PcrG, is incapable of blocking type III secretion in Y. pestis. A genetic selection was utilized to obtain a PcrG variant capable of blocking secretion. This PcrG variant allowed us to locate a region of LcrG involved in secretion blocking. Conclusion Our results demonstrate that LcrG interacts with LcrV via hydrophobic interactions located in the N-terminus of LcrG within a predicted coiled-coil motif. We also obtained preliminary evidence that the secretion blocking activity of LcrG is located between amino acids 39 and 53.

  17. Effects of hydrophobic drug-polyesteric core interactions on drug loading and release properties of poly(ethylene glycol)-polyester-poly(ethylene glycol) triblock core-shell nanoparticles

    International Nuclear Information System (INIS)

    Khoee, Sepideh; Hassanzadeh, Salman; Goliaie, Bahram

    2007-01-01

    BAB amphiphilic triblock copolymers consisting of poly(ethylene glycol) (B) (PEG) as the hydrophilic segment and different polyesters (A) as the hydrophobic block were prepared by a polycondensation reaction as efficient model core-shell nanoparticles to assay the effect of interactions between the hydrophobic drug and the polyesteric core in terms of drug loading content and release profile. PEG-poly(hexylene adipate)-PEG (PEG-PHA-PEG) and PEG-poly(butylene adipate)-PEG (PEG-PBA-PEG) to PEG-poly(ethylene adipate)-PEG (PEG-PEA-PEG) core-shell type nanoparticles entrapping quercetin (an anticarcinogenic, allergy inhibitor and antibacterial agent), were prepared by a nanoprecipitation method and characterized by dynamic light scattering (DLS), transmission electron microscopy (TEM) and x-ray diffraction (XRD) techniques. It was found that the obtained nanoparticles showed a smooth surface and spherical shape with controllable sizes in the range of 64-74 nm, while drug loading varied from 7.24% to 19% depending on the copolymer composition and the preparation conditions. The in vitro release behaviour exhibited a sustained release and was affected by the polymer-drug interactions. UV studies revealed the presence of hydrogen bonding as the main existing interaction between quercetin and polyesters in the nanosphere cores

  18. A thermodynamic study of peptides binding to carbon nanotubes based on a hydrophobic-polar lattice model using Monte Carlo simulations

    International Nuclear Information System (INIS)

    Cheng, Y; Lu, C; Liu, G R; Li, Z R; Mi, D

    2008-01-01

    Carbon nanotubes (CNTs) are outstanding novel materials that have great potential for a variety of chemical and biomedical applications. However, the mechanism of their interactions with biomaterials is still not fully understood, and more insightful research work is needed. In this work, we use the 2D hydrophobic-polar lattice model and the Monte Carlo simulation method to study the interactions between model peptides and CNTs. The energy parameters of the coarse-grained lattice model are qualitatively determined based on experimental data and molecular dynamics simulation results. Our model is capable of reproducing the essential phenomena of peptides folding in bulk water and binding to CNTs, as well as providing new insights into the thermodynamics and conformational properties of peptides interacting with nanotubes. The results suggest that both the internal energy and the peptide conformational entropy contribute to the binding process. Upon binding to the CNTs, peptides generally unfold into their denatured structures before they reach the lowest-accessible energy states of the system. Temperature has a significant influence on the adsorption process

  19. Combined effects of potassium chloride and ethanol as mobile phase modulators on hydrophobic interaction and reversed-phase chromatography of three insulin variants.

    Science.gov (United States)

    Johansson, Karolina; Frederiksen, Søren S; Degerman, Marcus; Breil, Martin P; Mollerup, Jørgen M; Nilsson, Bernt

    2015-02-13

    The two main chromatographic modes based on hydrophobicity, hydrophobic interaction chromatography (HIC) and reversed-phase chromatography (RPC), are widely used for both analytical and preparative chromatography of proteins in the pharmaceutical industry. Despite the extensive application of these separation methods, and the vast amount of studies performed on HIC and RPC over the decades, the underlying phenomena remain elusive. As part of a systematic study of the influence of mobile phase modulators in hydrophobicity-based chromatography, we have investigated the effects of both KCl and ethanol on the retention of three insulin variants on two HIC adsorbents and two RPC adsorbents. The focus was on the linear adsorption range, separating the modulator effects from the capacity effects, but some complementary experiments at higher load were included to further investigate observed phenomena. The results show that the modulators have the same effect on the two RPC adsorbents in the linear range, indicating that the modulator concentration only affects the activity of the solute in the mobile phase, and not that of the solute-ligand complex, or that of the ligand. Unfortunately, the HIC adsorbents did not show the same behavior. However, the insulin variants displayed a strong tendency toward self-association on both HIC adsorbents; on one in particular. Since this causes peak fronting, the retention is affected, and this could probably explain the lack of congruity. This conclusion was supported by the results from the non-linear range experiments which were indicative of double-layer adsorption on the HIC adsorbents, while the RPC adsorbents gave the anticipated increased tailing at higher load. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. Mixed micelles of 7,12-dioxolithocholic acid and selected hydrophobic bile acids: interaction parameter, partition coefficient of nitrazepam and mixed micelles haemolytic potential.

    Science.gov (United States)

    Poša, Mihalj; Tepavčević, Vesna

    2011-09-01

    The formation of mixed micelles built of 7,12-dioxolithocholic and the following hydrophobic bile acids was examined by conductometric method: cholic (C), deoxycholic (D), chenodeoxycholic (CD), 12-oxolithocholic (12-oxoL), 7-oxolithocholic (7-oxoL), ursodeoxycholic (UD) and hiodeoxycholic (HD). Interaction parameter (β) in the studied binary mixed micelles had negative value, suggesting synergism between micelle building units. Based on β value, the hydrophobic bile acids formed two groups: group I (C, D and CD) and group II (12-oxoL, 7-oxoL, UD and HD). Bile acids from group II had more negative β values than bile acids from group I. Also, bile acids from group II formed intermolecular hydrogen bonds in aggregates with both smaller (2) and higher (4) aggregation numbers, according to the analysis of their stereochemical (conformational) structures and possible structures of mixed micelles built of these bile acids and 7,12-dioxolithocholic acid. Haemolytic potential and partition coefficient of nitrazepam were higher in mixed micelles built of the more hydrophobic bile acids (C, D, CD) and 7,12-dioxolithocholic acid than in micelles built only of 7,12-dioxolithocholic acid. On the other hand, these mixed micelles still had lower values of haemolytic potential than micelles built of C, D or CD. The mixed micelles that included bile acids: 12-oxoL, 7-oxoL, UD or HD did not significantly differ from the micelles of 7,12-dioxolithocholic acid, observing the values of their haemolytic potential. Copyright © 2011 Elsevier B.V. All rights reserved.

  1. Native Hydrophobic Binding Interactions at the Transition State for Association between the TAZ1 Domain of CBP and the Disordered TAD-STAT2 Are Not a Requirement.

    Science.gov (United States)

    Lindström, Ida; Dogan, Jakob

    2017-08-15

    A significant fraction of the eukaryotic proteome consists of proteins that are either partially or completely disordered under native-like conditions. Intrinsically disordered proteins (IDPs) are common in protein-protein interactions and are involved in numerous cellular processes. Although many proteins have been identified as disordered, much less is known about the binding mechanisms of the coupled binding and folding reactions involving IDPs. Here we have analyzed the rate-limiting transition state for binding between the TAZ1 domain of CREB binding protein and the intrinsically disordered transactivation domain of STAT2 (TAD-STAT2) by site-directed mutagenesis and kinetic experiments (Φ-value analysis) and found that the native protein-protein binding interface is not formed at the transition state for binding. Instead, native hydrophobic binding interactions form late, after the rate-limiting barrier has been crossed. The association rate constant in the absence of electrostatic enhancement was determined to be rather high. This is consistent with the Φ-value analysis, which showed that there are few or no obligatory native contacts. Also, linear free energy relationships clearly demonstrate that native interactions are cooperatively formed, a scenario that has usually been observed for proteins that fold according to the so-called nucleation-condensation mechanism. Thus, native hydrophobic binding interactions at the rate-limiting transition state for association between TAD-STAT2 and TAZ1 are not a requirement, which is generally in agreement with previous findings on other IDP systems and might be a common mechanism for IDPs.

  2. Scattering Studies of Hydrophobic Monomers in Liposomal Bilayers: An Expanding Shell Model of Monomer Distribution

    International Nuclear Information System (INIS)

    Richter, Andrew; Dergunov, Sergey; Ganus, Bill; Thomas, Zachary; Pingali, Sai Venkatesh; Urban, Volker S.; Liu, Yun; Porcar, Lionel; Pinkhassik, Eugene

    2011-01-01

    Hydrophobic monomers partially phase separate from saturated lipids when loaded into lipid bilayers in amounts exceeding a 1:1 monomer/lipid molar ratio. This conclusion is based on the agreement between two independent methods of examining the structure of monomer-loaded bilayers. Complete phase separation of monomers from lipids would result in an increase in bilayer thickness and a slight increase in the diameter of liposomes. A homogeneous distribution of monomers within the bilayer would not change the bilayer thickness and would lead to an increase in the liposome diameter. The increase in bilayer thickness, measured by the combination of small-angle neutron scattering (SANS) and small-angle X-ray scattering (SAXS), was approximately half of what was predicted for complete phase separation. The increase in liposome diameter, measured by dynamic light scattering (DLS), was intermediate between values predicted for a homogeneous distribution and complete phase separation. Combined SANS, SAXS, and DLS data suggest that at a 1.2 monomer/lipid ratio approximately half of the monomers are located in an interstitial layer sandwiched between lipid sheets. These results expand our understanding of using self-assembled bilayers as scaffolds for the directed covalent assembly of organic nanomaterials. In particular, the partial phase separation of monomers from lipids corroborates the successful creation of nanothin polymer materials with uniform imprinted nanopores. Pore-forming templates do not need to span the lipid bilayer to create a pore in the bilayer-templated films.

  3. Defining process design space for a hydrophobic interaction chromatography (HIC) purification step: application of quality by design (QbD) principles.

    Science.gov (United States)

    Jiang, Canping; Flansburg, Lisa; Ghose, Sanchayita; Jorjorian, Paul; Shukla, Abhinav A

    2010-12-15

    The concept of design space has been taking root under the quality by design paradigm as a foundation of in-process control strategies for biopharmaceutical manufacturing processes. This paper outlines the development of a design space for a hydrophobic interaction chromatography (HIC) process step. The design space included the impact of raw material lot-to-lot variability and variations in the feed stream from cell culture. A failure modes and effects analysis was employed as the basis for the process characterization exercise. During mapping of the process design space, the multi-dimensional combination of operational variables were studied to quantify the impact on process performance in terms of yield and product quality. Variability in resin hydrophobicity was found to have a significant influence on step yield and high-molecular weight aggregate clearance through the HIC step. A robust operating window was identified for this process step that enabled a higher step yield while ensuring acceptable product quality. © 2010 Wiley Periodicals, Inc.

  4. Deciphering the perturbation effect of urea on the supramolecular host-guest interaction of biologically active hydrophobic molecule inside the nanocavity of cyclodextrins

    Energy Technology Data Exchange (ETDEWEB)

    Maity, Banibrata; Chatterjee, Aninda; Ahmed, Sayeed Ashique; Seth, Debabrata, E-mail: debabrata@iitp.ac.in

    2017-03-15

    The present work articulates the supramolecular interaction and the formation of host-guest complex between the biologically active hydrophobic coumarin derivative and cyclodextrins by using several spectroscopic, calorimetric and microscopic techniques. All the studies clearly revealed that in presence of cyclodextrins (CDs), coumarin forms 1:1 stoichiometric complex. From all the study, we have found that with gradual increasing the cavity diameter of the hosts, the binding efficiency of the complexes gradually increases. The small population of the non emissive twisted intramolecular charge transfer (TICT) state of coumarin molecule turns into highly emissive in presence of γ-CD owing to its greater cavity diameter. The emissive TICT band is not found in β-CD complex due to its comparative small hydrophilic exterior and less polar environment. The present finding also interpret the perturbation effect of urea on host-guest complexes. In the presence of urea, the TICT emissive band of γ-CD is completely diminished. From, {sup 1}H NMR study it was observed that –NEt{sub 2} moiety of 7-DCCAE molecule is deeply buried inside the hydrophobic cavity of the CDs and forms host-guest complexes. Isothermal titration calorimetry measurement also indicates the formation of 1:1 host-guest complexes.

  5. New insight in the structural features of haloadaptation in α-amylases from halophilic Archaea following homology modeling strategy: folded and stable conformation maintained through low hydrophobicity and highly negative charged surface

    Science.gov (United States)

    Zorgani, Mohamed Amine; Patron, Kevin; Desvaux, Mickaël

    2014-07-01

    Proteins from halophilic archaea, which live in extreme saline conditions, have evolved to remain folded, active and stable at very high ionic strengths. Understanding the mechanism of haloadaptation is the first step toward engineering of halostable biomolecules. Amylases are one of the main enzymes used in industry. Yet, no three-dimensional structure has been experimentally resolved for α-amylases from halophilic archaea. In this study, homology structure modeling of α-amylases from the halophilic archaea Haloarcula marismortui, Haloarcula hispanica, and Halalkalicoccus jeotgali were performed. The resulting models were subjected to energy minimization, evaluation, and structural analysis. Calculations of the amino acid composition, salt bridges and hydrophobic interactions were also performed and compared to a set of non-halophilic counterparts. It clearly appeared that haloarchaeal α-amylases exhibited lower propensities for helix formation and higher propensities for coil-forming regions. Furthermore, they could maintain a folded and stable conformation in high salt concentration through highly negative charged surface with over representation of acidic residues, especially Asp, and low hydrophobicity with increase of salt bridges and decrease in hydrophobic interactions on the protein surface. This study sheds some light on the stability of α-amylases from halophilic archaea and provides strong basis not only to understand haloadaptation mechanisms of proteins in microorganisms from hypersalines environments but also for biotechnological applications.

  6. Interactive Dimensioning of Parametric Models

    KAUST Repository

    Kelly, T.

    2015-06-22

    We propose a solution for the dimensioning of parametric and procedural models. Dimensioning has long been a staple of technical drawings, and we present the first solution for interactive dimensioning: A dimension line positioning system that adapts to the view direction, given behavioral properties. After proposing a set of design principles for interactive dimensioning, we describe our solution consisting of the following major components. First, we describe how an author can specify the desired interactive behavior of a dimension line. Second, we propose a novel algorithm to place dimension lines at interactive speeds. Third, we introduce multiple extensions, including chained dimension lines, controls for different parameter types (e.g. discrete choices, angles), and the use of dimension lines for interactive editing. Our results show the use of dimension lines in an interactive parametric modeling environment for architectural, botanical, and mechanical models.

  7. Recovery of infective virus particles in ion-exchange and hydrophobic interaction monolith chromatography is influenced by particle charge and total-to-infective particle ratio.

    Science.gov (United States)

    Sviben, Dora; Forcic, Dubravko; Ivancic-Jelecki, Jelena; Halassy, Beata; Brgles, Marija

    2017-06-01

    Viral particles are used in medical applications as vaccines or gene therapy vectors. In order to obtain product of high purity, potency and safety for medical use purification of virus particles is a prerequisite, and chromatography is gaining increased attention to meet this aim. Here, we report on the use of ion-exchange and hydrophobic interaction chromatography on monolithic columns for purification of mumps virus (MuV) and measles virus (MeV). Efficiency of the process was monitored by quantification of infective virus particles (by 50% cell culture infective dose assay) and total virus particles, and monitoring of their size (by Nanoparticle Tracking Analysis). Ion-exchange chromatography was shown to be inefficient for MuV and best results for MeV were obtained on QA column with recovery around 17%. Purification of MuV and MeV by hydrophobic interaction chromatography resulted in recoveries around 60%. Results showed that columns with small channels (d=1.4μm) are not suitable for MuV and MeV, although their size is below 400nm, whereas columns with large channels (6μm) showed to be efficient and recoveries independent on the flow rate up to 10mL/min. Heterogeneity of the virus suspension and its interday variability mostly regarding total-to-infective particle ratio was observed. Interestingly, a trend in recovery depending on the day of the harvest was also observed for both viruses, and it correlated with the total-to-infective particle ratio, indicating influence of the virus sample composition on the chromatography results. Copyright © 2017. Published by Elsevier B.V.

  8. Strong interactions - quark models

    International Nuclear Information System (INIS)

    Goto, M.; Ferreira, P.L.

    1979-01-01

    The variational method is used for the PSI and upsilon family spectra reproduction from the quark model, through several phenomenological potentials, viz.: linear, linear plus coulomb term and logarithmic. (L.C.) [pt

  9. Salt effects on hydrophobic interaction and charge screening in the folding of a negatively charged peptide to a coiled coil (leucine zipper).

    Science.gov (United States)

    Jelesarov, I; Dürr, E; Thomas, R M; Bosshard, H R

    1998-05-19

    The stability of a coiled coil or leucine zipper is controlled by hydrophobic interactions and electrostatic forces between the constituent helices. We have designed a 30-residue peptide with the repeating seven-residue pattern of a coiled coil, (abcdefg)n, and with Glu in positions e and g of each heptad. The glutamate side chains prevented folding at pH values above 6 because of electrostatic repulsion across the helix dimer interface as well as within the individual helices. Protonation of the carboxylates changed the conformation from a random coil monomer to a coiled coil dimer. Folding at alkaline pH where the peptide had a net charge of -7e was promoted by the addition of salts. The nature of the charge screening cation was less important than that of the anion. The high salt concentrations (>1 M) necessary to induce folding indicated that the salt-induced folding resulted from alterations in the protein-water interaction. Folding was promoted by the kosmotropic anions sulfate and fluoride and to a lesser extent by the weak kosmotrope formate, whereas chloride and the strong chaotrope perchlorate were ineffective. Kosmotropes are excluded from the protein surface, which is preferentially hydrated, and this promotes folding by strengthening hydrophobic interactions at the coiled coil interface. Although charge neutralization also contributed to folding, it was effective only when the screening cation was partnered by a good kosmotropic anion. Folding conformed to a two-state transition from random coil monomer to coiled coil dimer and was enthalpy driven and characterized by a change in the heat capacity of unfolding of 3.9 +/- 1.2 kJ mol-1 K-1. The rate of folding was analyzed by fluorescence stopped-flow measurements. Folding occurred in a biphasic reaction in which the rapid formation of an initial dimer (kf = 2 x 10(7) M-1 s-1) was followed by an equally rapid concentration-independent rearrangement to the folded dimer (k > 100 s-1).

  10. Sum Frequency Generation Vibrational Spectroscopy Studies on ModelPeptide Adsorption at the Hydrophobic Solid-Water and HydrophilicSolid-Water Interfaces

    Energy Technology Data Exchange (ETDEWEB)

    York, Roger L. [Univ. of California, Berkeley, CA (United States)

    2007-01-01

    Sum frequency generation (SFG) vibrational spectroscopy has been used to study the interfacial structure of several polypeptides and amino acids adsorbed to hydrophobic and hydrophilic surfaces under a variety of experimental conditions. Peptide sequence, peptide chain length, peptide hydrophobicity, peptide side-chain type, surface hydrophobicity, and solution ionic strength all affect an adsorbed peptide's interfacial structure. Herein, it is demonstrated that with the choice of simple, model peptides and amino acids, surface specific SFG vibrational spectroscopy can be a powerful tool to elucidate the interfacial structure of these adsorbates. Herein, four experiments are described. In one, a series of isosequential amphiphilic peptides are synthesized and studied when adsorbed to both hydrophobic and hydrophilic surfaces. On hydrophobic surfaces of deuterated polystyrene, it was determined that the hydrophobic part of the peptide is ordered at the solid-liquid interface, while the hydrophilic part of the peptide appears to have a random orientation at this interface. On a hydrophilic surface of silica, it was determined that an ordered peptide was only observed if a peptide had stable secondary structure in solution. In another experiment, the interfacial structure of a model amphiphilic peptide was studied as a function of the ionic strength of the solution, a parameter that could change the peptide's secondary structure in solution. It was determined that on a hydrophobic surface, the peptide's interfacial structure was independent of its structure in solution. This was in contrast to the adsorbed structure on a hydrophilic surface, where the peptide's interfacial structure showed a strong dependence on its solution secondary structure. In a third experiment, the SFG spectra of lysine and proline amino acids on both hydrophobic and hydrophilic surfaces were obtained by using a different experimental geometry that increases the SFG signal

  11. Experimental Results and Integrated Modeling of Bacterial Growth on an Insoluble Hydrophobic Substrate (Phenanthrene)

    DEFF Research Database (Denmark)

    Adam, Iris K. U.; Rein, Arno; Miltner, Anja

    2014-01-01

    Metabolism of a low-solubility substrate is limited by dissolution and availability and can hardly be determined. We developed a numerical model for simultaneously calculating dissolution kinetics of such substrates and their metabolism and microbial growth (Monod kinetics with decay) and tested ...

  12. Characterisation of nanomaterial hydrophobicity using engineered surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Desmet, Cloé; Valsesia, Andrea; Oddo, Arianna; Ceccone, Giacomo; Spampinato, Valentina; Rossi, François; Colpo, Pascal, E-mail: pascal.colpo@ec.europa.eu [Directorate Health, Consumer and Reference Materials, Consumer Products Safety Unit (Italy)

    2017-03-15

    Characterisation of engineered nanomaterials (NMs) is of outmost importance for the assessment of the potential risks arising from their extensive use. NMs display indeed a large variety of physico-chemical properties that drastically affect their interaction with biological systems. Among them, hydrophobicity is an important property that is nevertheless only slightly covered by the current physico-chemical characterisation techniques. In this work, we developed a method for the direct characterisation of NM hydrophobicity. The determination of the nanomaterial hydrophobic character is carried out by the direct measurement of the affinity of the NMs for different collectors. Each collector is an engineered surface designed in order to present specific surface charge and hydrophobicity degrees. Being thus characterised by a combination of surface energy components, the collectors enable the NM immobilisation with surface coverage in relation to their hydrophobicity. The experimental results are explained by using the extended DLVO theory, which takes into account the hydrophobic forces acting between NMs and collectors.

  13. Clustering structures of large proteins using multifractal analyses based on a 6-letter model and hydrophobicity scale of amino acids

    International Nuclear Information System (INIS)

    Yang Jianyi; Yu Zuguo; Anh, Vo

    2009-01-01

    The Schneider and Wrede hydrophobicity scale of amino acids and the 6-letter model of protein are proposed to study the relationship between the primary structure and the secondary structural classification of proteins. Two kinds of multifractal analyses are performed on the two measures obtained from these two kinds of data on large proteins. Nine parameters from the multifractal analyses are considered to construct the parameter spaces. Each protein is represented by one point in these spaces. A procedure is proposed to separate large proteins in the α, β, α + β and α/β structural classes in these parameter spaces. Fisher's linear discriminant algorithm is used to assess our clustering accuracy on the 49 selected large proteins. Numerical results indicate that the discriminant accuracies are satisfactory. In particular, they reach 100.00% and 84.21% in separating the α proteins from the {β, α + β, α/β} proteins in a parameter space; 92.86% and 86.96% in separating the β proteins from the {α + β, α/β} proteins in another parameter space; 91.67% and 83.33% in separating the α/β proteins from the α + β proteins in the last parameter space.

  14. Modelling land surface - atmosphere interactions

    DEFF Research Database (Denmark)

    Rasmussen, Søren Højmark

    representation of groundwater in the hydrological model is found to important and this imply resolving the small river valleys. Because, the important shallow groundwater is found in the river valleys. If the model does not represent the shallow groundwater then the area mean surface flux calculation......The study is investigates modelling of land surface – atmosphere interactions in context of fully coupled climatehydrological model. With a special focus of under what condition a fully coupled model system is needed. Regional climate model inter-comparison projects as ENSEMBLES have shown bias...... by the hydrological model is found to be insensitive to model resolution. Furthermore, this study highlights the effect of bias precipitation by regional climate model and it implications for hydrological modelling....

  15. Phenytoin-Bovine Serum Albumin interactions - modeling plasma protein - drug binding: A multi-spectroscopy and in silico-based correlation

    Science.gov (United States)

    Suresh, P. K.; Divya, Naik; Nidhi, Shah; Rajasekaran, R.

    2018-03-01

    The study focused on the analysis of the nature and site of binding of Phenytoin (PHT) -(a model hydrophobic drug) with Bovine Serum Albumin (BSA) (a model protein used as a surrogate for HSA). Interactions with defined amounts of Phenytoin and BSA demonstrated a blue shift (hypsochromic -change in the microenvironment of the tryptophan residue with decrease in the polar environment and more of hydrophobicity) with respect to the albumin protein and a red shift (bathochromic -hydrophobicity and polarity related changes) in the case of the model hydrophobic drug. This shift, albeit lower in magnitude, has been substantiated by a fairly convincing, Phenytoin-mediated quenching of the endogenous fluorophore in BSA. Spectral shifts studied at varying pH, temperatures and incubation periods (at varying concentrations of PHT with a defined/constant BSA concentration) showed no significant differences (data not shown). FTIR analysis provided evidence of the interaction of PHT with BSA with a stretching vibration of 1737.86 cm- 1, apart from the vibrations characteristically associated with the amine and carboxyl groups respectively. Our in vitro findings were extended to molecular docking of BSA with PHT (with the different ionized forms of the drug) and the subsequent LIGPLOT-based analysis. In general, a preponderance of hydrophobic interactions was observed. These hydrophobic interactions corroborate the tryptophan-based spectral shifts and the fluorescence quenching data. These results substantiates our hitherto unreported in vitro/in silico experimental flow and provides a basis for screening other hydrophobic drugs in its class.

  16. The joy of interactive modeling

    Science.gov (United States)

    Donchyts, Gennadii; Baart, Fedor; van Dam, Arthur; Jagers, Bert

    2013-04-01

    The conventional way of working with hydrodynamical models usually consists of the following steps: 1) define a schematization (e.g., in a graphical user interface, or by editing input files) 2) run model from start to end 3) visualize results 4) repeat any of the previous steps. This cycle commonly takes up from hours to several days. What if we can make this happen instantly? As most of the research done using numerical models is in fact qualitative and exploratory (Oreskes et al., 1994), why not use these models as such? How can we adapt models so that we can edit model input, run and visualize results at the same time? More and more, interactive models become available as online apps, mainly for demonstration and educational purposes. These models often simplify the physics behind flows and run on simplified model geometries, particularly when compared with state-of-the-art scientific simulation packages. Here we show how the aforementioned conventional standalone models ("static, run once") can be transformed into interactive models. The basic concepts behind turning existing (conventional) model engines into interactive engines are the following. The engine does not run the model from start to end, but is always available in memory, and can be fed by new boundary conditions, or state changes at any time. The model can be run continuously, per step, or up to a specified time. The Hollywood principle dictates how the model engine is instructed from 'outside', instead of the model engine taking all necessary actions on its own initiative. The underlying techniques that facilitate these concepts are introspection of the computation engine, which exposes its state variables, and control functions, e.g. for time stepping, via a standardized interface, such as BMI (Peckam et. al., 2012). In this work we have used a shallow water flow model engine D-Flow Flexible Mesh. The model was converted from executable to a library, and coupled to the graphical modelling

  17. Interactive differential equations modeling program

    International Nuclear Information System (INIS)

    Rust, B.W.; Mankin, J.B.

    1976-01-01

    Due to the recent emphasis on mathematical modeling, many ecologists are using mathematics and computers more than ever, and engineers, mathematicians and physical scientists are now included in ecological projects. However, the individual ecologist, with intuitive knowledge of the system, still requires the means to critically examine and adjust system models. An interactive program was developed with the primary goal of allowing an ecologist with minimal experience in either mathematics or computers to develop a system model. It has also been used successfully by systems ecologists, engineers, and mathematicians. This program was written in FORTRAN for the DEC PDP-10, a remote terminal system at Oak Ridge National Laboratory. However, with relatively minor modifications, it can be implemented on any remote terminal system with a FORTRAN IV compiler, or equivalent. This program may be used to simulate any phenomenon which can be described as a system of ordinary differential equations. The program allows the user to interactively change system parameters and/or initial conditions, to interactively select a set of variables to be plotted, and to model discontinuities in the state variables and/or their derivatives. One of the most useful features to the non-computer specialist is the ability to interactively address the system parameters by name and to interactively adjust their values between simulations. These and other features are described in greater detail

  18. Interacting boson model with surface delta interaction between nucleons

    International Nuclear Information System (INIS)

    Druce, C.; Moszkowski, S.A.

    1984-01-01

    The surface delta interaction is used as an effective nucleon-nucleon interaction to investigate the structure and interaction of the bosons in the interacting boson model. The authors have obtained analytical expressions for the coefficients of a multipole expansion of the neutron-boson proton-boson interaction for the case of degenerate orbits

  19. Interaction of methotrexate with trypsin analyzed by spectroscopic and molecular modeling methods

    Science.gov (United States)

    Wang, Yanqing; Zhang, Hongmei; Cao, Jian; Zhou, Qiuhua

    2013-11-01

    Trypsin is one of important digestive enzymes that have intimate correlation with human health and illness. In this work, the interaction of trypsin with methotrexate was investigated by spectroscopic and molecular modeling methods. The results revealed that methotrexate could interact with trypsin with about one binding site. Methotrexate molecule could enter into the primary substrate-binding pocket, resulting in inhibition of trypsin activity. Furthermore, the thermodynamic analysis implied that electrostatic force, hydrogen bonding, van der Waals and hydrophobic interactions were the main interactions for stabilizing the trypsin-methotrexate system, which agreed well with the results from the molecular modeling study.

  20. Introduction to interacting boson model

    International Nuclear Information System (INIS)

    Goutte, D.

    1986-01-01

    A very simple presentation of the interacting boson model is first given. The two computerized models which are presented allow, with few parameters, to reproduce an impressive quantity of data characterizing the deformed nuclei. Their excitation spectra, the reduced transition probabilities, the quadrupolar moments, the two nucleon transfer experiment results, ... Then a specific application of the model is given: radial extension reproduction of nuclear functions. It is shown first how the electron inelastic scattering allows to measure observables related to these radial functions, the transition charge densities, then, on some examples, how the model allows to reproduce them [fr

  1. Molecular interaction of PCB153 to human serum albumin: Insights from spectroscopic and molecular modeling studies

    Energy Technology Data Exchange (ETDEWEB)

    Han, Chao; Fang, Senbiao; Cao, Huiming; Lu, Yan; Ma, Yaqiong [School of Pharmacy, Lanzhou University, Lanzhou 730000 (China); Wei, Dongfeng [Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700 (China); Xie, Xiaoyun [College of Earth and Environmental Science, Lanzhou University, Lanzhou 730000 (China); Liu, Xiaohua [School of Pharmacy, Lanzhou University, Lanzhou 730000 (China); Li, Xin [College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471003 (China); Fei, Dongqing [School of Pharmacy, Lanzhou University, Lanzhou 730000 (China); Zhao, Chunyan, E-mail: zhaochy07@lzu.edu.cn [School of Pharmacy, Lanzhou University, Lanzhou 730000 (China)

    2013-03-15

    Highlights: ► We identify the binding mode of PCB153 to human serum albumin (HSA). ► Spectroscopic and molecular modeling results reveal that PCB153 binds at the site II. ► The interaction is mainly governed by hydrophobic and hydrogen bond forces. ► The work helps to probe transporting, distribution and toxicity effect of PCBs. -- Abstract: Polychlorinated biphenyls (PCBs) possessed much potential hazard to environment because of its chemical stability and biological toxicity. Here, we identified the binding mode of a representative compound, PCB153, to human serum albumin (HSA) using fluorescence and molecular dynamics simulation methods. The fluorescence study showed that the intrinsic fluorescence of HSA was quenched by addition of PCB153 through a static quenching mechanism. The thermodynamic analysis proved the binding behavior was mainly governed by hydrophobic force. Furthermore, as evidenced by site marker displacement experiments using two probe compounds, it revealed that PCB153 acted exactly on subdomain IIIA (site II) of HSA. On the other hand, the molecular dynamics studies as well as free energy calculations made another important contribution to understand the conformational changes of HSA and the stability of HSA-PCB153 system. Molecular docking revealed PCB153 can bind in a large hydrophobic activity of subdomain IIIA by the hydrophobic interaction and hydrogen bond interactions between chlorine atoms and residue ASN391. The present work provided reasonable models helping us further understand the transporting, distribution and toxicity effect of PCBs when it spread into human blood serum.

  2. Stochastic hyperfine interactions modeling library

    Science.gov (United States)

    Zacate, Matthew O.; Evenson, William E.

    2011-04-01

    The stochastic hyperfine interactions modeling library (SHIML) provides a set of routines to assist in the development and application of stochastic models of hyperfine interactions. The library provides routines written in the C programming language that (1) read a text description of a model for fluctuating hyperfine fields, (2) set up the Blume matrix, upon which the evolution operator of the system depends, and (3) find the eigenvalues and eigenvectors of the Blume matrix so that theoretical spectra of experimental techniques that measure hyperfine interactions can be calculated. The optimized vector and matrix operations of the BLAS and LAPACK libraries are utilized; however, there was a need to develop supplementary code to find an orthonormal set of (left and right) eigenvectors of complex, non-Hermitian matrices. In addition, example code is provided to illustrate the use of SHIML to generate perturbed angular correlation spectra for the special case of polycrystalline samples when anisotropy terms of higher order than A can be neglected. Program summaryProgram title: SHIML Catalogue identifier: AEIF_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIF_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU GPL 3 No. of lines in distributed program, including test data, etc.: 8224 No. of bytes in distributed program, including test data, etc.: 312 348 Distribution format: tar.gz Programming language: C Computer: Any Operating system: LINUX, OS X RAM: Varies Classification: 7.4 External routines: TAPP [1], BLAS [2], a C-interface to BLAS [3], and LAPACK [4] Nature of problem: In condensed matter systems, hyperfine methods such as nuclear magnetic resonance (NMR), Mössbauer effect (ME), muon spin rotation (μSR), and perturbed angular correlation spectroscopy (PAC) measure electronic and magnetic structure within Angstroms of nuclear probes through the hyperfine interaction. When

  3. Drug-model membrane interactions

    International Nuclear Information System (INIS)

    Deniz, Usha K.

    1994-01-01

    In the present day world, drugs play a very important role in medicine and it is necessary to understand their mode of action at the molecular level, in order to optimise their use. Studies of drug-biomembrane interactions are essential for gaining such as understanding. However, it would be prohibitively difficult to carry out such studies, since biomembranes are highly complex systems. Hence, model membranes (made up of these lipids which are important components of biomembranes) of varying degrees of complexity are used to investigate drug-membrane interactions. Bio- as well as model-membranes undergo a chain melting transition when heated, the chains being in a disordered state above the transition point, T CM . This transition is of physiological importance since biomembranes select their components such that T CM is less than the ambient temperature but not very much so, so that membrane flexibility is ensured and porosity, avoided. The influence of drugs on the transition gives valuable clues about various parameters such as the location of the drug in the membrane. Deep insights into drug-membrane interactions are obtained by observing the effect of drugs on membrane structure and the mobilities of the various groups in lipids, near T CM . Investigation of such changes have been carried out with several drugs, using techniques such as DSC, XRD and NMR. The results indicate that the drug-membrane interaction not only depends on the nature of drug and lipids but also on the form of the model membrane - stacked bilayer or vesicles. The light that these results shed on the nature of drug-membrane interactions is discussed. (author). 13 refs., 13 figs., 1 tab

  4. Interactions of Model Cell Membranes with Nanoparticles

    Science.gov (United States)

    D'Angelo, S. M.; Camesano, T. A.; Nagarajan, R.

    2011-12-01

    or pores in the cell membrane. The dissipation changes were small, which indicates that even with the membrane destabilization that occurs, the overall structure of the bilayer is not greatly perturbed. For the 80 nm nanoparticles, we initially saw the same pattern as the smaller nanoparticles with a mass loss from the membrane, but eventually we saw a large decrease in frequency, representing an increase in mass. This addition of mass may be attributed to adsorption of the gold nanoparticles onto the bilayer. The 80 nm particles also created a change in the energy dissipation, which suggests that the formation of the bilayer was altered with the adsorbed particles. This study suggests that nanoparticle size controls the mechanism by which nanoparticles interact with model cell membranes. We are extending this work to other types of gold nanoparticles. We are interested in examining the role of nanoparticle hydrophobicity and type of chemical functionalization on the interactions of the nanoparticle with a model membrane. We are also conducting studies on environmental bacteria, to correlate the mechanisms of nanoparticle cytoxicity with killing data on bacterial cells.

  5. Efficiency of clay--TiO2 nanocomposites on the photocatalytic elimination of a model hydrophobic air pollutant.

    Science.gov (United States)

    Kibanova, Daria; Cervini-Silva, Javiera; Destaillats, Hugo

    2009-03-01

    Clay-supported TiO2 photocatalysts can potentially improve the performance of air treatment technologies via enhanced adsorption and reactivity of target volatile organic compounds (VOCs). In this study, a benchtop photocatalytic flow reactor was used to evaluate the efficiency of hectorite-TiO2 and kaolinite-TiO2, two novel composite materials synthesized in our laboratory. Toluene, a model hydrophobic VOC and a common indoor air pollutant, was introduced in the air stream at realistic concentrations, and reacted under UVA (lamda(max) = 365 nm) or UVC (lamda(max) = 254 nm) irradiation. The UVC lamp generated secondary emission at 185 nm, leading to the formation of ozone and other short-lived reactive species. Performance of clay-Ti02 composites was compared with that of pure TiO2 (Degussa P25), and with UV irradiation in the absence of photocatalyst under identical conditions. Films of clay-TiO2 composites and of P25 were prepared by a dip-coating method on the surface of Raschig rings, which were placed inside the flow reactor. An upstream toluene concentration of approximately 170 ppbv was generated by diluting a constant flow of toluene vapor from a diffusion source with dry air, or with humid air at 10, 33, and 66% relative humidity (RH). Toluene concentrations were determined by collecting Tenax-TA sorbent tubes downstream of the reactor, with subsequent thermal desorption--GC/MS analysis. The fraction of toluene removed, %R, and the reaction rate, Tr, were calculated for each experimental condition from the concentrations measured with and without UV irradiation. Use of UVC light (UV/TiO2/O3) led to overall higher reactivity, which can be partially attributed to the contribution of gas phase reactions by short-lived radical species. When the reaction rate was normalized to the light irradiance, Tr/Ilamda,the UV/TiO2 reaction under UVA irradiation was more efficient for samples with a higher content of TiO2 (P25 and Hecto-TiO2), but notfor Kao-TiO2. In all

  6. Temperature dependence of the evaporation lengthscale for water confined between two hydrophobic plates.

    Science.gov (United States)

    Djikaev, Yuri S; Ruckenstein, Eli

    2015-07-01

    Liquid water in a hydrophobic confinement is the object of high interest in physicochemical sciences. Confined between two macroscopic hydrophobic surfaces, liquid water transforms into vapor if the distance between surfaces is smaller than a critical separation, referred to as the evaporation lengthscale. To investigate the temperature dependence of the evaporation lengthscale of water confined between two hydrophobic parallel plates, we use the combination of the density functional theory (DFT) with the probabilistic hydrogen bond (PHB) model for water-water hydrogen bonding. The PHB model provides an analytic expression for the average number of hydrogen bonds per water molecule as a function of its distance to a hydrophobic surface and its curvature. Knowing this expression, one can implement the effect of hydrogen bonding between water molecules on their interaction with the hydrophobe into DFT, which is then employed to determine the distribution of water molecules between two macroscopic hydrophobic plates at various interplate distances and various temperatures. For water confined between hydrophobic plates, our results suggest the evaporation lengthscale to be of the order of several nanometers and a linearly increasing function of temperature from T=293 K to T=333 K, qualitatively consistent with previous results. Copyright © 2015 Elsevier Inc. All rights reserved.

  7. Efficiency of clay-TiO2 nanocomposites on the photocatalytic eliminationof a model hydrophobic air pollutant

    Energy Technology Data Exchange (ETDEWEB)

    Kibanova, Daria; Cervini-Silva, Javiera; Destaillats, Hugo

    2009-01-01

    Clay-supported TiO2 photocatalysts can potentially improve the performance of air treatment technologies via enhanced adsorption and reactivity of target volatile organic compounds (VOCs). In this study, a bench-top photocatalytic flow reactor was used to evaluate the efficiency of hectorite-TiO2 and kaolinite-TiO2, two novel composite materials synthesized in our laboratory. Toluene, a model hydrophobic VOC and a common indoor air pollutant, was introduced in the air stream at realistic concentrations, and reacted under UVA (gamma max = 365 nm) or UVC (gamma max = 254 nm) irradiation. The UVC lamp generated secondary emission at 185 nm, leading to the formation of ozone and other short-lived reactive species. Performance of clay-TiO2 composites was compared with that of pure TiO2 (Degussa P25), and with UV irradiation in the absence of photocatalyst under identical conditions. Films of clay-TiO2 composites and of P25 were prepared by a dip-coating method on the surface of Raschig rings, which were placed inside the flow reactor. An upstream toluene concentration of ~;;170 ppbv was generated by diluting a constant flow of toluene vapor from a diffusion source with dry air, or with humid air at 10, 33 and 66percent relative humidity (RH). Toluene concentrations were determined by collecting Tenax-TA (R) sorbent tubes downstream of the reactor, with subsequent thermal desorption -- GC/MS analysis. The fraction of toluene removed, percentR, and the reaction rate, Tr, were calculated for each experimental condition from the concentration changes measured with and without UV irradiation. Use of UVC light (UV/TiO2/O3) led to overall higher reactivity, which can be partially attributed to the contribution of gas phase reactions by short-lived radical species. When the reaction rate was normalized to the light irradiance, Tr/I gamma, the UV/TiO2 reaction under UVA irradiation was more efficient for samples with a higher content of TiO2 (P25 and Hecto-TiO2), but not for Kao

  8. Towards understanding hydrophobic recovery of plasma treated polymers: Storing in high polarity liquids suppresses hydrophobic recovery

    International Nuclear Information System (INIS)

    Bormashenko, Edward; Chaniel, Gilad; Grynyov, Roman

    2013-01-01

    The phenomenon of hydrophobic recovery was studied for cold air plasma treated polyethylene films. Plasma-treated polymer films were immersed into liquids with very different polarities such as ethanol, acetone, carbon tetrachloride, benzene and carbon disulphide. Hydrophobic recovery was studied by measurement of contact angles. Immersion into high polarity liquids slows markedly the hydrophobic recovery. We relate this slowing to dipole–dipole interaction of polar groups of the polymer with those of the liquids. This kind of interaction becomes decisive when polar groups of polymer chains are at least partially spatially fixed.

  9. Water-based adhesives with tailored hydrophobic association: dilution resistance and improved setting behavior.

    Science.gov (United States)

    Dundua, Alexander; Landfester, Katharina; Taden, Andreas

    2014-11-01

    Hydrophobic association and stimuli-responsiveness is a powerful tool towards water-based adhesives with strongly improved properties, which is demonstrated based on the example of hydrophobically modified alkali-soluble latexes (HASE) with modulated association. Their rheological properties are highly tunable due to the hydrophobic domains that act as physical crosslinking sites of adjustable interaction strength. Ethanol, propanol, and butanol are used as water-soluble model additives with different hydrophobicity in order to specifically target the association sites and impact the viscoelastic properties and stimuli-responsiveness. The rheological and mechanical property response upon dilution with water can be tailored, and dilution-resistant or even dilution-thickening systems are obtained. The investigations are of high importance for water-based adhesives, as our findings provide insight into general structure-property relationships to improve their setting behavior, especially upon contact with wet substrates. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Measurement error models with interactions

    Science.gov (United States)

    Midthune, Douglas; Carroll, Raymond J.; Freedman, Laurence S.; Kipnis, Victor

    2016-01-01

    An important use of measurement error models is to correct regression models for bias due to covariate measurement error. Most measurement error models assume that the observed error-prone covariate (\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}$W$\\end{document}) is a linear function of the unobserved true covariate (\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}$X$\\end{document}) plus other covariates (\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}$Z$\\end{document}) in the regression model. In this paper, we consider models for \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}$W$\\end{document} that include interactions between \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}$X$\\end{document} and \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}$Z$\\end{document}. We derive the conditional distribution of

  11. Modelling the fate of hydrophobic organic contaminants in a boreal forest catchment: A cross disciplinary approach to assessing diffuse pollution to surface waters

    International Nuclear Information System (INIS)

    Bergknut, Magnus; Meijer, Sandra; Halsall, Crispin; Agren, Anneli; Laudon, Hjalmar; Koehler, Stephan; Jones, Kevin C.; Tysklind, Mats; Wiberg, Karin

    2010-01-01

    The fate of hydrophobic organic compounds (HOCs) in soils and waters in a northern boreal catchment was explored through the development of a chemical fate model in a well-characterised catchment system dominated by two land types: forest and mire. Input was based solely on atmospheric deposition, dominated by accumulation in the winter snowpack. Release from soils was governed by the HOC concentration in soil, the soil organic carbon fraction and soil-water DOC content. The modelled export of selected HOCs in surface waters ranged between 11 and 250 ng day -1 during the snow covered period, compared to 200 and 9600 ng/d during snow-melt; highlighting the importance of the snow pack as a source of these chemicals. The predicted levels of HOCs in surface water were in reasonable agreement to a limited set of measured values, although the model tended to over predict concentrations of HOCs for the forested sub-catchment, by over an order of magnitude in the case of hexachlorobenzene and PCB 180. This possibly reflects both the heterogeneity of the forest soils and the complicated and changing hydrology experienced between the different seasons. - The fate of hydrophobic organic contaminants in a boreal forest catchment is connected to the flux of dissolved organic carbon and seasonal deposition.

  12. Interacting boson model with surface delta interaction between nucleons: Structure and interaction of bosons

    International Nuclear Information System (INIS)

    Druce, C.H.; Moszkowski, S.A.

    1986-01-01

    The surface delta interaction is used as an effective nucleon-nucleon interaction to investigate the structure and interaction of the bosons in the interacting boson model. We have obtained analytical expressions for the coefficients of a multipole expansion of the neutron-boson-proton-boson interaction for the case of degenerate orbits. A connection is made between these coefficients and the parameters of the interaction boson model Hamiltonian. A link between the latter parameters and the single boson energies is suggested

  13. Interacting boson model with surface delta interaction between nucleons: Structure and interaction of bosons

    Energy Technology Data Exchange (ETDEWEB)

    Druce, C.H.; Moszkowski, S.A.

    1986-01-01

    The surface delta interaction is used as an effective nucleon-nucleon interaction to investigate the structure and interaction of the bosons in the interacting boson model. We have obtained analytical expressions for the coefficients of a multipole expansion of the neutron-boson-proton-boson interaction for the case of degenerate orbits. A connection is made between these coefficients and the parameters of the interaction boson model Hamiltonian. A link between the latter parameters and the single boson energies is suggested.

  14. Nanocarriers from GRAS Zein Proteins to Encapsulate Hydrophobic Actives.

    Science.gov (United States)

    Weissmueller, Nikolas T; Lu, Hoang D; Hurley, Amanda; Prud'homme, Robert K

    2016-11-14

    One factor limiting the expansion of nanomedicines has been the high cost of the materials and processes required for their production. We present a continuous, scalable, low cost nanoencapsulation process, Flash Nanoprecipitation (FNP) that enables the production of nanocarriers (NCs) with a narrow size distribution using zein corn proteins. Zein is a low cost, GRAS protein (having the FDA status of "Generally Regarded as Safe") currently used in food applications, which acts as an effective encapsulant for hydrophobic compounds using FNP. The four-stream FNP configuration allows the encapsulation of very hydrophobic compounds in a way that is not possible with previous precipitation processes. We present the encapsulation of several model active compounds with as high as 45 wt % drug loading with respect to zein concentration into ∼100 nm nanocarriers. Three examples are presented: (1) the pro-drug antioxidant, vitamin E-acetate, (2) an anticholera quorum-sensing modulator CAI-1 ((S)-3-hydroxytridecan-4-one; CAI-1 that reduces Vibrio cholerae virulence by modulating cellular communication), and (3) hydrophobic fluorescent dyes with a range of hydrophobicities. The specific interaction between zein and the milk protein, sodium caseinate, provides stabilization of the NCs in PBS, LB medium, and in pH 2 solutions. The stability and size changes in the three media provide information on the mechanism of assembly of the zein/active/casein NC.

  15. Is Br2 hydration hydrophobic?

    Science.gov (United States)

    Alcaraz-Torres, A; Gamboa-Suárez, A; Bernal-Uruchurtu, M I

    2017-02-28

    The spectroscopic properties of bromine in aqueous systems suggest it can behave as either hydrophilic or hydrophobic solute. In small water clusters, the halogen bond and the hydrogen-halogen interaction are responsible for its specific way of binding. In water hydrates, it is efficiently hosted by two different cages forming the crystal structure and it has been frequently assumed that there is little or no interaction between the guest and the host. Bromine in liquid solution poses a challenging question due to its non-negligible solubility and the large blue shift measured in its absorption spectra. Using a refined semi-empirical force field, PM3-PIF, we performed a Born-Oppenheimer molecular dynamics study of bromine in liquid water. Here we present a detailed study in which we retrieved the most representative hydration structures in terms of the most frequent positions around bromine and the most common water orientations. Albeit being an approximate description of the total hydration phenomenon, it captures the contribution of the leading molecular interactions in form of the recurrent structures. Our findings confirm that the spectroscopic signature is mainly caused by the closest neighbors. The dynamics of the whole first hydration shell strongly suggests that the external molecules in that structure effectively isolate the bulk from the presence of bromine. The solvation structure fluctuates from a hydrophilic to a hydrophobic-like environment along the studied trajectory.

  16. Chitosan derivatives targeting lipid bilayers: Synthesis, biological activity and interaction with model membranes.

    Science.gov (United States)

    Martins, Danubia Batista; Nasário, Fábio Domingues; Silva-Gonçalves, Laiz Costa; de Oliveira Tiera, Vera Aparecida; Arcisio-Miranda, Manoel; Tiera, Marcio José; Dos Santos Cabrera, Marcia Perez

    2018-02-01

    The antimicrobial activity of chitosan and derivatives to human and plant pathogens represents a high-valued prospective market. Presently, two low molecular weight derivatives, endowed with hydrophobic and cationic character at different ratios were synthesized and characterized. They exhibit antimicrobial activity and increased performance in relation to the intermediate and starting compounds. However, just the derivative with higher cationic character showed cytotoxicity towards human cervical carcinoma cells. Considering cell membranes as targets, the mode of action was investigated through the interaction with model lipid vesicles mimicking bacterial, tumoral and erythrocyte membranes. Intense lytic activity and binding are demonstrated for both derivatives in anionic bilayers. The less charged compound exhibits slightly improved selectivity towards bacterial model membranes, suggesting that balancing its hydrophobic/hydrophilic character may improve efficiency. Observing the aggregation of vesicles, we hypothesize that the "charge cluster mechanism", ascribed to some antimicrobial peptides, could be applied to these chitosan derivatives. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Molecular modeling of proteinlike inclusions in lipid bilayers: lipid-mediated interactions.

    Science.gov (United States)

    Kik, Richard A; Leermakers, Frans A M; Kleijn, J Mieke

    2010-02-01

    We investigated the insertion of transmembrane structures in a lipid bilayer and their interactions using self-consistent field theory. The lipids are coarse-grained on a united-atom level and consist of a phosphatidylcholinelike headgroup and two hydrophobic tails. The inclusions, acting as simple models for proteins that span biological membranes, are rigid rods (radius R ) with a hydrophobic surface and hydrophilic end caps. The insertion free energy Omega of an individual rod is strongly regulated by the affinity between its hydrophobic surface and the lipid tails. This affinity also controls the best match of the hydrophobic length of the rod with that of the bilayer. The line tension tau(=Omega/2piR) is practically independent of R . The perturbations in the bilayer as a function of distance from the inclusion, have the shape of a damped oscillation. The wavelength and decay length are related to the elastic properties of the bilayer and do not depend on R . These results are used to analyze how the lipid matrix affects the interaction between transmembrane objects, for computational reasons considering the limit of R-->infinity . Contributions on different length scales can be distinguished: (i) a long-range elastic interaction, which is an exponentially decaying oscillation; (ii) an exponentially decaying repulsion on an intermediate length scale, resulting from the loss of conformational entropy of the lipid tails; and (iii) a short-range interaction due to the finite compressibility of the lipid tails, which manifests either as a depletion attraction if there is no affinity between the tails and the inclusions' surface or, otherwise, as an oscillatory structural force.

  18. An analytical model for interactive failures

    International Nuclear Information System (INIS)

    Sun Yong; Ma Lin; Mathew, Joseph; Zhang Sheng

    2006-01-01

    In some systems, failures of certain components can interact with each other, and accelerate the failure rates of these components. These failures are defined as interactive failure. Interactive failure is a prevalent cause of failure associated with complex systems, particularly in mechanical systems. The failure risk of an asset will be underestimated if the interactive effect is ignored. When failure risk is assessed, interactive failures of an asset need to be considered. However, the literature is silent on previous research work in this field. This paper introduces the concepts of interactive failure, develops an analytical model to analyse this type of failure quantitatively, and verifies the model using case studies and experiments

  19. A feature-based approach to modeling protein-protein interaction hot spots.

    Science.gov (United States)

    Cho, Kyu-il; Kim, Dongsup; Lee, Doheon

    2009-05-01

    Identifying features that effectively represent the energetic contribution of an individual interface residue to the interactions between proteins remains problematic. Here, we present several new features and show that they are more effective than conventional features. By combining the proposed features with conventional features, we develop a predictive model for interaction hot spots. Initially, 54 multifaceted features, composed of different levels of information including structure, sequence and molecular interaction information, are quantified. Then, to identify the best subset of features for predicting hot spots, feature selection is performed using a decision tree. Based on the selected features, a predictive model for hot spots is created using support vector machine (SVM) and tested on an independent test set. Our model shows better overall predictive accuracy than previous methods such as the alanine scanning methods Robetta and FOLDEF, and the knowledge-based method KFC. Subsequent analysis yields several findings about hot spots. As expected, hot spots have a larger relative surface area burial and are more hydrophobic than other residues. Unexpectedly, however, residue conservation displays a rather complicated tendency depending on the types of protein complexes, indicating that this feature is not good for identifying hot spots. Of the selected features, the weighted atomic packing density, relative surface area burial and weighted hydrophobicity are the top 3, with the weighted atomic packing density proving to be the most effective feature for predicting hot spots. Notably, we find that hot spots are closely related to pi-related interactions, especially pi . . . pi interactions.

  20. Interaction Modeling at PROS Research Center

    OpenAIRE

    Panach , José ,; Aquino , Nathalie; PASTOR , Oscar

    2011-01-01

    Part 1: Long and Short Papers; International audience; This paper describes how the PROS Research Center deals with interaction in the context of a model-driven approach for the development of information systems. Interaction is specified in a conceptual model together with the structure and behavior of the system. Major achievements and current research challenges of PROS in the field of interaction modeling are presented.

  1. Hydrophobic treatment of concrete

    NARCIS (Netherlands)

    Vries, J. de; Polder, R.B.

    1996-01-01

    As part of the maintenance policy of the Dutch Ministry of Transport, Civil Engineering Division, hydrophobic treatment of concrete was considered as an additional protective measure against penetration of aggressive substances, for instance deicing salts in bridge decks. A set of tests was designed

  2. Interactive Dimensioning of Parametric Models

    KAUST Repository

    Kelly, T.; Wonka, Peter; Mueller, P.

    2015-01-01

    that adapts to the view direction, given behavioral properties. After proposing a set of design principles for interactive dimensioning, we describe our solution consisting of the following major components. First, we describe how an author can specify

  3. Surface analysis of selected hydrophobic materials

    Science.gov (United States)

    Wisniewska, Sylwia Katarzyna

    This dissertation contains a series of studies on hydrophobic surfaces by various surface sensitive techniques such as contact angle measurements, Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), and atomic force microscopy (AFM). Hydrophobic surfaces have been classified as mineral surfaces, organic synthetic surfaces, or natural biological surfaces. As a model hydrophobic mineral surface, elemental sulfur has been selected. The sulfur surface has been characterized for selected allotropic forms of sulfur such as rhombic, monoclinic, plastic, and cyclohexasulfur. Additionally, dextrin adsorption at the sulfur surface was measured. The structure of a dextrin molecule showing hydrophobic sites has been presented to support the proposed hydrophobic bonding nature of dextrin adsorption at the sulfur surface. As a model organic hydrophobic surface, primary fatty amines such as dodecylamine, hexadecylamine, and octadecylamine were chosen. An increase of hydrophobicity, significant changes of infrared bands, and surface topographical changes with time were observed for each amine. Based on the results it was concluded that hydrocarbon chain rearrangement associated with recrystallization took place at the surface during contact with air. A barley straw surface was selected as a model of biological hydrophobic surfaces. The differences in the contact angles for various straw surfaces were explained by the presence of a wax layer. SEM images confirmed the heterogeneity and complexity of the wax crystal structure. AFM measurements provided additional structural details including a measure of surface roughness. Additionally, straw degradation as a result of conditioning in an aqueous environment was studied. Significant contact angle changes were observed as soon as one day after conditioning. FTIR studies showed a gradual wax layer removal due to straw surface decomposition. SEM and AFM images revealed topographical changes and biological

  4. In vitro evaluation of tissue adhesives composed of hydrophobically modified gelatins and disuccinimidyl tartrate

    Directory of Open Access Journals (Sweden)

    Miyuki Matsuda

    2012-01-01

    Full Text Available The effect of the hydrophobic group content in gelatin on the bonding strength of novel tissue–penetrating tissue adhesives was evaluated. The hydrophobic groups introduced into gelatin were the saturated hexanoyl, palmitoyl, and stearoyl groups, and the unsaturated oleoyl group. A collagen casing was employed as an adherend to model soft tissue for the in vitro determination of bonding strength of tissue adhesives composed of various hydrophobically modified gelatins and disuccinimidyl tartrate. The adhesive composed of stearoyl-modified gelatin (7.4% stearoyl; 10Ste and disuccinimidyl tartrate showed the highest bonding strength. The bonding strength of the adhesives decreased as the degree of substitution of the hydrophobic groups increased. Cell culture experiments demonstrated that fluorescein isothiocyanate-labeled 10Ste was integrated onto the surface of smooth muscle cells and showed no cytotoxicity. These results suggest that 10Ste interacted with the hydrophobic domains of collagen casings, such as hydrophobic amino acid residues and cell membranes. Therefore, 10Ste–disuccinimidyl tartrate is a promising adhesive for use in aortic dissection.

  5. Tuning the hydrophobicity of mica surfaces by hyperthermal Ar ion irradiation

    International Nuclear Information System (INIS)

    Keller, Adrian; Ogaki, Ryosuke; Bald, Ilko; Dong Mingdong; Kingshott, Peter; Fritzsche, Monika; Facsko, Stefan; Besenbacher, Flemming

    2011-01-01

    The hydrophobicity of surfaces has a strong influence on their interactions with biomolecules such as proteins. Therefore, for in vitro studies of bio-surface interactions model surfaces with tailored hydrophobicity are of utmost importance. Here, we present a method for tuning the hydrophobicity of atomically flat mica surfaces by hyperthermal Ar ion irradiation. Due to the sub-100 eV energies, only negligible roughening of the surface is observed at low ion fluences and also the chemical composition of the mica crystal remains almost undisturbed. However, the ion irradiation induces the preferential removal of the outermost layer of K + ions from the surface, leading to the exposure of the underlying aluminosilicate sheets which feature a large number of centers for C adsorption. The irradiated surface thus exhibits an enhanced chemical reactivity toward hydrocarbons, resulting in the adsorption of a thin hydrocarbon film from the environment. Aging these surfaces under ambient conditions leads to a continuous increase of their contact angle until a fully hydrophobic surface with a contact angle >80 deg. is obtained after a period of about 3 months. This method thus enables the fabrication of ultrasmooth biological model surfaces with precisely tailored hydrophobicity.

  6. Semantic models for adaptive interactive systems

    CERN Document Server

    Hussein, Tim; Lukosch, Stephan; Ziegler, Jürgen; Calvary, Gaëlle

    2013-01-01

    Providing insights into methodologies for designing adaptive systems based on semantic data, and introducing semantic models that can be used for building interactive systems, this book showcases many of the applications made possible by the use of semantic models.Ontologies may enhance the functional coverage of an interactive system as well as its visualization and interaction capabilities in various ways. Semantic models can also contribute to bridging gaps; for example, between user models, context-aware interfaces, and model-driven UI generation. There is considerable potential for using

  7. Using Interaction Scenarios to Model Information Systems

    DEFF Research Database (Denmark)

    Bækgaard, Lars; Bøgh Andersen, Peter

    The purpose of this paper is to define and discuss a set of interaction primitives that can be used to model the dynamics of socio-technical activity systems, including information systems, in a way that emphasizes structural aspects of the interaction that occurs in such systems. The primitives...... a number of case studies that indicate that interaction primitives can be useful modeling tools for supplementing conventional flow-oriented modeling of business processes....... are based on a unifying, conceptual definition of the disparate interaction types - a robust model of the types. The primitives can be combined and may thus represent mediated interaction. We present a set of visualizations that can be used to define multiple related interactions and we present and discuss...

  8. Fragmentary model of exchange interactions

    CERN Document Server

    Kotov, V M

    2000-01-01

    This article makes attempt to refusal from using neutrino for explanation continuous distribution of beta particle energy by conversion to characteristic exchange interaction particles in nucleolus. It is taking formulation for nuclear position with many different fragments. It is computing half-value period of spontaneous fission of heavy nucleolus. (author)

  9. The modeling of predator-prey interactions

    OpenAIRE

    Muhammad Shakil; H. A. Wahab; Muhammad Naeem, et al.

    2015-01-01

    In this paper, we aim to study the interactions between the territorial animals like foxes and the rabbits. The territories for the foxes are considered to be the simple cells. The interactions between predator and its prey are represented by the chemical reactions which obey the mass action law. In this sense, we apply the mass action law for predator prey models and the quasi chemical approach is applied for the interactions between the predator and its prey to develop the modeled equations...

  10. Modeling multimodal human-computer interaction

    NARCIS (Netherlands)

    Obrenovic, Z.; Starcevic, D.

    2004-01-01

    Incorporating the well-known Unified Modeling Language into a generic modeling framework makes research on multimodal human-computer interaction accessible to a wide range off software engineers. Multimodal interaction is part of everyday human discourse: We speak, move, gesture, and shift our gaze

  11. Gravitational interactions of integrable models

    International Nuclear Information System (INIS)

    Abdalla, E.; Abdalla, M.C.B.

    1995-10-01

    We couple non-linear σ-models to Liouville gravity, showing that integrability properties of symmetric space models still hold for the matter sector. Using similar arguments for the fermionic counterpart, namely Gross-Neveu-type models, we verify that such conclusions must also hold for them, as recently suggested. (author). 18 refs

  12. Contribution of hydrophobic effect to the sorption of phenanthrene, 9-phenanthrol and 9, 10-phenanthrenequinone on carbon nanotubes.

    Science.gov (United States)

    Peng, Hongbo; Zhang, Di; Pan, Bo; Peng, Jinhui

    2017-02-01

    Polycyclic aromatic hydrocarbons (PAHs), with diverse sources and acute toxicity, are categorized as priority pollutants. Previous studies have stated that the hydrophobic effect controls PAH sorption, but no study has been conducted to quantify the exact contribution of the hydrophobic effect. Considering the well-defined structure of carbon nanotubes and their stable chemical composition in organic solvents, three multi-walled carbon nanotubes (MWCNTs) were selected as a model adsorbent. Phenanthrene (PHE) and its degradation intermediates 9-phenanthrol (PTR) and 9, 10-phenanthrenequinone (PQN) were used as model adsorbates. To quantify the contribution of the hydrophobic effect for these three chemicals, the effect of organic solvent (methanol and hexadecane) was investigated. Adsorption isotherms for PHE, PTR and PQN were well fitted by the Freundlich isotherm model. A positive relationship between adsorption affinities of these three chemicals and specific surface area (SSA) was observed in hexadecane but not in water or methanol. Other factors should be included other than SSA. Adsorption of PQN on MWCNTs with oxygen functional groups was higher than that on pristine MWCNTs due to π-π EDA interactions. The contribution of hydrophobic effect was 50%-85% for PHE, suggesting that hydrophobic effect was the predominant mechanism. This contribution was lower than 30% for PTR/PQN on functionalized MWCNTs. Hydrogen bonds control the adsorption of PTR, and π-π bonding interactions control PQN sorption after screening out the hydrophobic effect in hexadecane. Hydrophobic effect is the control mechanism for nonpolar chemicals, while functional groups of CNTs and solvent types control the adsorption of polar compounds. Extended work on quantifying the relationship between chemical structure and the contribution of the hydrophobic effect will provide a useful technique for PAH fate modeling. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Deep Predictive Models in Interactive Music

    OpenAIRE

    Martin, Charles P.; Ellefsen, Kai Olav; Torresen, Jim

    2018-01-01

    Automatic music generation is a compelling task where much recent progress has been made with deep learning models. In this paper, we ask how these models can be integrated into interactive music systems; how can they encourage or enhance the music making of human users? Musical performance requires prediction to operate instruments, and perform in groups. We argue that predictive models could help interactive systems to understand their temporal context, and ensemble behaviour. Deep learning...

  14. Phactr3/scapinin, a member of protein phosphatase 1 and actin regulator (phactr family, interacts with the plasma membrane via basic and hydrophobic residues in the N-terminus.

    Directory of Open Access Journals (Sweden)

    Akihiro Itoh

    Full Text Available Proteins that belong to the protein phosphatase 1 and actin regulator (phactr family are involved in cell motility and morphogenesis. However, the mechanisms that regulate the actin cytoskeleton are poorly understood. We have previously shown that phactr3, also known as scapinin, localizes to the plasma membrane, including lamellipodia and membrane ruffles. In the present study, experiments using deletion and point mutants showed that the basic and hydrophobic residues in the N-terminus play crucial roles in the localization to the plasma membrane. A BH analysis (http://helixweb.nih.gov/bhsearch is a program developed to identify membrane-binding domains that comprise basic and hydrophobic residues in membrane proteins. We applied this program to phactr3. The results of the BH plot analysis agreed with the experimentally determined region that is responsible for the localization of phactr3 to the plasma membrane. In vitro experiments showed that the N-terminal itself binds to liposomes and acidic phospholipids. In addition, we showed that the interaction with the plasma membrane via the N-terminal membrane-binding sequence is required for phactr3-induced morphological changes in Cos7 cells. The membrane-binding sequence in the N-terminus is highly conserved in all members of the phactr family. Our findings may provide a molecular basis for understanding the mechanisms that allow phactr proteins to regulate cell morphogenesis.

  15. Mapping Hydrophobicity on the Protein Molecular Surface at Atom-Level Resolution

    Science.gov (United States)

    Nicolau Jr., Dan V.; Paszek, Ewa; Fulga, Florin; Nicolau, Dan V.

    2014-01-01

    A precise representation of the spatial distribution of hydrophobicity, hydrophilicity and charges on the molecular surface of proteins is critical for the understanding of the interaction with small molecules and larger systems. The representation of hydrophobicity is rarely done at atom-level, as this property is generally assigned to residues. A new methodology for the derivation of atomic hydrophobicity from any amino acid-based hydrophobicity scale was used to derive 8 sets of atomic hydrophobicities, one of which was used to generate the molecular surfaces for 35 proteins with convex structures, 5 of which, i.e., lysozyme, ribonuclease, hemoglobin, albumin and IgG, have been analyzed in more detail. Sets of the molecular surfaces of the model proteins have been constructed using spherical probes with increasingly large radii, from 1.4 to 20 Å, followed by the quantification of (i) the surface hydrophobicity; (ii) their respective molecular surface areas, i.e., total, hydrophilic and hydrophobic area; and (iii) their relative densities, i.e., divided by the total molecular area; or specific densities, i.e., divided by property-specific area. Compared with the amino acid-based formalism, the atom-level description reveals molecular surfaces which (i) present an approximately two times more hydrophilic areas; with (ii) less extended, but between 2 to 5 times more intense hydrophilic patches; and (iii) 3 to 20 times more extended hydrophobic areas. The hydrophobic areas are also approximately 2 times more hydrophobicity-intense. This, more pronounced “leopard skin”-like, design of the protein molecular surface has been confirmed by comparing the results for a restricted set of homologous proteins, i.e., hemoglobins diverging by only one residue (Trp37). These results suggest that the representation of hydrophobicity on the protein molecular surfaces at atom-level resolution, coupled with the probing of the molecular surface at different geometric resolutions

  16. Insights into the Hendra virus NTAIL-XD complex: Evidence for a parallel organization of the helical MoRE at the XD surface stabilized by a combination of hydrophobic and polar interactions.

    Science.gov (United States)

    Erales, Jenny; Beltrandi, Matilde; Roche, Jennifer; Maté, Maria; Longhi, Sonia

    2015-08-01

    The Hendra virus is a member of the Henipavirus genus within the Paramyxoviridae family. The nucleoprotein, which consists of a structured core and of a C-terminal intrinsically disordered domain (N(TAIL)), encapsidates the viral genome within a helical nucleocapsid. N(TAIL) partly protrudes from the surface of the nucleocapsid being thus capable of interacting with the C-terminal X domain (XD) of the viral phosphoprotein. Interaction with XD implies a molecular recognition element (MoRE) that is located within N(TAIL) residues 470-490, and that undergoes α-helical folding. The MoRE has been proposed to be embedded in the hydrophobic groove delimited by helices α2 and α3 of XD, although experimental data could not discriminate between a parallel and an antiparallel orientation of the MoRE. Previous studies also showed that if the binding interface is enriched in hydrophobic residues, charged residues located close to the interface might play a role in complex formation. Here, we targeted for site directed mutagenesis two acidic and two basic residues within XD and N(TAIL). ITC studies showed that electrostatics plays a crucial role in complex formation and pointed a parallel orientation of the MoRE as more likely. Further support for a parallel orientation was afforded by SAXS studies that made use of two chimeric constructs in which XD and the MoRE were covalently linked to each other. Altogether, these studies unveiled the multiparametric nature of the interactions established within this complex and contribute to shed light onto the molecular features of protein interfaces involving intrinsically disordered regions. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. A Method for Model Checking Feature Interactions

    DEFF Research Database (Denmark)

    Pedersen, Thomas; Le Guilly, Thibaut; Ravn, Anders Peter

    2015-01-01

    This paper presents a method to check for feature interactions in a system assembled from independently developed concurrent processes as found in many reactive systems. The method combines and refines existing definitions and adds a set of activities. The activities describe how to populate the ...... the definitions with models to ensure that all interactions are captured. The method is illustrated on a home automation example with model checking as analysis tool. In particular, the modelling formalism is timed automata and the analysis uses UPPAAL to find interactions....

  18. Porous models for wave-seabed interactions

    Energy Technology Data Exchange (ETDEWEB)

    Jeng, Dong-Sheng [Shanghai Jiaotong Univ., SH (China)

    2013-02-01

    Detailed discussion about the phenomenon of wave-seabed interactions. Novel models for wave-induced seabed response. Intensive theoretical derivations for wave-seabed interactions. Practical examples for engineering applications. ''Porous Models for Wave-seabed Interactions'' discusses the Phenomenon of wave-seabed interactions, which is a vital issue for coastal and geotechnical engineers involved in the design of foundations for marine structures such as pipelines, breakwaters, platforms, etc. The most important sections of this book will be the fully detailed theoretical models of wave-seabed interaction problem, which are particularly useful for postgraduate students and junior researchers entering the discipline of marine geotechnics and offshore engineering. This book also converts the research outcomes of theoretical studies to engineering applications that will provide front-line engineers with practical and effective tools in the assessment of seabed instability in engineering design.

  19. The Monash University Interactive Simple Climate Model

    Science.gov (United States)

    Dommenget, D.

    2013-12-01

    The Monash university interactive simple climate model is a web-based interface that allows students and the general public to explore the physical simulation of the climate system with a real global climate model. It is based on the Globally Resolved Energy Balance (GREB) model, which is a climate model published by Dommenget and Floeter [2011] in the international peer review science journal Climate Dynamics. The model simulates most of the main physical processes in the climate system in a very simplistic way and therefore allows very fast and simple climate model simulations on a normal PC computer. Despite its simplicity the model simulates the climate response to external forcings, such as doubling of the CO2 concentrations very realistically (similar to state of the art climate models). The Monash simple climate model web-interface allows you to study the results of more than a 2000 different model experiments in an interactive way and it allows you to study a number of tutorials on the interactions of physical processes in the climate system and solve some puzzles. By switching OFF/ON physical processes you can deconstruct the climate and learn how all the different processes interact to generate the observed climate and how the processes interact to generate the IPCC predicted climate change for anthropogenic CO2 increase. The presentation will illustrate how this web-base tool works and what are the possibilities in teaching students with this tool are.

  20. The Color Mutation Model for soft interaction

    International Nuclear Information System (INIS)

    Hwa, R.C.

    1998-01-01

    A comprehensive model for soft interaction is presented. It overcomes all the shortcomings of the existing models - in particular, the failure of Fritiof and Venus models in predicting the correct multiplicity fluctuations as observed in the intermittency data. The Color Mutation Model incorporates all the main features of hadronic interaction: eikonal formalism, parton model, evolution in color space according to QCD, branching of color neutral clusters, contraction due to confinement forces, dynamical self-similarity, resonance production, and power-law behavior of factorial moments. (author)

  1. N-barN interaction theoretical models

    International Nuclear Information System (INIS)

    Loiseau, B.

    1991-12-01

    In the framework of antinucleon-nucleon interaction theoretical models, our present understanding on the N-barN interaction is discussed, either from quark- or/and meson- and baryon-degrees of freedom, by considering the N-barN annihilation into mesons and the N-barN elastic and charge-exchange scattering. (author) 52 refs., 11 figs., 2 tabs

  2. Numerical modeling of magma-repository interactions

    NARCIS (Netherlands)

    Bokhove, Onno

    2001-01-01

    This report explains the numerical programs behind a comprehensive modeling effort of magma-repository interactions. Magma-repository interactions occur when a magma dike with high-volatile content magma ascends through surrounding rock and encounters a tunnel or drift filled with either a magmatic

  3. Discrete choice models for commuting interactions

    DEFF Research Database (Denmark)

    Rouwendal, Jan; Mulalic, Ismir; Levkovich, Or

    An emerging quantitative spatial economics literature models commuting interactions by a gravity equation that is mathematically equivalent to a multinomial logit model. This model is widely viewed as restrictive because of the independence of irrelevant alternatives (IIA) property that links sub...

  4. Modeling of soil-water-structure interaction

    DEFF Research Database (Denmark)

    Tang, Tian

    as the developed nonlinear soil displacements and stresses under monotonic and cyclic loading. With the FVM nonlinear coupled soil models as a basis, multiphysics modeling of wave-seabed-structure interaction is carried out. The computations are done in an open source code environment, OpenFOAM, where FVM models...

  5. Syndetic model of fundamental interactions

    Directory of Open Access Journals (Sweden)

    Ernest Ma

    2015-02-01

    Full Text Available The standard model of quarks and leptons is extended to connect three outstanding issues in particle physics and astrophysics: (1 the absence of strong CP nonconservation, (2 the existence of dark matter, and (3 the mechanism of nonzero neutrino masses, and that of the first family of quarks and leptons, all in the context of having only one Higgs boson in a renormalizable theory. Some phenomenological implications are discussed.

  6. Electron scattering in the interacting boson model

    NARCIS (Netherlands)

    Dieperink, AEL; Iachello, F; Rinat, A; Creswell, C

    1978-01-01

    It is suggested that the interacting boson model be used in the analysis of electron scattering data. Qualitative features of the expected behavior of the inelastic excitation of some 2 ÷ states inthe transitional Sm-Nd region are discussed

  7. A physiologically based toxicokinetic (PBTK) model for moderately hydrophobic organic chemicals in the European eel (Anguilla anguilla)

    Energy Technology Data Exchange (ETDEWEB)

    Brinkmann, Markus [Department of Ecosystem Analysis, Institute for Environmental Research, ABBt — Aachen Biology and Biotechnology, RWTH Aachen University, Aachen (Germany); Freese, Marko; Pohlmann, Jan-Dag; Kammann, Ulrike [Thünen Institute of Fisheries Ecology, Hamburg (Germany); Preuss, Thomas G. [Environmental Biology and Chemodynamics, Institute for Environmental Research, ABBt — Aachen Biology and Biotechnology, RWTH Aachen University, Aachen (Germany); Buchinger, Sebastian; Reifferscheid, Georg [Federal Institute of Hydrology (BFG), Department G3: Biochemistry, Ecotoxicology, Koblenz (Germany); Beiermeister, Anne; Hanel, Reinhold [Thünen Institute of Fisheries Ecology, Hamburg (Germany); Hollert, Henner, E-mail: Henner.hollert@bio5.rwth-aachen.de [Department of Ecosystem Analysis, Institute for Environmental Research, ABBt — Aachen Biology and Biotechnology, RWTH Aachen University, Aachen (Germany); State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing (China); College of Resources and Environmental Science, Chongqing University, Chongqing (China); Key Laboratory of Yangtze Water Environment, Ministry of Education, Tongji University, Shanghai 200092 (China)

    2015-12-01

    The European eel (Anguilla anguilla) is a facultatively catadromous fish species with a complex life cycle. Its current population status is alarming: recruitment has decreased drastically since the 1980s and its stock is still considered to be outside safe biological limits. Although there is no consensus on the reasons for this situation, it is currently thought to have resulted from a combination of different stressors, including anthropogenic contaminants. To deepen our understanding of the processes leading to the accumulation of lipophilic organic contaminants in yellow eels (i.e. the feeding, continental growth stage), we developed a physiologically based toxicokinetic model using our own data and values from the literature. Such models can predict the uptake and distribution of water-borne organic chemicals in the whole fish and in different tissues at any time during exposure. The predictive power of the model was tested against experimental data for six chemicals with n-octanol-water partitioning coefficient (log K{sub ow}) values ranging from 2.13–4.29. Model performance was excellent, with a root mean squared error of 0.28 log units. This model has the potential to help identify suitable habitats for restocking under eel management plans. - Highlights: • A PBTK model was developed for European eel (Anguilla anguilla). • Own experimental data and data from the literature were used for parameterization. • The predictive power of the model was excellent, with RMSE of 0.28 log units. • The developed model can be amended with sub-models for dietary and dermal exposure.

  8. A physiologically based toxicokinetic (PBTK) model for moderately hydrophobic organic chemicals in the European eel (Anguilla anguilla)

    International Nuclear Information System (INIS)

    Brinkmann, Markus; Freese, Marko; Pohlmann, Jan-Dag; Kammann, Ulrike; Preuss, Thomas G.; Buchinger, Sebastian; Reifferscheid, Georg; Beiermeister, Anne; Hanel, Reinhold; Hollert, Henner

    2015-01-01

    The European eel (Anguilla anguilla) is a facultatively catadromous fish species with a complex life cycle. Its current population status is alarming: recruitment has decreased drastically since the 1980s and its stock is still considered to be outside safe biological limits. Although there is no consensus on the reasons for this situation, it is currently thought to have resulted from a combination of different stressors, including anthropogenic contaminants. To deepen our understanding of the processes leading to the accumulation of lipophilic organic contaminants in yellow eels (i.e. the feeding, continental growth stage), we developed a physiologically based toxicokinetic model using our own data and values from the literature. Such models can predict the uptake and distribution of water-borne organic chemicals in the whole fish and in different tissues at any time during exposure. The predictive power of the model was tested against experimental data for six chemicals with n-octanol-water partitioning coefficient (log K ow ) values ranging from 2.13–4.29. Model performance was excellent, with a root mean squared error of 0.28 log units. This model has the potential to help identify suitable habitats for restocking under eel management plans. - Highlights: • A PBTK model was developed for European eel (Anguilla anguilla). • Own experimental data and data from the literature were used for parameterization. • The predictive power of the model was excellent, with RMSE of 0.28 log units. • The developed model can be amended with sub-models for dietary and dermal exposure

  9. On gel electrophoresis of dielectric charged particles with hydrophobic surface: A combined theoretical and numerical study.

    Science.gov (United States)

    Majee, Partha Sarathi; Bhattacharyya, Somnath; Gopmandal, Partha Pratim; Ohshima, Hiroyuki

    2018-03-01

    A theoretical study on the gel electrophoresis of a charged particle incorporating the effects of dielectric polarization and surface hydrophobicity at the particle-liquid interface is made. A simplified model based on the weak applied field and low charge density assumption is also presented and compared with the full numerical model for a nonpolarizable particle to elucidate the nonlinear effects such as double layer polarization and relaxation as well as surface conduction. The main motivation of this study is to analyze the electrophoresis of the surface functionalized nanoparticle with tunable hydrophobicity or charged fluid drop in gel medium by considering the electrokinetic effects and hydrodynamic interactions between the particle and the gel medium. An effective medium approach, in which the transport in the electrolyte-saturated hydrogel medium is governed by the Brinkman equation, is adopted in the present analysis. The governing electrokinetic equations based on the conservation principles are solved numerically. The Navier-slip boundary condition along with the continuity condition of dielectric displacement are imposed on the surface of the hydrophobic polarizable particle. The impact of the slip length on the electrophoresis is profound for a thinner Debye layer, however, surface conduction effect also becomes significant for a hydrophobic particle. Impact of hydrophobicity and relaxation effects are higher for a larger particle. Dielectric polarization creates a reduction in its electrophoretic propulsion and has negligible impact at the thinner Debye length as well as lower gel screening length. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Characterization of the Interaction between Eupatorin and Bovine Serum Albumin by Spectroscopic and Molecular Modeling Methods

    Science.gov (United States)

    Xu, Hongliang; Yao, Nannan; Xu, Haoran; Wang, Tianshi; Li, Guiying; Li, Zhengqiang

    2013-01-01

    This study investigated the interaction between eupatorin and bovine serum albumin (BSA) using ultraviolet-visible (UV-vis) absorption, fluorescence, synchronous fluorescence, circular dichroism (CD) spectroscopies, and molecular modeling at pH 7.4. Results of UV-vis and fluorescence spectroscopies illustrated that BSA fluorescence was quenched by eupatorin via a static quenching mechanism. Thermodynamic parameters revealed that hydrophobic and electrostatic interactions played major roles in the interaction. Moreover, the efficiency of energy transfer, and the distance between BSA and acceptor eupatorin, were calculated. The effects of eupatorin on the BSA conformation were analyzed using UV-vis, CD, and synchronous fluorescence. Finally, the binding of eupatorin to BSA was modeled using the molecular docking method. PMID:23839090

  11. Hydrophobic and electrostatic interactions between cell penetrating peptides and plasmid DNA are important for stable non-covalent complexation and intracellular delivery.

    Science.gov (United States)

    Upadhya, Archana; Sangave, Preeti C

    2016-10-01

    Cell penetrating peptides are useful tools for intracellular delivery of nucleic acids. Delivery of plasmid DNA, a large nucleic acid, poses a challenge for peptide mediated transport. The paper investigates and compares efficacy of five novel peptide designs for complexation of plasmid DNA and subsequent delivery into cells. The peptides were designed to contain reported DNA condensing agents and basic cell penetrating sequences, octa-arginine (R 8 ) and CHK 6 HC coupled to cell penetration accelerating peptides such as Bax inhibitory mutant peptide (KLPVM) and a peptide derived from the Kaposi fibroblast growth factor (kFGF) membrane translocating sequence. A tryptophan rich peptide, an analogue of Pep-3, flanked with CH 3 on either ends was also a part of the study. The peptides were analysed for plasmid DNA complexation, protection of peptide-plasmid DNA complexes against DNase I, serum components and competitive ligands by simple agarose gel electrophoresis techniques. Hemolysis of rat red blood corpuscles (RBCs) in the presence of the peptides was used as a measure of peptide cytotoxicity. Plasmid DNA delivery through the designed peptides was evaluated in two cell lines, human cervical cancer cell line (HeLa) and (NIH/3 T3) mouse embryonic fibroblasts via expression of the secreted alkaline phosphatase (SEAP) reporter gene. The importance of hydrophobic sequences in addition to cationic sequences in peptides for non-covalent plasmid DNA complexation and delivery has been illustrated. An alternative to the employment of fatty acid moieties for enhanced gene transfer has been proposed. Comparison of peptides for plasmid DNA complexation and delivery of peptide-plasmid DNA complexes to cells estimated by expression of a reporter gene, SEAP. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

  12. Functional Modeling of Neural-Glia Interaction

    DEFF Research Database (Denmark)

    Postnov, D.E.; Brazhe, N.A.; Sosnovtseva, Olga

    2012-01-01

    Functional modeling is an approach that focuses on the representation of the qualitative dynamics of the individual components (e.g. cells) of a system and on the structure of the interaction network.......Functional modeling is an approach that focuses on the representation of the qualitative dynamics of the individual components (e.g. cells) of a system and on the structure of the interaction network....

  13. Mathematical models for plant-herbivore interactions

    Science.gov (United States)

    Feng, Zhilan; DeAngelis, Donald L.

    2017-01-01

    Mathematical Models of Plant-Herbivore Interactions addresses mathematical models in the study of practical questions in ecology, particularly factors that affect herbivory, including plant defense, herbivore natural enemies, and adaptive herbivory, as well as the effects of these on plant community dynamics. The result of extensive research on the use of mathematical modeling to investigate the effects of plant defenses on plant-herbivore dynamics, this book describes a toxin-determined functional response model (TDFRM) that helps explains field observations of these interactions. This book is intended for graduate students and researchers interested in mathematical biology and ecology.

  14. The new view of hydrophobic free energy.

    Science.gov (United States)

    Baldwin, Robert L

    2013-04-17

    In the new view, hydrophobic free energy is measured by the work of solute transfer of hydrocarbon gases from vapor to aqueous solution. Reasons are given for believing that older values, measured by solute transfer from a reference solvent to water, are not quantitatively correct. The hydrophobic free energy from gas-liquid transfer is the sum of two opposing quantities, the cavity work (unfavorable) and the solute-solvent interaction energy (favorable). Values of the interaction energy have been found by simulation for linear alkanes and are used here to find the cavity work, which scales linearly with molar volume, not accessible surface area. The hydrophobic free energy is the dominant factor driving folding as judged by the heat capacity change for transfer, which agrees with values for solvating hydrocarbon gases. There is an apparent conflict with earlier values of hydrophobic free energy from studies of large-to-small mutations and an explanation is given. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  15. Vector-Interaction-Enhanced Bag Model

    Science.gov (United States)

    Cierniak, Mateusz; Klähn, Thomas; Fischer, Tobias; Bastian, Niels-Uwe

    2018-02-01

    A commonly applied quark matter model in astrophysics is the thermodynamic bag model (tdBAG). The original MIT bag model approximates the effect of quark confinement, but does not explicitly account for the breaking of chiral symmetry, an important property of Quantum Chromodynamics (QCD). It further ignores vector repulsion. The vector-interaction-enhanced bag model (vBag) improves the tdBAG approach by accounting for both dynamical chiral symmetry breaking and repulsive vector interactions. The latter is of particular importance to studies of dense matter in beta-equilibriumto explain the two solar mass maximum mass constraint for neutron stars. The model is motivated by analyses of QCD based Dyson-Schwinger equations (DSE), assuming a simple quark-quark contact interaction. Here, we focus on the study of hybrid neutron star properties resulting from the application of vBag and will discuss possible extensions.

  16. Temperature effects on the hydrophobic force between two ...

    Indian Academy of Sciences (India)

    TUHIN SAMANTA

    2018-03-02

    Mar 2, 2018 ... We perform the molecular dynamics simulations to investigate ... molecular assemblies and in the formation of protein complexes.1–7 One of the important manifestations of the hydrophobic interactions is observed in oil-water.

  17. Relativistic direct interaction and hadron models

    International Nuclear Information System (INIS)

    Biswas, T.

    1984-01-01

    Direct interaction theories at a nonrelativistic level have been used successfully in several areas earlier (e.g. nuclear physics). But for hadron spectroscopy relativistic effects are important and hence the need for a relativistic direct interaction theory arises. It is the goal of this thesis to suggest such a theory which has the simplicity and the flexibility required for phenomenological model building. In general the introduction of relativity in a direct interaction theory is shown to be non-trivial. A first attempt leads to only an approximate form for allowed interactions. Even this is far too complex for phenomenological applicability. To simplify the model an extra spacelike particle called the vertex is introduced in any set of physical (timelike) particles. The vertex model is successfully used to fit and to predict experimental data on hadron spectra, γ and psi states fit very well with an interaction function inspired by QCD. Light mesons also fit reasonably well. Better forms of hyperfine interaction functions would be needed to improve the fitting of light mesons. The unexpectedly low pi meson mass is partially explained. Baryon ground states are fitted with unprecedented accuracy with very few adjustable parameters. For baryon excited states it is shown that better QCD motivated interaction functions are needed for a fit. Predictions for bb states in e + e - experiments are made to assist current experiments

  18. Modeling of hydrogen interactions with beryllium

    Energy Technology Data Exchange (ETDEWEB)

    Longhurst, G.R. [Lockheed Martin Idaho Technologies Co., Idaho Falls, ID (United States)

    1998-01-01

    In this paper, improved mathematical models are developed for hydrogen interactions with beryllium. This includes the saturation effect observed for high-flux implantation of ions from plasmas and retention of tritium produced from neutronic transmutations in beryllium. Use of the models developed is justified by showing how they can replicated experimental data using the TMAP4 tritium transport code. (author)

  19. Interacting p- Boson model with isospin

    International Nuclear Information System (INIS)

    Chen, C.H.-T.

    A description of collective states in self-conjugate nuclei is proposed, both odd-odd and even-even, in terms of an interacting isoscalar p-boson model. Within this model, two limiting cases can be identified with the anharmonic vibrator and axial rotor limits of the classical geometrical description. (Author) [pt

  20. Learning models of activities involving interacting objects

    DEFF Research Database (Denmark)

    Manfredotti, Cristina; Pedersen, Kim Steenstrup; Hamilton, Howard J.

    2013-01-01

    We propose the LEMAIO multi-layer framework, which makes use of hierarchical abstraction to learn models for activities involving multiple interacting objects from time sequences of data concerning the individual objects. Experiments in the sea navigation domain yielded learned models that were t...

  1. The Spiral-Interactive Program Evaluation Model.

    Science.gov (United States)

    Khaleel, Ibrahim Adamu

    1988-01-01

    Describes the spiral interactive program evaluation model, which is designed to evaluate vocational-technical education programs in secondary schools in Nigeria. Program evaluation is defined; utility oriented and process oriented models for evaluation are described; and internal and external evaluative factors and variables that define each…

  2. An introduction to the interacting boson model

    International Nuclear Information System (INIS)

    Iachello, F.

    1981-01-01

    This chapter introduces an alternative, algebraic, description of the properties of nuclei with several particles outside the closed shells. Focuses on the group theory of the interacting boson model. Discusses the group structure of the boson Hamiltonian; subalgebras; the classification of states; dynamical symmetry; electromagnetic transition rates; transitional classes; and general cases. Omits a discussion of the latest developments (e.g., the introduction of proton and neutron degrees of freedom); the spectra of odd-A nuclei; and the bosonfermion model. Concludes that the major new feature of the interacting boson model is the introduction and systematic exploitation of algebraic techniques, which allows a simple and detailed description of many nuclear properties

  3. Effect of particle size on droplet infiltration into hydrophobic porous media as a model of water repellent soil.

    Science.gov (United States)

    Hamlett, Christopher A E; Shirtcliffe, Neil J; McHale, Glen; Ahn, Sujung; Bryant, Robert; Doerr, Stefan H; Newton, Michael I

    2011-11-15

    The wettability of soil is of great importance for plants and soil biota, and in determining the risk for preferential flow, surface runoff, flooding,and soil erosion. The molarity of ethanol droplet (MED) test is widely used for quantifying the severity of water repellency in soils that show reduced wettability and is assumed to be independent of soil particle size. The minimum ethanol concentration at which droplet penetration occurs within a short time (≤ 10 s) provides an estimate of the initial advancing contact angle at which spontaneous wetting is expected. In this study, we test the assumption of particle size independence using a simple model of soil, represented by layers of small (~0.2-2 mm) diameter beads that predict the effect of changing bead radius in the top layer on capillary driven imbibition. Experimental results using a three-layer bead system show broad agreement with the model and demonstrate a dependence of the MED test on particle size. The results show that the critical initial advancing contact angle for penetration can be considerably less than 90° and varies with particle size, demonstrating that a key assumption currently used in the MED testing of soil is not necessarily valid.

  4. Multisite Interactions in Lattice-Gas Models

    Science.gov (United States)

    Einstein, T. L.; Sathiyanarayanan, R.

    For detailed applications of lattice-gas models to surface systems, multisite interactions often play at least as significant a role as interactions between pairs of adatoms that are separated by a few lattice spacings. We recall that trio (3-adatom, non-pairwise) interactions do not inevitably create phase boundary asymmetries about half coverage. We discuss a sophisticated application to an experimental system and describe refinements in extracting lattice-gas energies from calculations of total energies of several different ordered overlayers. We describe how lateral relaxations complicate matters when there is direct interaction between the adatoms, an issue that is important when examining the angular dependence of step line tensions. We discuss the connector model as an alternative viewpoint and close with a brief account of recent work on organic molecule overlayers.

  5. Cranking model and attenuation of Coriolis interaction

    International Nuclear Information System (INIS)

    Lyutorovich, N.A.

    1987-01-01

    Description of rotational bands of odd deformed nuclei in the self-consistent Cranking model (SCM) is given. Causes of attenuation of the Coriolis interaction in the nuclei investigated are studied, and account of bound of one-particle degrees of freedom with rotation of the Hartree-Fock-Bogolyubov (HFB) self-consistent method is introduced additionally to SCM for qualitative agreement with experimental data. Merits and shortages of SCM in comparison with the quadruparticle-rotor (QR) model are discussed. All know ways for constructing the Hamiltonian QR model (or analog of such Hamiltonian) on the basis of the microscopic theory are shown to include two more approximations besides others: quasi-particle-rotational interaction leading to pair break is taken into account in the second order of the perturbation theory; some exchange diagrams are neglected among diagrams of the second order according to this interaction. If one makes the same approximations in SCM instead of HFB method, then the dependence of level energies on spin obtained in this case is turned out to be close to the results of the QR model. Besides, the problem on renormalization of matrix elements of quasi-rotational interaction occurs in such nonself-consistent approach as in the QR model. In so far as the similar problem does not occur in SCM, one can make the conclusion that the problem of attenuation of Coriolis interaction involves the approximations given above

  6. Interactive wood combustion for botanical tree models

    KAUST Repository

    Pirk, Sören

    2017-11-22

    We present a novel method for the combustion of botanical tree models. Tree models are represented as connected particles for the branching structure and a polygonal surface mesh for the combustion. Each particle stores biological and physical attributes that drive the kinetic behavior of a plant and the exothermic reaction of the combustion. Coupled with realistic physics for rods, the particles enable dynamic branch motions. We model material properties, such as moisture and charring behavior, and associate them with individual particles. The combustion is efficiently processed in the surface domain of the tree model on a polygonal mesh. A user can dynamically interact with the model by initiating fires and by inducing stress on branches. The flames realistically propagate through the tree model by consuming the available resources. Our method runs at interactive rates and supports multiple tree instances in parallel. We demonstrate the effectiveness of our approach through numerous examples and evaluate its plausibility against the combustion of real wood samples.

  7. Modeling of interaction effects in granular systems

    International Nuclear Information System (INIS)

    El-Hilo, M.; Shatnawy, M.; Al-Rsheed, A.

    2000-01-01

    Interaction effects on the magnetic behavior of granular solid systems are examined using a numerical model which is capable of predicting the field, temperature and time dependence of magnetization. In this work, interaction effects on the temperature dependence of time viscosity coefficient S(T) and formation of minor hysteresis loops have been studied. The results for the time- and temperature dependence of remanence ratio have showed that the distribution of energy barriers f(ΔE) obtained depend critically on the strength and nature of interactions. These interactions-based changes in f(ΔE) can easily give a temperature-independent behavior of S(T) when these changes give a 1/ΔE behavior to the distribution of energy barriers. Thus, conclusions about macroscopic quantum tunneling must be carefully drawn when the temperature dependence of S(T) is used to probe for MQT effects. For minor hysteresis effects, the result shows that for the non-interacting case, no minor hysteresis loops occur and the loops are only predicted when the interaction field is positive. From these predictions, minor loops will form when the interaction field is strong enough to magnetize some moments during the recoil process back to zero field. Thus, these minor loops are originated from interaction driving irreversible changes along the recoil curve and the irreversible component of magnetization has no direct influence on the formation of these minor loops

  8. Quark interchange model of baryon interactions

    Energy Technology Data Exchange (ETDEWEB)

    Maslow, J.N.

    1983-01-01

    The strong interactions at low energy are traditionally described by meson field theories treating hadrons as point-like particles. Here a mesonic quark interchange model (QIM) is presented which takes into account the finite size of the baryons and the internal quark structure of hadrons. The model incorporates the basic quark-gluon coupling of quantum chromodynamics (QCD) and the MIT bag model for color confinement. Because the quark-gluon coupling constant is large and it is assumed that confinement excludes overlap of hadronic quark bags except at high momenta, a non-perturbative method of nuclear interactions is presented. The QIM allows for exchange of quark quantum numbers at the bag boundary between colliding hadrons mediated at short distances by a gluon exchange between two quarks within the hadronic interior. This generates, via a Fierz transformation, an effective space-like t channel exchange of color singlet (q anti-q) states that can be identified with the low lying meson multiplets. Thus, a one boson exchange (OBE) model is obtained that allows for comparison with traditional phenomenological models of nuclear scattering. Inclusion of strange quarks enables calculation of YN scattering. The NN and YN coupling constants and the nucleon form factors show good agreement with experimental values as do the deuteron low energy data and the NN low energy phase shifts. Thus, the QIM provides a simple model of strong interactions that is chirally invariant, includes confinement and allows for an OBE form of hadronic interaction at low energies and momentum transfers.

  9. Quark interchange model of baryon interactions

    International Nuclear Information System (INIS)

    Maslow, J.N.

    1983-01-01

    The strong interactions at low energy are traditionally described by meson field theories treating hadrons as point-like particles. Here a mesonic quark interchange model (QIM) is presented which takes into account the finite size of the baryons and the internal quark structure of hadrons. The model incorporates the basic quark-gluon coupling of quantum chromodynamics (QCD) and the MIT bag model for color confinement. Because the quark-gluon coupling constant is large and it is assumed that confinement excludes overlap of hadronic quark bags except at high momenta, a non-perturbative method of nuclear interactions is presented. The QIM allows for exchange of quark quantum numbers at the bag boundary between colliding hadrons mediated at short distances by a gluon exchange between two quarks within the hadronic interior. This generates, via a Fierz transformation, an effective space-like t channel exchange of color singlet (q anti-q) states that can be identified with the low lying meson multiplets. Thus, a one boson exchange (OBE) model is obtained that allows for comparison with traditional phenomenological models of nuclear scattering. Inclusion of strange quarks enables calculation of YN scattering. The NN and YN coupling constants and the nucleon form factors show good agreement with experimental values as do the deuteron low energy data and the NN low energy phase shifts. Thus, the QIM provides a simple model of strong interactions that is chirally invariant, includes confinement and allows for an OBE form of hadronic interaction at low energies and momentum transfers

  10. Single Molecule Sensors to Study Hydrophobic Phenomena

    OpenAIRE

    Geisler, Michael

    2010-01-01

    The nature and magnitude of the hydrophobic interaction is crucial for many technical and biological processes. In the current study a molecular probe was developed which consists of a single polymer that is bound onto the tip of an AFM cantilever in order to study these effects on the molecular scale. In the following, equilibrium forces are measured and factors of influence such as temperature, cosolvents and chemical composition are varied. Thereby, the system under investigation is so sma...

  11. Modelling of molten fuel/concrete interactions

    International Nuclear Information System (INIS)

    Muir, J.F.; Benjamin, A.S.

    1980-01-01

    A computer program modelling the interaction between molten core materials and structural concrete (CORCON) is being developed to provide quantitative estimates of fuel-melt accident consequences suitable for risk assessment of light water reactors. The principal features of CORCON are reviewed. Models developed for the principal interaction phenomena, inter-component heat transfer, concrete erosion, and melt/gas chemical reactions, are described. Alternative models for the controlling phenomenon, heat transfer from the molten pool to the surrounding concrete, are presented. These models, formulated in conjunction with the development of CORCON, are characterized by the presence or absence of either a gas film or viscous layer of molten concrete at the melt/concrete interface. Predictions of heat transfer based on these models compare favorably with available experimental data

  12. A feature-based approach to modeling protein–protein interaction hot spots

    Science.gov (United States)

    Cho, Kyu-il; Kim, Dongsup; Lee, Doheon

    2009-01-01

    Identifying features that effectively represent the energetic contribution of an individual interface residue to the interactions between proteins remains problematic. Here, we present several new features and show that they are more effective than conventional features. By combining the proposed features with conventional features, we develop a predictive model for interaction hot spots. Initially, 54 multifaceted features, composed of different levels of information including structure, sequence and molecular interaction information, are quantified. Then, to identify the best subset of features for predicting hot spots, feature selection is performed using a decision tree. Based on the selected features, a predictive model for hot spots is created using support vector machine (SVM) and tested on an independent test set. Our model shows better overall predictive accuracy than previous methods such as the alanine scanning methods Robetta and FOLDEF, and the knowledge-based method KFC. Subsequent analysis yields several findings about hot spots. As expected, hot spots have a larger relative surface area burial and are more hydrophobic than other residues. Unexpectedly, however, residue conservation displays a rather complicated tendency depending on the types of protein complexes, indicating that this feature is not good for identifying hot spots. Of the selected features, the weighted atomic packing density, relative surface area burial and weighted hydrophobicity are the top 3, with the weighted atomic packing density proving to be the most effective feature for predicting hot spots. Notably, we find that hot spots are closely related to π–related interactions, especially π · · · π interactions. PMID:19273533

  13. Interactive Visual Analysis within Dynamic Ocean Models

    Science.gov (United States)

    Butkiewicz, T.

    2012-12-01

    The many observation and simulation based ocean models available today can provide crucial insights for all fields of marine research and can serve as valuable references when planning data collection missions. However, the increasing size and complexity of these models makes leveraging their contents difficult for end users. Through a combination of data visualization techniques, interactive analysis tools, and new hardware technologies, the data within these models can be made more accessible to domain scientists. We present an interactive system that supports exploratory visual analysis within large-scale ocean flow models. The currents and eddies within the models are illustrated using effective, particle-based flow visualization techniques. Stereoscopic displays and rendering methods are employed to ensure that the user can correctly perceive the complex 3D structures of depth-dependent flow patterns. Interactive analysis tools are provided which allow the user to experiment through the introduction of their customizable virtual dye particles into the models to explore regions of interest. A multi-touch interface provides natural, efficient interaction, with custom multi-touch gestures simplifying the otherwise challenging tasks of navigating and positioning tools within a 3D environment. We demonstrate the potential applications of our visual analysis environment with two examples of real-world significance: Firstly, an example of using customized particles with physics-based behaviors to simulate pollutant release scenarios, including predicting the oil plume path for the 2010 Deepwater Horizon oil spill disaster. Secondly, an interactive tool for plotting and revising proposed autonomous underwater vehicle mission pathlines with respect to the surrounding flow patterns predicted by the model; as these survey vessels have extremely limited energy budgets, designing more efficient paths allows for greater survey areas.

  14. The hydrophobic effect: Molecular dynamics simulations of water confined between extended hydrophobic and hydrophilic surfaces

    DEFF Research Database (Denmark)

    Jensen, Morten Østergaard; Mouritsen, Ole G.; Peters, Günther H.J.

    2004-01-01

    Structural and dynamic properties of water confined between two parallel, extended, either hydrophobic or hydrophilic crystalline surfaces of n-alkane C36H74 or n-alcohol C35H71OH, are studied by molecular dynamics simulations. Electron density profiles, directly compared with corresponding......-correlation functions reveal that water molecules have characteristic diffusive behavior and orientational ordering due to the lack of hydrogen bonding interactions with the surface. These observations suggest that the altered dynamical properties of water in contact with extended hydrophobic surfaces together...... at both surfaces. The ordering is characteristically different between the surfaces and of longer range at the hydrophilic surface. Furthermore, the dynamic properties of water are different at the two surfaces and different from the bulk behavior. In particular, at the hydrophobic surface, time...

  15. Modelling Safe Interface Interactions in Web Applications

    Science.gov (United States)

    Brambilla, Marco; Cabot, Jordi; Grossniklaus, Michael

    Current Web applications embed sophisticated user interfaces and business logic. The original interaction paradigm of the Web based on static content pages that are browsed by hyperlinks is, therefore, not valid anymore. In this paper, we advocate a paradigm shift for browsers and Web applications, that improves the management of user interaction and browsing history. Pages are replaced by States as basic navigation nodes, and Back/Forward navigation along the browsing history is replaced by a full-fledged interactive application paradigm, supporting transactions at the interface level and featuring Undo/Redo capabilities. This new paradigm offers a safer and more precise interaction model, protecting the user from unexpected behaviours of the applications and the browser.

  16. New aspects of the interacting boson model

    International Nuclear Information System (INIS)

    Nadzakov, E.G.; Mikhajlov, I.N.

    1987-01-01

    In the framework of the boson space extension called interacting multiboson model: conserving the model basic dynamic symmetries, the s p d f boson model is considered. It does not destruct the intermediate mass nuclei simple description, and at the same time includes the number of levels and transitions, inaccessible to the usual s d boson model. Its applicability, even in a brief version, to the recently observed asymmetric nuclear shape effect in the Ra-Th-U region (and in other regions) with possible octupole and dipole deformation is demonstrated. It is done by reproducing algebraically the yrast lines of nuclei with vibrational, transitional and rotational spectra

  17. Modelling hadronic interactions in HEP MC generators

    CERN Document Server

    Skands, Peter

    2015-01-01

    HEP event generators aim to describe high-energy collisions in full exclusive detail. They combine perturbative matrix elements and parton showers with dynamical models of less well-understood phenomena such as hadronization, diffraction, and the so-called underlying event. We briefly summarise some of the main concepts relevant to the modelling of soft/inclusive hadron interactions in MC generators, in particular PYTHIA, with emphasis on questions recently highlighted by LHC data.

  18. Interacting dark energy model and thermal stability

    Energy Technology Data Exchange (ETDEWEB)

    Bhandari, Pritikana; Haldar, Sourav; Chakraborty, Subenoy [Jadavpur University, Department of Mathematics, Kolkata, West Bengal (India)

    2017-12-15

    In the background of the homogeneous and isotropic FLRW model, the thermodynamics of the interacting DE fluid is investigated in the present work. By studying the thermodynamical parameters, namely the heat capacities and the compressibilities, both thermal and mechanical stability are discussed and the restrictions on the equation of state parameter of the dark fluid are analyzed. (orig.)

  19. Intuitionistic preference modeling and interactive decision making

    CERN Document Server

    Xu, Zeshui

    2014-01-01

    This book offers an in-depth and comprehensive introduction to the priority methods of intuitionistic preference relations, the consistency and consensus improving procedures for intuitionistic preference relations, the approaches to group decision making based on intuitionistic preference relations, the approaches and models for interactive decision making with intuitionistic fuzzy information, and the extended results in interval-valued intuitionistic fuzzy environments.

  20. QSO evolution in the interaction model

    International Nuclear Information System (INIS)

    De Robertis, M.

    1985-01-01

    QSO evolution is investigated according to the interaction hypothesis described most recently by Stockton (1982), in which activity results from an interaction between two galaxies resulting in the transfer of gas onto a supermassive black hole (SBH) at the center of at least one participant. Explicit models presented here for interactions in cluster environments show that a peak QSO population can be formed in this way at zroughly-equal2--3, with little activity prior to this epoch. Calculated space densities match those inferred from observations for this epoch. Substantial density evolution is expected in such models, since, after virialization, conditions in the cores of rich clusters lead to the depletion of gas-rich systems through ram-pressure stripping. Density evolution parameters of 6--12 are easily accounted for. At smaller redshifts, however, QSOs should be found primarily in poor clusters or groups. Probability estimates provided by this model are consistent with local estimates for the observed number of QSOs per interaction. Significant luminosity-dependent evolution might also be expected in these models. It is suggested that the mean SBH mass increases with lookback time, leading to a statistical brightening with redshift. Undoubtedly, both forms of evolution contribute to the overall QSO luminosity function

  1. Sphericity in the interacting boson model

    International Nuclear Information System (INIS)

    Ogata, H.

    1977-01-01

    The interacting boson model (IBM) of Arima and Iachello is examined. The transition between the rotational and vibrational modes of even-even nuclei is presented as a function of a sphericity parameter, which is determined primarily from yrast band spectra. The backbending feature is reasonably reproduced. (author)

  2. Electron scattering in the interacting boson model

    International Nuclear Information System (INIS)

    Dieperink, A.E.L.; Iachello, F.; Creswell, C.

    1978-01-01

    It is suggested that the interacting boson model be used in the analysis of electron scattering data. Qualitative features of the expected behavior of the inelastic excitation of some 2 + states in the transitional Sm-Nd region are discussed. (Auth.)

  3. Interacting dark energy model and thermal stability

    International Nuclear Information System (INIS)

    Bhandari, Pritikana; Haldar, Sourav; Chakraborty, Subenoy

    2017-01-01

    In the background of the homogeneous and isotropic FLRW model, the thermodynamics of the interacting DE fluid is investigated in the present work. By studying the thermodynamical parameters, namely the heat capacities and the compressibilities, both thermal and mechanical stability are discussed and the restrictions on the equation of state parameter of the dark fluid are analyzed. (orig.)

  4. A fashion model with social interaction

    Science.gov (United States)

    Nakayama, Shoichiro; Nakamura, Yasuyuki

    2004-06-01

    In general, it is difficult to investigate social phenomena mathematically or quantitatively due to non-linear interactions. Statistical physics can provide powerful methods for studying social phenomena with interactions, and could be very useful for them. In this study, we take a focus on fashion as a social phenomenon with interaction. The social interaction considered here are “bandwagon effect” and “snob effect.” In the bandwagon effect, the correlation between one's behavior and others is positive. People feel fashion weary or boring when it is overly popular. This is the snob effect. It is assumed that the fashion phenomenon is formed by the aggregation of individual's binary choice, that is, the fashion is adopted or not. We formulate the fashion phenomenon as the logit model, which is based on the random utility theory in social science, especially economics. The model derived here basically has the similarity with the pioneering model by Weidlich (Phys. Rep. 204 (1991) 1), which was derived from the master equation, the Langevin equation, or the Fokker-Planck equation. This study seems to give the behavioral or behaviormetrical foundation to his model. As a result of dynamical analysis, it is found that in the case that both the bandwagon effect and the snob effect work, periodic or chaotic behavior of fashion occurs under certain conditions.

  5. Statistical pairwise interaction model of stock market

    Science.gov (United States)

    Bury, Thomas

    2013-03-01

    Financial markets are a classical example of complex systems as they are compound by many interacting stocks. As such, we can obtain a surprisingly good description of their structure by making the rough simplification of binary daily returns. Spin glass models have been applied and gave some valuable results but at the price of restrictive assumptions on the market dynamics or they are agent-based models with rules designed in order to recover some empirical behaviors. Here we show that the pairwise model is actually a statistically consistent model with the observed first and second moments of the stocks orientation without making such restrictive assumptions. This is done with an approach only based on empirical data of price returns. Our data analysis of six major indices suggests that the actual interaction structure may be thought as an Ising model on a complex network with interaction strengths scaling as the inverse of the system size. This has potentially important implications since many properties of such a model are already known and some techniques of the spin glass theory can be straightforwardly applied. Typical behaviors, as multiple equilibria or metastable states, different characteristic time scales, spatial patterns, order-disorder, could find an explanation in this picture.

  6. Synthetic models related to DNA-intercalating molecules. Interactions between 8-alkoxypsoralen and adenine

    International Nuclear Information System (INIS)

    Decout, J.L.; Lhomme, J.

    1983-01-01

    To investigate the interactions and the photoreactions between furocoumarins and adenine, compounds in which a psoralen molecule is linked by different polymethylene bridges have been synthesised. Ring-ring intramolecular interactions are observed by UV spectroscopy. Thermodynamic parameters of these hydrophobic interactions are determined by the study of the variation of the hypochromic effect with temperature. (author)

  7. Understanding and modelling Man-Machine Interaction

    International Nuclear Information System (INIS)

    Cacciabue, P.C.

    1991-01-01

    This paper gives an overview of the current state of the art in man machine systems interaction studies, focusing on the problems derived from highly automated working environments and the role of humans in the control loop. In particular, it is argued that there is a need for sound approaches to design and analysis of Man-Machine Interaction (MMI), which stem from the contribution of three expertises in interfacing domains, namely engineering, computer science and psychology: engineering for understanding and modelling plants and their material and energy conservation principles; psychology for understanding and modelling humans and their cognitive behaviours; computer science for converting models in sound simulations running in appropriate computer architectures. (author)

  8. Understanding and modelling man-machine interaction

    International Nuclear Information System (INIS)

    Cacciabue, P.C.

    1996-01-01

    This paper gives an overview of the current state of the art in man-machine system interaction studies, focusing on the problems derived from highly automated working environments and the role of humans in the control loop. In particular, it is argued that there is a need for sound approaches to the design and analysis of man-machine interaction (MMI), which stem from the contribution of three expertises in interfacing domains, namely engineering, computer science and psychology: engineering for understanding and modelling plants and their material and energy conservation principles; psychology for understanding and modelling humans an their cognitive behaviours; computer science for converting models in sound simulations running in appropriate computer architectures. (orig.)

  9. Geometrical analysis of the interacting boson model

    International Nuclear Information System (INIS)

    Dieperink, A.E.L.

    1983-01-01

    The Interacting Boson Model is considered, in relation with geometrical models and the application of mean field techniques to algebraic models, in three lectures. In the first, several methods are reviewed to establish a connection between the algebraic formulation of collective nuclear properties in terms of the group SU(6) and the geometric approach. In the second lecture the geometric interpretation of new degrees of freedom that arise in the neutron-proton IBA is discussed, and in the third one some further applications of algebraic techniques to the calculation of static and dynamic collective properties are presented. (U.K.)

  10. Localisation in a Growth Model with Interaction

    Science.gov (United States)

    Costa, M.; Menshikov, M.; Shcherbakov, V.; Vachkovskaia, M.

    2018-05-01

    This paper concerns the long term behaviour of a growth model describing a random sequential allocation of particles on a finite cycle graph. The model can be regarded as a reinforced urn model with graph-based interaction. It is motivated by cooperative sequential adsorption, where adsorption rates at a site depend on the configuration of existing particles in the neighbourhood of that site. Our main result is that, with probability one, the growth process will eventually localise either at a single site, or at a pair of neighbouring sites.

  11. Modeling of interaction effects in granular systems

    CERN Document Server

    El-Hilo, M; Al-Rsheed, A

    2000-01-01

    Interaction effects on the magnetic behavior of granular solid systems are examined using a numerical model which is capable of predicting the field, temperature and time dependence of magnetization. In this work, interaction effects on the temperature dependence of time viscosity coefficient S(T) and formation of minor hysteresis loops have been studied. The results for the time- and temperature dependence of remanence ratio have showed that the distribution of energy barriers f(DELTA E) obtained depend critically on the strength and nature of interactions. These interactions-based changes in f(DELTA E) can easily give a temperature-independent behavior of S(T) when these changes give a 1/DELTA E behavior to the distribution of energy barriers. Thus, conclusions about macroscopic quantum tunneling must be carefully drawn when the temperature dependence of S(T) is used to probe for MQT effects. For minor hysteresis effects, the result shows that for the non-interacting case, no minor hysteresis loops occur an...

  12. A two-particle exchange interaction model

    International Nuclear Information System (INIS)

    Lyubina, Julia; Mueller, Karl-Hartmut; Wolf, Manfred; Hannemann, Ullrich

    2010-01-01

    The magnetisation reversal of two interacting particles was investigated within a simple model describing exchange coupling of magnetically uniaxial single-domain particles. Depending on the interaction strength W, the reversal may be cooperative or non-cooperative. A non-collinear reversal mode is obtained even for two particles with parallel easy axes. The model yields different phenomena as observed in spring magnets such as recoil hysteresis in the second quadrant of the field-magnetisation-plane, caused by exchange bias, as well as the mentioned reversal-rotation mode. The Wohlfarth's remanence analysis performed on aggregations of such pairs of interacting particles shows that the deviation δM(H m ) usually being considered as a hallmark of magnetic interaction vanishes for all maximum applied fields H m not only at W=0, but also for sufficiently large values of W. Furthermore, this so-called δM-plot depends on whether the sample is ac-field or thermally demagnetised.

  13. A two-particle exchange interaction model

    Energy Technology Data Exchange (ETDEWEB)

    Lyubina, Julia, E-mail: j.lyubina@ifw-dresden.d [IFW Dresden, Institute for Metallic Materials, P.O. Box 270016, D-01171 Dresden (Germany); Mueller, Karl-Hartmut; Wolf, Manfred; Hannemann, Ullrich [IFW Dresden, Institute for Metallic Materials, P.O. Box 270016, D-01171 Dresden (Germany)

    2010-10-15

    The magnetisation reversal of two interacting particles was investigated within a simple model describing exchange coupling of magnetically uniaxial single-domain particles. Depending on the interaction strength W, the reversal may be cooperative or non-cooperative. A non-collinear reversal mode is obtained even for two particles with parallel easy axes. The model yields different phenomena as observed in spring magnets such as recoil hysteresis in the second quadrant of the field-magnetisation-plane, caused by exchange bias, as well as the mentioned reversal-rotation mode. The Wohlfarth's remanence analysis performed on aggregations of such pairs of interacting particles shows that the deviation {delta}M(H{sub m}) usually being considered as a hallmark of magnetic interaction vanishes for all maximum applied fields H{sub m} not only at W=0, but also for sufficiently large values of W. Furthermore, this so-called {delta}M-plot depends on whether the sample is ac-field or thermally demagnetised.

  14. Motion Model Employment using interacting Motion Model Algorithm

    DEFF Research Database (Denmark)

    Hussain, Dil Muhammad Akbar

    2006-01-01

    The paper presents a simulation study to track a maneuvering target using a selective approach in choosing Interacting Multiple Models (IMM) algorithm to provide a wider coverage to track such targets.  Initially, there are two motion models in the system to track a target.  Probability of each m...

  15. Microscopic foundation of the interacting boson model

    International Nuclear Information System (INIS)

    Arima, Akito

    1994-01-01

    A microscopic foundation of the interacting boson model is described. The importance of monopole and quadrupole pairs of nucleons is emphasized. Those pairs are mapped onto the s and d bosons. It is shown that this mapping provides a good approximation in vibrational and transitional nuclei. In appendix, it is shown that the monopole pair of electrons plays possibly an important role in metal clusters. (orig.)

  16. Interactive Procedural Modelling of Coherent Waterfall Scenes

    OpenAIRE

    Emilien , Arnaud; Poulin , Pierre; Cani , Marie-Paule; Vimont , Ulysse

    2015-01-01

    International audience; Combining procedural generation and user control is a fundamental challenge for the interactive design of natural scenery. This is particularly true for modelling complex waterfall scenes where, in addition to taking charge of geometric details, an ideal tool should also provide a user with the freedom to shape the running streams and falls, while automatically maintaining physical plausibility in terms of flow network, embedding into the terrain, and visual aspects of...

  17. Nonlinear interaction model of subsonic jet noise.

    Science.gov (United States)

    Sandham, Neil D; Salgado, Adriana M

    2008-08-13

    Noise generation in a subsonic round jet is studied by a simplified model, in which nonlinear interactions of spatially evolving instability modes lead to the radiation of sound. The spatial mode evolution is computed using linear parabolized stability equations. Nonlinear interactions are found on a mode-by-mode basis and the sound radiation characteristics are determined by solution of the Lilley-Goldstein equation. Since mode interactions are computed explicitly, it is possible to find their relative importance for sound radiation. The method is applied to a single stream jet for which experimental data are available. The model gives Strouhal numbers of 0.45 for the most amplified waves in the jet and 0.19 for the dominant sound radiation. While in near field axisymmetric and the first azimuthal modes are both important, far-field sound is predominantly axisymmetric. These results are in close correspondence with experiment, suggesting that the simplified model is capturing at least some of the important mechanisms of subsonic jet noise.

  18. Modeling Users' Experiences with Interactive Systems

    CERN Document Server

    Karapanos, Evangelos

    2013-01-01

    Over the past decade the field of Human-Computer Interaction has evolved from the study of the usability of interactive products towards a more holistic understanding of how they may mediate desired human experiences.  This book identifies the notion of diversity in usersʼ experiences with interactive products and proposes methods and tools for modeling this along two levels: (a) interpersonal diversity in usersʽ responses to early conceptual designs, and (b) the dynamics of usersʼ experiences over time. The Repertory Grid Technique is proposed as an alternative to standardized psychometric scales for modeling interpersonal diversity in usersʼ responses to early concepts in the design process, and new Multi-Dimensional Scaling procedures are introduced for modeling such complex quantitative data. iScale, a tool for the retrospective assessment of usersʼ experiences over time is proposed as an alternative to longitudinal field studies, and a semi-automated technique for the analysis of the elicited exper...

  19. Oil transformation sector modelling: price interactions

    International Nuclear Information System (INIS)

    Maurer, A.

    1992-01-01

    A global oil and oil product prices evolution model is proposed that covers the transformation sector incidence and the final user price establishment together with price interactions between gaseous and liquid hydrocarbons. High disparities among oil product prices in the various consumer zones (North America, Western Europe, Japan) are well described and compared with the low differences between oil supply prices in these zones. Final user price fluctuations are shown to be induced by transformation differences and competition; natural gas market is also modelled

  20. Some dynamical aspects of interacting quintessence model

    Science.gov (United States)

    Choudhury, Binayak S.; Mondal, Himadri Shekhar; Chatterjee, Devosmita

    2018-04-01

    In this paper, we consider a particular form of coupling, namely B=σ (\\dot{ρ _m}-\\dot{ρ _φ }) in spatially flat (k=0) Friedmann-Lemaitre-Robertson-Walker (FLRW) space-time. We perform phase-space analysis for this interacting quintessence (dark energy) and dark matter model for different numerical values of parameters. We also show the phase-space analysis for the `best-fit Universe' or concordance model. In our analysis, we observe the existence of late-time scaling attractors.

  1. Hydrophobic effect of silica functionalized with silylated Ti ...

    Indian Academy of Sciences (India)

    aCentre for Sustainable Nanomaterials, Ibnu Sina Institute for Scientific and Industrial Research,. Universiti ... rate of water adsorption capacity for the hydrophobic catalysts prepared. .... analyzed by Gas Chromatography, Shimadzu model.

  2. Ferromagnetic Potts models with multisite interaction

    Science.gov (United States)

    Schreiber, Nir; Cohen, Reuven; Haber, Simi

    2018-03-01

    We study the q -state Potts model with four-site interaction on a square lattice. Based on the asymptotic behavior of lattice animals, it is argued that when q ≤4 the system exhibits a second-order phase transition and when q >4 the transition is first order. The q =4 model is borderline. We find 1 /lnq to be an upper bound on Tc, the exact critical temperature. Using a low-temperature expansion, we show that 1 /(θ lnq ) , where θ >1 is a q -dependent geometrical term, is an improved upper bound on Tc. In fact, our findings support Tc=1 /(θ lnq ) . This expression is used to estimate the finite correlation length in first-order transition systems. These results can be extended to other lattices. Our theoretical predictions are confirmed numerically by an extensive study of the four-site interaction model using the Wang-Landau entropic sampling method for q =3 ,4 ,5 . In particular, the q =4 model shows an ambiguous finite-size pseudocritical behavior.

  3. Pre-relaxation in weakly interacting models

    Science.gov (United States)

    Bertini, Bruno; Fagotti, Maurizio

    2015-07-01

    We consider time evolution in models close to integrable points with hidden symmetries that generate infinitely many local conservation laws that do not commute with one another. The system is expected to (locally) relax to a thermal ensemble if integrability is broken, or to a so-called generalised Gibbs ensemble if unbroken. In some circumstances expectation values exhibit quasi-stationary behaviour long before their typical relaxation time. For integrability-breaking perturbations, these are also called pre-thermalisation plateaux, and emerge e.g. in the strong coupling limit of the Bose-Hubbard model. As a result of the hidden symmetries, quasi-stationarity appears also in integrable models, for example in the Ising limit of the XXZ model. We investigate a weak coupling limit, identify a time window in which the effects of the perturbations become significant and solve the time evolution through a mean-field mapping. As an explicit example we study the XYZ spin-\\frac{1}{2} chain with additional perturbations that break integrability. One of the most intriguing results of the analysis is the appearance of persistent oscillatory behaviour. To unravel its origin, we study in detail a toy model: the transverse-field Ising chain with an additional nonlocal interaction proportional to the square of the transverse spin per unit length (2013 Phys. Rev. Lett. 111 197203). Despite being nonlocal, this belongs to a class of models that emerge as intermediate steps of the mean-field mapping and shares many dynamical properties with the weakly interacting models under consideration.

  4. Hydrophobic interactions of phenoxazine modulators with bovine ...

    Indian Academy of Sciences (India)

    effect of the displacing activities of hydroxyzine and acetylsalicylic acid on the ... concentration of the drugs, higher numbers being obtained at higher drug ... derivatives4 and have been claimed to be nervous system depressants, in particular ...

  5. Interactions between baryon octets by quark model

    Energy Technology Data Exchange (ETDEWEB)

    Nakamoto, S. [Suzuka National College of Technology, Suzuka, Mie (Japan); Fujiwara, Y. [Kyoto Univ., Faculty of Science, Kyoto (Japan); Suzuki, Y. [Niigata Univ., Faculty of Science, Niigata (Japan); Kohno, M. [Kyushu Dental College, Kita-kyushu, Fukuoka (Japan)

    2003-03-01

    Interactions between the baryon octets are studied by using the two spin flavor SU{sub 6} quark models, namely fss2 and FSS. In all channels, results that can be systematically understood along with the flavor symmetry are obtained. Effect of the channel coupling in the {sup 1}S{sub 0} state of the system of strangeness-2 shows a tendency to be weak in the system of isospin 0 while strong in the system of isospin 1. It is shown that this tendency is due to the competitive contributions of the color magnetic term and the effective meson exchange potential to the transition potential. Flavor symmetry breaking weakens both the repulsive force in the short range and the attractive force in the intermediate range. It is revealed that the overall qualitative behavior is determined as the result of the competitive effect of those interactions. (S. Funahashi)

  6. On dark degeneracy and interacting models

    International Nuclear Information System (INIS)

    Carneiro, S.; Borges, H.A.

    2014-01-01

    Cosmological background observations cannot fix the dark energy equation of state, which is related to a degeneracy in the definition of the dark sector components. Here we show that this degeneracy can be broken at perturbation level by imposing two observational properties on dark matter. First, dark matter is defined as the clustering component we observe in large scale structures. This definition is meaningful only if dark energy is unperturbed, which is achieved if we additionally assume, as a second condition, that dark matter is cold, i.e. non-relativistic. As a consequence, dark energy models with equation-of-state parameter −1 ≤ ω < 0 are reduced to two observationally distinguishable classes with ω = −1, equally competitive when tested against observations. The first comprises the ΛCDM model with constant dark energy density. The second consists of interacting models with an energy flux from dark energy to dark matter

  7. Influence of Hydrophobicity on Polyelectrolyte Complexation

    Energy Technology Data Exchange (ETDEWEB)

    Sadman, Kazi [Department; amp, Engineering, Northwestern University, Evanston, Illinois 60208, United States; Wang, Qifeng [Department; amp, Engineering, Northwestern University, Evanston, Illinois 60208, United States; Chen, Yaoyao [Department; amp, Engineering, Northwestern University, Evanston, Illinois 60208, United States; Keshavarz, Bavand [Department; Jiang, Zhang [X-ray; Shull, Kenneth R. [Department; amp, Engineering, Northwestern University, Evanston, Illinois 60208, United States

    2017-11-16

    Polyelectrolyte complexes are a fascinating class of soft materials that can span the full spectrum of mechanical properties from low viscosity fluids to glassy solids. This spectrum can be accessed by modulating the extent of electrostatic association in these complexes. However, to realize the full potential of polyelectrolyte complexes as functional materials their molecular level details need to be clearly correlated with their mechanical response. The present work demonstrates that by making simple amendments to the chain architecture it is possible to affect the salt responsiveness of polyelectrolyte complexes in a systematic manner. This is achieved by quaternizing poly(4-vinylpyridine) (QVP) with methyl, ethyl and propyl substituents– thereby increasing the hydrophobicity with increasing side chain length– and complexing them with a common anionic polyelectrolyte, poly(styrene sulfonate). The mechanical 1 ACS Paragon Plus Environment behavior of these complexes is compared to the more hydrophilic system of poly(styrene sulfonate) and poly(diallyldimethylammonium) by quantifying the swelling behavior in response to salt stimuli. More hydrophobic complexes are found to be more resistant to doping by salt, yet the mechanical properties of the complex remain contingent on the overall swelling ratio of the complex itself, following near universal swelling-modulus master curves that are quantified in this work. The rheological behavior of QVP complex coacervates are found to be approximately the same, only requiring higher salt concentrations to overcome strong hydrophobic interactions, demonstrating that hydrophobicity can be used as an important parameter for tuning the stability of polyelectrolyte complexes in general, while still preserving the ability to be processed “saloplastically”.

  8. Estimation of the solubility parameters of model plant surfaces and agrochemicals: a valuable tool for understanding plant surface interactions.

    Science.gov (United States)

    Khayet, Mohamed; Fernández, Victoria

    2012-11-14

    Most aerial plant parts are covered with a hydrophobic lipid-rich cuticle, which is the interface between the plant organs and the surrounding environment. Plant surfaces may have a high degree of hydrophobicity because of the combined effects of surface chemistry and roughness. The physical and chemical complexity of the plant cuticle limits the development of models that explain its internal structure and interactions with surface-applied agrochemicals. In this article we introduce a thermodynamic method for estimating the solubilities of model plant surface constituents and relating them to the effects of agrochemicals. Following the van Krevelen and Hoftyzer method, we calculated the solubility parameters of three model plant species and eight compounds that differ in hydrophobicity and polarity. In addition, intact tissues were examined by scanning electron microscopy and the surface free energy, polarity, solubility parameter and work of adhesion of each were calculated from contact angle measurements of three liquids with different polarities. By comparing the affinities between plant surface constituents and agrochemicals derived from (a) theoretical calculations and (b) contact angle measurements we were able to distinguish the physical effect of surface roughness from the effect of the chemical nature of the epicuticular waxes. A solubility parameter model for plant surfaces is proposed on the basis of an increasing gradient from the cuticular surface towards the underlying cell wall. The procedure enabled us to predict the interactions among agrochemicals, plant surfaces, and cuticular and cell wall components, and promises to be a useful tool for improving our understanding of biological surface interactions.

  9. Modeling Drug-Carrier Interaction in the Drug Release from Nanocarriers

    Directory of Open Access Journals (Sweden)

    Like Zeng

    2011-01-01

    Full Text Available Numerous nanocarriers of various compositions and geometries have been developed for the delivery and release of therapeutic and imaging agents. Due to the high specific surface areas of nanocarriers, different mechanisms such as ion pairing and hydrophobic interaction need to be explored for achieving sustained release. Recently, we developed a three-parameter model that considers reversible drug-carrier interaction and first-order drug release from liposomes. A closed-form analytical solution was obtained. Here, we further explore the ability of the model to capture the release of bioactive molecules such as drugs and growth factors from various nanocarriers. A parameter study demonstrates that the model is capable of resembling major categories of drug release kinetics. We further fit the model to 60 sets of experimental data from various drug release systems, including nanoparticles, hollow particles, fibers, and hollow fibers. Additionally, bootstrapping is used to evaluate the accuracy of parameter determination and validate the model in selected cases. The simplicity and universality of the model and the clear physical meanings of each model parameter render the model useful for the design and development of new drug delivery systems.

  10. Separation of very hydrophobic analytes by micellar electrokinetic chromatography IV. Modeling of the effective electrophoretic mobility from carbon number equivalents and octanol-water partition coefficients.

    Science.gov (United States)

    Huhn, Carolin; Pyell, Ute

    2008-07-11

    It is investigated whether those relationships derived within an optimization scheme developed previously to optimize separations in micellar electrokinetic chromatography can be used to model effective electrophoretic mobilities of analytes strongly differing in their properties (polarity and type of interaction with the pseudostationary phase). The modeling is based on two parameter sets: (i) carbon number equivalents or octanol-water partition coefficients as analyte descriptors and (ii) four coefficients describing properties of the separation electrolyte (based on retention data for a homologous series of alkyl phenyl ketones used as reference analytes). The applicability of the proposed model is validated comparing experimental and calculated effective electrophoretic mobilities. The results demonstrate that the model can effectively be used to predict effective electrophoretic mobilities of neutral analytes from the determined carbon number equivalents or from octanol-water partition coefficients provided that the solvation parameters of the analytes of interest are similar to those of the reference analytes.

  11. Investigation of the Interaction between Patulin and Human Serum Albumin by a Spectroscopic Method, Atomic Force Microscopy, and Molecular Modeling

    Directory of Open Access Journals (Sweden)

    Li Yuqin

    2014-01-01

    Full Text Available The interaction of patulin with human serum albumin (HSA was studied in vitro under normal physiological conditions. The study was performed using fluorescence, ultraviolet-visible spectroscopy (UV-Vis, circular dichroism (CD, atomic force microscopy (AFM, and molecular modeling techniques. The quenching mechanism was investigated using the association constants, the number of binding sites, and basic thermodynamic parameters. A dynamic quenching mechanism occurred between HSA and patulin, and the binding constants (K were 2.60 × 104, 4.59 × 104, and 7.01 × 104 M−1 at 288, 300, and 310 K, respectively. Based on fluorescence resonance energy transfer, the distance between the HSA and patulin was determined to be 2.847 nm. The ΔG0, ΔH0, and ΔS0 values across various temperatures indicated that hydrophobic interaction was the predominant binding force. The UV-Vis and CD results confirmed that the secondary structure of HSA was altered in the presence of patulin. The AFM results revealed that the individual HSA molecule dimensions were larger after interaction with patulin. In addition, molecular modeling showed that the patulin-HSA complex was stabilized by hydrophobic and hydrogen bond forces. The study results suggested that a weak intermolecular interaction occurred between patulin and HSA. Overall, the results are potentially useful for elucidating the toxigenicity of patulin when it is combined with the biomolecular function effect, transmembrane transport, toxicological, testing and other experiments.

  12. The interaction of 2-mercaptobenzimidazole with human serum albumin as determined by spectroscopy, atomic force microscopy and molecular modeling.

    Science.gov (United States)

    Li, Yuqin; Jia, Baoxiu; Wang, Hao; Li, Nana; Chen, Gaopan; Lin, Yuejuan; Gao, Wenhua

    2013-04-01

    The interaction of 2-mercaptobenzimidazole (MBI) with human serum albumin (HSA) was studied in vitro by equilibrium dialysis under normal physiological conditions. This study used fluorescence, ultraviolet-visible spectroscopy (UV-vis), Fourier transform infrared (FT-IR), circular dichroism (CD) and Raman spectroscopy, atomic force microscopy (AFM) and molecular modeling techniques. Association constants, the number of binding sites and basic thermodynamic parameters were used to investigate the quenching mechanism. Based on the fluorescence resonance energy transfer, the distance between the HSA and MBI was 2.495 nm. The ΔG(0), ΔH(0), and ΔS(0) values across temperature indicated that the hydrophobic interaction was the predominant binding Force. The UV, FT-IR, CD and Raman spectra confirmed that the HSA secondary structure was altered in the presence of MBI. In addition, the molecular modeling showed that the MBI-HSA complex was stabilized by hydrophobic forces, which resulted from amino acid residues. The AFM results revealed that the individual HSA molecule dimensions were larger after interaction with MBI. Overall, this study suggested a method for characterizing the weak intermolecular interaction. In addition, this method is potentially useful for elucidating the toxigenicity of MBI when it is combined with the biomolecular function effect, transmembrane transport, toxicological testing and other experiments. Copyright © 2012 Elsevier B.V. All rights reserved.

  13. Role of air bubbles overlooked in the adsorption of perfluorooctanesulfonate on hydrophobic carbonaceous adsorbents.

    Science.gov (United States)

    Meng, Pingping; Deng, Shubo; Lu, Xinyu; Du, Ziwen; Wang, Bin; Huang, Jun; Wang, Yujue; Yu, Gang; Xing, Baoshan

    2014-12-02

    Hydrophobic interaction has been considered to be responsible for adsorption of perfluorooctanesulfonate (PFOS) on the surface of hydrophobic adsorbents, but the long C-F chain in PFOS is not only hydrophobic but also oleophobic. In this study, for the first time we propose that air bubbles on the surface of hydrophobic carbonaceous adsorbents play an important role in the adsorption of PFOS. The level of adsorption of PFOS on carbon nanotubes (CNTs), graphite (GI), graphene (GE), and powdered activated carbon (PAC) decreases after vacuum degassing. Vacuum degassing time and pressure significantly affect the removal of PFOS by these adsorbents. After vacuum degassing at 0.01 atm for 36 h, the extent of removal of PFOS by the pristine CNTs and GI decreases 79% and 74%, respectively, indicating the main contribution of air bubbles to PFOS adsorption. When the degassed solution is recontacted with air during the adsorption process, the removal of PFOS recovers to the value obtained without vacuum degassing, further verifying the key role of air bubbles in PFOS adsorption. By theoretical calculation, the distribution of PFOS in air bubbles on the adsorbent surfaces is discussed, and a new schematic sorption model of PFOS on carbonaceous adsorbents in the presence of air bubbles is proposed. The accumulation of PFOS at the interface of air bubbles on the adsorbents is primarily responsible for its adsorption, providing a new mechanistic insight into the transport, fate, and removal of PFOS.

  14. The interacting boson-fermion model

    International Nuclear Information System (INIS)

    Iachello, F.; Van Isacker, P.

    1990-01-01

    The interacting boson-fermion model has become in recent years the standard model for the description of atomic nuclei with an odd number of protons and/or neutrons. This book describes the mathematical framework on which the interacting boson-fermion model is built and presents applications to a variety of situations encountered in nuclei. The book addresses both the analytical and the numerical aspects of the problem. The analytical aspect requires the introduction of rather complex group theoretic methods, including the use of graded (or super) Lie algebras. The first (and so far only) example of supersymmetry occurring in nature is also discussed. The book is the first comprehensive treatment of the subject and will appeal to both theoretical and experimental physicists. The large number of explicit formulas for level energies, electromagnetic transition rates and intensities of transfer reactions presented in the book provide a simple but detailed way to analyze experimental data. This book can also be used as a textbook for advanced graduate students

  15. Interaction of Mastoparan with Model Membranes

    Science.gov (United States)

    Haloot, Justin

    2010-10-01

    The use of antimicrobial agents began during the 20th century to reduce the effects of infectious diseases. Since the 1990s, antimicrobial resistance has become an ever-increasing global problem. Our laboratory recently found that small antimicrobial peptides (AMPs) have potent antimicrobial activity against a wide range of Gram-negative and Gram-positive organisms including antibiotic resistant organisms. These AMPs are potential therapeutic agents against the growing problem of antimicrobial resistance. AMPs are small peptides produced by plants, insects and animals. Several hypotheses concede that these peptides cause some type of structural perturbations and increased membrane permeability in bacteria however, how AMPs kill bacteria remains unclear. The goal of this study was to design an assay that would allow us to evaluate and monitor the pore forming ability of an AMP, Mastoparan, on model membrane structures called liposomes. Development of this model will facilitate the study of how mastoparan and related AMPs interact with the bacterial membrane.

  16. Laser interaction with biological material mathematical modeling

    CERN Document Server

    Kulikov, Kirill

    2014-01-01

    This book covers the principles of laser interaction with biological cells and tissues of varying degrees of organization. The problems of biomedical diagnostics are considered. Scattering of laser irradiation of blood cells is modeled for biological structures (dermis, epidermis, vascular plexus). An analytic theory is provided which is based on solving the wave equation for the electromagnetic field. It allows the accurate analysis of interference effects arising from the partial superposition of scattered waves. Treated topics of mathematical modeling are: optical characterization of biological tissue with large-scale and small-scale inhomogeneities in the layers, heating blood vessel under laser irradiation incident on the outer surface of the skin and thermo-chemical denaturation of biological structures at the example of human skin.

  17. Interaction of Defensins with Model Cell Membranes

    Science.gov (United States)

    Sanders, Lori K.; Schmidt, Nathan W.; Yang, Lihua; Mishra, Abhijit; Gordon, Vernita D.; Selsted, Michael E.; Wong, Gerard C. L.

    2009-03-01

    Antimicrobial peptides (AMPs) comprise a key component of innate immunity for a wide range of multicellular organisms. For many AMPs, activity comes from their ability to selectively disrupt and lyse bacterial cell membranes. There are a number of proposed models for this action, but the detailed molecular mechanism of selective membrane permeation remains unclear. Theta defensins are circularized peptides with a high degree of selectivity. We investigate the interaction of model bacterial and eukaryotic cell membranes with theta defensins RTD-1, BTD-7, and compare them to protegrin PG-1, a prototypical AMP, using synchrotron small angle x-ray scattering (SAXS). The relationship between membrane composition and peptide induced changes in membrane curvature and topology is examined. By comparing the membrane phase behavior induced by these different peptides we will discuss the importance of amino acid composition and placement on membrane rearrangement.

  18. An interactive program for pharmacokinetic modeling.

    Science.gov (United States)

    Lu, D R; Mao, F

    1993-05-01

    A computer program, PharmK, was developed for pharmacokinetic modeling of experimental data. The program was written in C computer language based on the high-level user-interface Macintosh operating system. The intention was to provide a user-friendly tool for users of Macintosh computers. An interactive algorithm based on the exponential stripping method is used for the initial parameter estimation. Nonlinear pharmacokinetic model fitting is based on the maximum likelihood estimation method and is performed by the Levenberg-Marquardt method based on chi 2 criterion. Several methods are available to aid the evaluation of the fitting results. Pharmacokinetic data sets have been examined with the PharmK program, and the results are comparable with those obtained with other programs that are currently available for IBM PC-compatible and other types of computers.

  19. Repetition-based Interactive Facade Modeling

    KAUST Repository

    AlHalawani, Sawsan

    2012-07-01

    Modeling and reconstruction of urban environments has gained researchers attention throughout the past few years. It spreads in a variety of directions across multiple disciplines such as image processing, computer graphics and computer vision as well as in architecture, geoscience and remote sensing. Having a virtual world of our real cities is very attractive in various directions such as entertainment, engineering, governments among many others. In this thesis, we address the problem of processing a single fa cade image to acquire useful information that can be utilized to manipulate the fa cade and generate variations of fa cade images which can be later used for buildings\\' texturing. Typical fa cade structures exhibit a rectilinear distribution where in windows and other elements are organized in a grid of horizontal and vertical repetitions of similar patterns. In the firt part of this thesis, we propose an efficient algorithm that exploits information obtained from a single image to identify the distribution grid of the dominant elements i.e. windows. This detection method is initially assisted with the user marking the dominant window followed by an automatic process for identifying its repeated instances which are used to define the structure grid. Given the distribution grid, we allow the user to interactively manipulate the fa cade by adding, deleting, resizing or repositioning the windows in order to generate new fa cade structures. Having the utility for the interactive fa cade is very valuable to create fa cade variations and generate new textures for building models. Ultimately, there is a wide range of interesting possibilities of interactions to be explored.

  20. Marginal and Interaction Effects in Ordered Response Models

    OpenAIRE

    Debdulal Mallick

    2009-01-01

    In discrete choice models the marginal effect of a variable of interest that is interacted with another variable differs from the marginal effect of a variable that is not interacted with any variable. The magnitude of the interaction effect is also not equal to the marginal effect of the interaction term. I present consistent estimators of both marginal and interaction effects in ordered response models. This procedure is general and can easily be extended to other discrete choice models. I ...

  1. Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the “Hydrophobic Wall” of Carbonic Anhydrase

    Energy Technology Data Exchange (ETDEWEB)

    J Mecinovic; P Snyder; K Mirica; S Bai; E Mack; R Kwant; D Moustakas; A Heroux; G Whitesides

    2011-12-31

    entropic contributions to the hydrophobic effect in this representative system of protein and ligand: hydrophobic interactions, here, seem to comprise approximately equal contributions from enthalpy (plausibly from strengthening networks of hydrogen bonds among molecules of water) and entropy (from release of water from configurationally restricted positions).

  2. Modeling energy-economy interactions using integrated models

    International Nuclear Information System (INIS)

    Uyterlinde, M.A.

    1994-06-01

    Integrated models are defined as economic energy models that consist of several submodels, either coupled by an interface module, or embedded in one large model. These models can be used for energy policy analysis. Using integrated models yields the following benefits. They provide a framework in which energy-economy interactions can be better analyzed than in stand-alone models. Integrated models can represent both energy sector technological details, as well as the behaviour of the market and the role of prices. Furthermore, the combination of modeling methodologies in one model can compensate weaknesses of one approach with strengths of another. These advantages motivated this survey of the class of integrated models. The purpose of this literature survey therefore was to collect and to present information on integrated models. To carry out this task, several goals were identified. The first goal was to give an overview of what is reported on these models in general. The second one was to find and describe examples of such models. Other goals were to find out what kinds of models were used as component models, and to examine the linkage methodology. Solution methods and their convergence properties were also a subject of interest. The report has the following structure. In chapter 2, a 'conceptual framework' is given. In chapter 3 a number of integrated models is described. In a table, a complete overview is presented of all described models. Finally, in chapter 4, the report is summarized, and conclusions are drawn regarding the advantages and drawbacks of integrated models. 8 figs., 29 refs

  3. Interactions in heated milk model systems with different ratios of nanoparticulated whey protein at varying pH

    DEFF Research Database (Denmark)

    Liu, Guanchen; Jæger, Tanja C.; Nielsen, Søren B.

    2017-01-01

    To better understand the interactions between nanoparticulated whey protein (NWP) and other milk proteins during acidification, milk model systems were diluted to 0.5% protein concentration and adjusted to pH of 6.0-4.5 following homogenisation and heat treatment. The diluted systems with different...... concentrations of NWP (0-0.5%) were characterised in terms of particle size, viscosity, surface charge and hydrophobicity. When pH was adjusted to 5.5, aggregation was initiated at levels of NWP (0.25-0.5%) leading to significant increase in particle size and viscosity. Pure NWP (0.5%) showed largest initial...

  4. Preparation of inorganic hydrophobic catalysts

    International Nuclear Information System (INIS)

    Yang, Yong; Wang, Heyi; Du, Yang

    2009-04-01

    In order to catalyse the oxidation of tritium gas, two inorganic hydrophobic catalysts are prepared. Under room temperature, the catalysed oxidation ratio of 0.3%-1% (V/V) hydrogen gas in air is higher than 95%. Pt-II inorganic hydrophobic catalysts has obviously better catalysing ability than Pt-PTFE and lower ability than Pt-SDB in H 2 -HTO isotopic exchange, because the pressure resistence of Pt-II is much higher than Pt-SDB, it can be used to the CECE cell of heavy water detritium system. (authors)

  5. Modeling mechanical interactions between cancerous mammary acini

    Science.gov (United States)

    Wang, Jeffrey; Liphardt, Jan; Rycroft, Chris

    2015-03-01

    The rules and mechanical forces governing cell motility and interactions with the extracellular matrix of a tissue are often critical for understanding the mechanisms by which breast cancer is able to spread through the breast tissue and eventually metastasize. Ex vivo experimentation has demonstrated the the formation of long collagen fibers through collagen gels between the cancerous mammary acini responsible for milk production, providing a fiber scaffolding along which cancer cells can disorganize. We present a minimal mechanical model that serves as a potential explanation for the formation of these collagen fibers and the resultant motion. Our working hypothesis is that cancerous cells induce this fiber formation by pulling on the gel and taking advantage of the specific mechanical properties of collagen. To model this system, we employ a new Eulerian, fixed grid simulation method to model the collagen as a nonlinear viscoelastic material subject to various forces coupled with a multi-agent model to describe individual cancer cells. We find that these phenomena can be explained two simple ideas: cells pull collagen radially inwards and move towards the tension gradient of the collagen gel, while being exposed to standard adhesive and collision forces.

  6. Integrating interactive computational modeling in biology curricula.

    Directory of Open Access Journals (Sweden)

    Tomáš Helikar

    2015-03-01

    Full Text Available While the use of computer tools to simulate complex processes such as computer circuits is normal practice in fields like engineering, the majority of life sciences/biological sciences courses continue to rely on the traditional textbook and memorization approach. To address this issue, we explored the use of the Cell Collective platform as a novel, interactive, and evolving pedagogical tool to foster student engagement, creativity, and higher-level thinking. Cell Collective is a Web-based platform used to create and simulate dynamical models of various biological processes. Students can create models of cells, diseases, or pathways themselves or explore existing models. This technology was implemented in both undergraduate and graduate courses as a pilot study to determine the feasibility of such software at the university level. First, a new (In Silico Biology class was developed to enable students to learn biology by "building and breaking it" via computer models and their simulations. This class and technology also provide a non-intimidating way to incorporate mathematical and computational concepts into a class with students who have a limited mathematical background. Second, we used the technology to mediate the use of simulations and modeling modules as a learning tool for traditional biological concepts, such as T cell differentiation or cell cycle regulation, in existing biology courses. Results of this pilot application suggest that there is promise in the use of computational modeling and software tools such as Cell Collective to provide new teaching methods in biology and contribute to the implementation of the "Vision and Change" call to action in undergraduate biology education by providing a hands-on approach to biology.

  7. Integrating interactive computational modeling in biology curricula.

    Science.gov (United States)

    Helikar, Tomáš; Cutucache, Christine E; Dahlquist, Lauren M; Herek, Tyler A; Larson, Joshua J; Rogers, Jim A

    2015-03-01

    While the use of computer tools to simulate complex processes such as computer circuits is normal practice in fields like engineering, the majority of life sciences/biological sciences courses continue to rely on the traditional textbook and memorization approach. To address this issue, we explored the use of the Cell Collective platform as a novel, interactive, and evolving pedagogical tool to foster student engagement, creativity, and higher-level thinking. Cell Collective is a Web-based platform used to create and simulate dynamical models of various biological processes. Students can create models of cells, diseases, or pathways themselves or explore existing models. This technology was implemented in both undergraduate and graduate courses as a pilot study to determine the feasibility of such software at the university level. First, a new (In Silico Biology) class was developed to enable students to learn biology by "building and breaking it" via computer models and their simulations. This class and technology also provide a non-intimidating way to incorporate mathematical and computational concepts into a class with students who have a limited mathematical background. Second, we used the technology to mediate the use of simulations and modeling modules as a learning tool for traditional biological concepts, such as T cell differentiation or cell cycle regulation, in existing biology courses. Results of this pilot application suggest that there is promise in the use of computational modeling and software tools such as Cell Collective to provide new teaching methods in biology and contribute to the implementation of the "Vision and Change" call to action in undergraduate biology education by providing a hands-on approach to biology.

  8. Bound water at protein-protein interfaces: partners, roles and hydrophobic bubbles as a conserved motif.

    Directory of Open Access Journals (Sweden)

    Mostafa H Ahmed

    Full Text Available There is a great interest in understanding and exploiting protein-protein associations as new routes for treating human disease. However, these associations are difficult to structurally characterize or model although the number of X-ray structures for protein-protein complexes is expanding. One feature of these complexes that has received little attention is the role of water molecules in the interfacial region.A data set of 4741 water molecules abstracted from 179 high-resolution (≤ 2.30 Å X-ray crystal structures of protein-protein complexes was analyzed with a suite of modeling tools based on the HINT forcefield and hydrogen-bonding geometry. A metric termed Relevance was used to classify the general roles of the water molecules.The water molecules were found to be involved in: a (bridging interactions with both proteins (21%, b favorable interactions with only one protein (53%, and c no interactions with either protein (26%. This trend is shown to be independent of the crystallographic resolution. Interactions with residue backbones are consistent for all classes and account for 21.5% of all interactions. Interactions with polar residues are significantly more common for the first group and interactions with non-polar residues dominate the last group. Waters interacting with both proteins stabilize on average the proteins' interaction (-0.46 kcal mol(-1, but the overall average contribution of a single water to the protein-protein interaction energy is unfavorable (+0.03 kcal mol(-1. Analysis of the waters without favorable interactions with either protein suggests that this is a conserved phenomenon: 42% of these waters have SASA ≤ 10 Å(2 and are thus largely buried, and 69% of these are within predominantly hydrophobic environments or "hydrophobic bubbles". Such water molecules may have an important biological purpose in mediating protein-protein interactions.

  9. Geodynamo Modeling of Core-Mantle Interactions

    Science.gov (United States)

    Kuang, Wei-Jia; Chao, Benjamin F.; Smith, David E. (Technical Monitor)

    2001-01-01

    Angular momentum exchange between the Earth's mantle and core influences the Earth's rotation on time scales of decades and longer, in particular in the length of day (LOD) which have been measured with progressively increasing accuracy for the last two centuries. There are four possible coupling mechanisms for transferring the axial angular momentum across the core-mantle boundary (CMB): viscous, magnetic, topography, and gravitational torques. Here we use our scalable, modularized, fully dynamic geodynamo model for the core to assess the importance of these torques. This numerical model, as an extension of the Kuang-Bloxham model that has successfully simulated the generation of the Earth's magnetic field, is used to obtain numerical results in various physical conditions in terms of specific parameterization consistent with the dynamical processes in the fluid outer core. The results show that depending on the electrical conductivity of the lower mantle and the amplitude of the boundary topography at CMB, both magnetic and topographic couplings can contribute significantly to the angular momentum exchange. This implies that the core-mantle interactions are far more complex than has been assumed and that there is unlikely a single dominant coupling mechanism for the observed decadal LOD variation.

  10. Interaction of elaiophylin with model bilayer membrane

    Science.gov (United States)

    Genova, J.; Dencheva-Zarkova, M.

    2017-01-01

    Elaiophylin is a new macrodiolide antibiotic, which is produced by the Streptomyces strains [1]. It displays biological activities against Gram-positive bacteria and fungi. The mode of action of this antibiotic has been attributed to an alteration of the membrane permeability. When this antibiotic is inserted into the bilayer membranes destabilization of the membrane and formation of ion-penetrable channels is observed. The macrodiolide antibiotic forms stable cation selective ion channels in synthetic lipid bilayer membranes. The aim of this work was to study the interactions of Elaiophylin with model bilayer membranes and to get information on the mechanical properties of lipid bilayers in presence of this antibiotic. Patch-clamp technique [2] were used in the study

  11. Neutron matter with a model interaction

    International Nuclear Information System (INIS)

    Amusia, M.Ya.; Shaginyan, V.R.

    2000-01-01

    An infinite system of neutrons interacting by a model pair potential is considered. We investigate a case when this potential is sufficiently strong attractive, so that its scattering length a tends to infinity, a →-∞. It appeared, that if the structure of the potential is simple enough, including no finite parameters, reliable evidences can be presented that such a system is completely unstable at any finite density. The incompressibility as a function of the density is negative, reaching zero value when the density tends to zero. If the potential contains a sufficiently strong repulsive core then the system possesses an equilibrium density. The main features of a theory describing such systems are considered. (orig.)

  12. Neutron matter with a model interaction

    Energy Technology Data Exchange (ETDEWEB)

    Amusia, M.Ya. [Hebrew Univ., Jerusalem (Israel). Racah Inst. of Physics; A.F. Ioffe Physical-Technical Institute, 194021 St. Petersburg (Russian Federation); Shaginyan, V.R. [Petersburg Institute of Nuclear Physics, 188350 Gatchina (Russian Federation); Department of Physics, University of Washington, Seattle, WA 98195 (United States)

    2000-05-01

    An infinite system of neutrons interacting by a model pair potential is considered. We investigate a case when this potential is sufficiently strong attractive, so that its scattering length a tends to infinity, a {yields}-{infinity}. It appeared, that if the structure of the potential is simple enough, including no finite parameters, reliable evidences can be presented that such a system is completely unstable at any finite density. The incompressibility as a function of the density is negative, reaching zero value when the density tends to zero. If the potential contains a sufficiently strong repulsive core then the system possesses an equilibrium density. The main features of a theory describing such systems are considered. (orig.)

  13. sdg Interacting boson model: two nucleon transfer

    International Nuclear Information System (INIS)

    Devi, Y.D.; Kota, V.K.B.

    1996-01-01

    A brief overview of the sdg interacting boson model (sdg IBM) is given. The two examples: (i) spectroscopic properties (spectra, B(E2)s, B(E4)s etc) of the rotor-γ unstable transitional Os-Pt isotopes and (ii) the analytical formulation of two nucleon transfer spectroscopic factors and sum-rule quantities are described in detail. They demonstrate that sdg IBM can be employed for systematic description of spectroscopic properties of nuclei and that large number of analytical formulas, which facilitate rapid analysis of data and provide a clear insight into the underlying structures, can be derived using sdg IBM dynamical symmetries respectively. (author). 24 refs., 5 figs., 3 tabs

  14. Hydrophobic patches on protein surfaces

    NARCIS (Netherlands)

    Lijnzaad, P.

    2007-01-01

    Hydrophobicity is a prime determinant of the structure and function of proteins. It is the driving force behind the folding of soluble proteins, and when exposed on the surface, it is frequently involved in recognition and binding of ligands and other proteins. The energetic cost of

  15. Breakout character of islet amyloid polypeptide hydrophobic mutations at the onset of type-2 diabetes

    Science.gov (United States)

    Frigori, Rafael B.

    2014-11-01

    Toxic fibrillar aggregates of islet amyloid polypeptide (IAPP) appear as the physical outcome of a peptidic phase transition signaling the onset of type-2 diabetes mellitus in different mammalian species. In particular, experimentally verified mutations on the amyloidogenic segment 20-29 in humans, cats, and rats are highly correlated with the molecular aggregation propensities. Through a microcanonical analysis of the aggregation of IAPP20 -29 isoforms, we show that a minimalist one-bead hydrophobic-polar continuum model for protein interactions properly quantifies those propensities from free-energy barriers. Our results highlight the central role of sequence-dependent hydrophobic mutations on hot spots for stabilization, and thus for the engineering, of such biological peptides.

  16. Institute for Multiscale Modeling of Biological Interactions

    Energy Technology Data Exchange (ETDEWEB)

    Paulaitis, Michael E; Garcia-Moreno, Bertrand; Lenhoff, Abraham

    2009-12-26

    The Institute for Multiscale Modeling of Biological Interactions (IMMBI) has two primary goals: Foster interdisciplinary collaborations among faculty and their research laboratories that will lead to novel applications of multiscale simulation and modeling methods in the biological sciences and engineering; and Building on the unique biophysical/biology-based engineering foundations of the participating faculty, train scientists and engineers to apply computational methods that collectively span multiple time and length scales of biological organization. The success of IMMBI will be defined by the following: Size and quality of the applicant pool for pre-doctoral and post-doctoral fellows; Academic performance; Quality of the pre-doctoral and post-doctoral research; Impact of the research broadly and to the DOE (ASCR program) mission; Distinction of the next career step for pre-doctoral and post-doctoral fellows; and Faculty collaborations that result from IMMBI activities. Specific details about accomplishments during the three years of DOE support for IMMBI have been documented in Annual Progress Reports (April 2005, June 2006, and March 2007) and a Report for a National Academy of Sciences Review (October 2005) that were submitted to DOE on the dates indicated. An overview of these accomplishments is provided.

  17. Are N-methyl groups of Tetramethylurea (TMU) Hydrophobic? A ...

    Indian Academy of Sciences (India)

    of three dimensional tetrahedral H-bond network to two dimensional zig-zag chain-like structure often found in alcohols. A comparison to ... All these results indicate hydrophobic interaction-induced aggregation of TMU in dilute aqueous solutions which .... off by gently blowing hot air around the outer surface of the cuvette.

  18. Measuring hydrophobic micropore volumes in geosorbents from trichloroethylene desorption data.

    Science.gov (United States)

    Cheng, Hefa; Reinhard, Martin

    2006-06-01

    Hydrophobic micropores can play a significant role in controlling the long-term release of organic contaminants from geosorbents. We describe a technique for quantifying the total and the hydrophobic mineral micropore volumes based on the mass of trichloroethylene (TCE) sorbed in the slow-releasing pores under dry and wet conditions, respectively. Micropore desorption models were used to differentiate the fast- and slow-desorbing fractions in desorption profiles. The micropore environment in which organic molecules were sorbed in the presence of water was probed by studying the transformation of a water-reactive compound (2,2-dichloropropane or 2,2-DCP). For sediment from an alluvial aquifer, the total and hydrophobic micropore volumes estimated using this technique were 4.65 microL/g and 0.027 microL/g (0.58% of total), respectively. In microporous silica gel A, a hydrophobic micropore volume of 0.038 microL/g (0.035% of reported total) was measured. The dehydrohalogenation rate of 2,2-DCP sorbed in hydrophobic micropores of the sediment was slower than that reported in bulk water, indicating an environment of low water activity. The results suggest that hydrolyzable organic contaminants sorbed in hydrophobic micropores react slower than in bulk water, consistent with the reported persistence of reactive contaminants in natural soils.

  19. Matrix models with Penner interaction inspired by interacting ...

    Indian Academy of Sciences (India)

    distribution of structure with temperature calculated from the NL model .... where φi are the random Hermitian matrices of size (N × N) placed at each base position ..... PB thanks UGC for research fellowships and ND thanks CSIR Project No.

  20. Transparent Hydrophobic Coating by Sol Gel Method

    International Nuclear Information System (INIS)

    Mohd Hamzah Harun; Nik Ghazali Nik Salleh; Mahathir Mohamed; Mohd Sofian Alias

    2016-01-01

    Transparent hydrophobic coating of inorganic based tetra orthosilicate (TEOS) was prepared by sol gel method by varying fluoroalkylsilane (FAS) content which works as hydrophobic agent. Surface contact angle, transmittance degree and surface morphology were characterized for each sample. All samples show good transparency which was confirmed by UV visible spectroscopy. The hydrophobicity obtained increases with FAS content indicates that FAS is best candidate to induce hydrophobicity for inorganic coating. (author)

  1. 21 CFR 584.700 - Hydrophobic silicas.

    Science.gov (United States)

    2010-04-01

    ...) Product. Amorphous fumed hydrophobic silica or precipitated hydrophobic silica (CAS Reg. No. 68611-0944... 21 Food and Drugs 6 2010-04-01 2010-04-01 false Hydrophobic silicas. 584.700 Section 584.700 Food... DRUGS, FEEDS, AND RELATED PRODUCTS FOOD SUBSTANCES AFFIRMED AS GENERALLY RECOGNIZED AS SAFE IN FEED AND...

  2. Hydrophobic Calcium Carbonate for Cement Surface

    Directory of Open Access Journals (Sweden)

    Shashi B. Atla

    2017-12-01

    Full Text Available This report describes a novel way to generate a highly effective hydrophobic cement surface via a carbonation route using sodium stearate. Carbonation reaction was carried out at different temperatures to investigate the hydrophobicity and morphology of the calcium carbonate formed with this process. With increasing temperatures, the particles changed from irregular shapes to more uniform rod-like structures and then aggregated to form a plate-like formation. The contact angle against water was found to increase with increasing temperature; after 90 °C there was no further increase. The maximum contact angle of 129° was obtained at the temperature of 60 °C. It was also found that carbonation increased the micro hardness of the cement material. The micro hardness was found to be dependent on the morphology of the CaCO3 particles. The rod like structures which caused increased mineral filler produced a material with enhanced strength. The 13C cross polarization magic-angle spinning NMR spectra gave plausible explanation of the interaction of organic-inorganic moieties.

  3. Rheological Properties in Aqueous Solution for Hydrophobically Modified Polyacrylamides Prepared in Inverse Emulsion Polymerization

    Directory of Open Access Journals (Sweden)

    Shirley Carro

    2017-01-01

    Full Text Available Inverse emulsion polymerization technique was employed to synthesize hydrophobically modified polyacrylamide polymers with hydrophobe contents near to feed composition. Three different structures were obtained: multisticker, telechelic, and combined. N-Dimethyl-acrylamide (DMAM, n-dodecylacrylamide (DAM, and n-hexadecylacrylamide (HDAM were used as hydrophobic comonomers. The effect of the hydrophobe length of comonomer, the initial monomer, and surfactant concentrations on shear viscosity was studied. Results show that the molecular weight of copolymer increases with initial monomer concentration and by increasing emulsifier concentration it remained almost constant. Shear viscosity measurements results show that the length of the hydrophobic comonomer augments the hydrophobic interactions causing an increase in viscosity and that the polymer thickening ability is higher for combined polymers.

  4. Improved gel electrophoresis matrix for hydrophobic protein separation and identification.

    Science.gov (United States)

    Tokarski, Caroline; Fillet, Marianne; Rolando, Christian

    2011-03-01

    We propose an improved acrylamide gel for the separation of hydrophobic proteins. The separation strategy is based on the incorporation of N-alkylated and N,N'-dialkylated acrylamide monomers in the gel composition in order to increase hydrophobic interactions between the gel matrix and the membrane proteins. Focusing on the most efficient monomer, N,N'-dimethylacrylamide, the potentiality of the new matrix was evaluated on membrane proteins of the human colon HCT-116 cell line. Protein analysis was performed using an adapted analytical strategy based on FT-ICR tandem mass spectrometry. As a result of this comparative study, including advanced reproducibility experiments, more hydrophobic proteins were identified in the new gel (average GRAVY: -0.085) than in the classical gel (average GRAVY: -0.411). Highly hydrophobic peptides were identified reaching a GRAVY value up to 1.450, therefore indicating their probable locations in the membrane. Focusing on predicted transmembrane domains, it can be pointed out that 27 proteins were identified in the hydrophobic gel containing up to 11 transmembrane domains; in the classical gel, only 5 proteins containing 1 transmembrane domain were successfully identified. For example, multiple ionic channels and receptors were characterized in the hydrophobic gel such as the sodium/potassium channel and the glutamate or the transferrin receptors whereas they are traditionally detected using specific enrichment techniques such as immunoprecipitation. In total, membrane proteins identified in the classical gel are well documented in the literature, while most of the membrane proteins only identified on the hydrophobic gel have rarely or never been described using a proteomic-based approach. 2010 Elsevier Inc. All rights reserved.

  5. Modeling of interactions between nanoparticles and cell membranes

    Science.gov (United States)

    Ban, Young-Min

    Rapid development of nanotechnology and ability to manufacture materials and devices with nanometer feature size leads to exciting innovations in many areas including the medical and electronic fields. However, the possible health and environmental impacts of manufactured nanomaterials are not fully known. Recent experimental reports suggest that some of the manufactured nanomaterials, such as fullerenes and carbon nanotubes, are highly toxic even in small concentrations. The goal of the current work is to understand the mechanisms responsible for the toxicity of nanomaterials. In the current study coarse-grained molecular dynamics simulations are employed to investigate the interactions between NPs and cellular membranes at a molecular level. One of the possible toxicity mechanisms of the nanomaterials is membrane disruption. Possibility of membrane disruption exposed to the manufactured nanomaterials are examined by considering chemical reactions and non-reactive physical interactions as chemical as well as physical mechanisms. Mechanisms of transport of carbon-based nanoparticles (fullerene and its derivative) across a phospholipid bilayer are investigated. The free energy profile is obtained using constrained simulations. It is shown that the considered nanoparticles are hydrophobic and therefore they tend to reside in the interior of the lipid bilayer. In addition, the dynamics of the membrane fluctuations is significantly affected by the nanoparticles at the bilayer-water interface. The hydrophobic interaction between the particles and membrane core induces the strong coupling between the nanoparticle motion and membrane deformation. It is observed that the considered nanoparticles affect several physical properties of the membrane. The nanoparticles embedded into the membrane interior lead to the membrane softening, which becomes more significant with increase in CNT length and concentration. The lateral pressure profile and membrane energy in the membrane

  6. Hydrophobic environment is a key factor for the stability of thermophilic proteins.

    Science.gov (United States)

    Gromiha, M Michael; Pathak, Manish C; Saraboji, Kadhirvel; Ortlund, Eric A; Gaucher, Eric A

    2013-04-01

    The stability of thermophilic proteins has been viewed from different perspectives and there is yet no unified principle to understand this stability. It would be valuable to reveal the most important interactions for designing thermostable proteins for such applications as industrial protein engineering. In this work, we have systematically analyzed the importance of various interactions by computing different parameters such as surrounding hydrophobicity, inter-residue interactions, ion-pairs and hydrogen bonds. The importance of each interaction has been determined by its predicted relative contribution in thermophiles versus the same contribution in mesophilic homologues based on a dataset of 373 protein families. We predict that hydrophobic environment is the major factor for the stability of thermophilic proteins and found that 80% of thermophilic proteins analyzed showed higher hydrophobicity than their mesophilic counterparts. Ion pairs, hydrogen bonds, and interaction energy are also important and favored in 68%, 50%, and 62% of thermophilic proteins, respectively. Interestingly, thermophilic proteins with decreased hydrophobic environments display a greater number of hydrogen bonds and/or ion pairs. The systematic elimination of mesophilic proteins based on surrounding hydrophobicity, interaction energy, and ion pairs/hydrogen bonds, led to correctly identifying 95% of the thermophilic proteins in our analyses. Our analysis was also applied to another, more refined set of 102 thermophilic-mesophilic pairs, which again identified hydrophobicity as a dominant property in 71% of the thermophilic proteins. Further, the notion of surrounding hydrophobicity, which characterizes the hydrophobic behavior of residues in a protein environment, has been applied to the three-dimensional structures of elongation factor-Tu proteins and we found that the thermophilic proteins are enriched with a hydrophobic environment. The results obtained in this work highlight the

  7. Functionalized anatomical models for EM-neuron Interaction modeling

    Science.gov (United States)

    Neufeld, Esra; Cassará, Antonino Mario; Montanaro, Hazael; Kuster, Niels; Kainz, Wolfgang

    2016-06-01

    The understanding of interactions between electromagnetic (EM) fields and nerves are crucial in contexts ranging from therapeutic neurostimulation to low frequency EM exposure safety. To properly consider the impact of in vivo induced field inhomogeneity on non-linear neuronal dynamics, coupled EM-neuronal dynamics modeling is required. For that purpose, novel functionalized computable human phantoms have been developed. Their implementation and the systematic verification of the integrated anisotropic quasi-static EM solver and neuronal dynamics modeling functionality, based on the method of manufactured solutions and numerical reference data, is described. Electric and magnetic stimulation of the ulnar and sciatic nerve were modeled to help understanding a range of controversial issues related to the magnitude and optimal determination of strength-duration (SD) time constants. The results indicate the importance of considering the stimulation-specific inhomogeneous field distributions (especially at tissue interfaces), realistic models of non-linear neuronal dynamics, very short pulses, and suitable SD extrapolation models. These results and the functionalized computable phantom will influence and support the development of safe and effective neuroprosthetic devices and novel electroceuticals. Furthermore they will assist the evaluation of existing low frequency exposure standards for the entire population under all exposure conditions.

  8. Effect of hydrophobic groups on the adsorption conformation of modified polycarboxylate superplasticizer investigated by molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Hongxia [State Key Laboratory of High Performance Civil Engineering Materials, Nanjing 210008, Jiangsu (China); Jiangsu Sobute New Materials Co. Ltd., Nanjing 211103, Jiangsu (China); Wang, Yanwei, E-mail: wangyanwei@cnjsjk.cn [State Key Laboratory of High Performance Civil Engineering Materials, Nanjing 210008, Jiangsu (China); Jiangsu Sobute New Materials Co. Ltd., Nanjing 211103, Jiangsu (China); Yang, Yong; Shu, Xin; Yan, Han [State Key Laboratory of High Performance Civil Engineering Materials, Nanjing 210008, Jiangsu (China); Jiangsu Sobute New Materials Co. Ltd., Nanjing 211103, Jiangsu (China); Ran, Qianping, E-mail: qpran@cnjsjk.cn [State Key Laboratory of High Performance Civil Engineering Materials, Nanjing 210008, Jiangsu (China); Jiangsu Sobute New Materials Co. Ltd., Nanjing 211103, Jiangsu (China)

    2017-06-15

    Highlights: • Adsorption conformation of comb-like PCE was studied by all-atom MD simulations. • A comparison is made between vacuum-based and solution-based simulations. • Effects of hydrophobic modifications on adsorption properties are elucidated. - Abstract: All-atom molecular dynamics (MD) simulations were used to study the adsorption conformations of hydrophobically-modified comb-shaped polycarboxylate ether-based (PCE) superplasticizer molecules on a model surface of dicalcium silicate (C{sub 2}S) in vacuum and in an explicit solution, respectively. Three different hydrophobic modifying groups, namely, the ethyl group, the n-butyl group and the phenyl group, decorated to the backbone, were examined. Comparing the hydrophobically-modified PCEs to the unmodified one, differences were found in the binding energy, the adsorption conformation and the water density at the interface. The interaction between PCE molecules and C{sub 2}S was weakened in a solution with explicit solvents than that obtained from vacuum-based simulations. The presence of hydrophobic groups lowered the polymer-surface binding energy, decreased the radius of gyration (Rg) of the adsorbed polymer, increased the peak position in the heavy-atom density profiles in the direction perpendicular to the surface, and also caused the adsorbed conformations to be more globular in shape. The parallel and perpendicular components (relative to the surface plane) of the geometric sizes of the adsorbed polymers were calculated, and the results showed that the presence of hydrophobically modifying groups decreased the in-plane radius while increased the adsorption layer thickness compared to the unmodified control. The presence of PCEs perturbed the dense water layer above the C{sub 2}S surface and lowered the water density. Perturbations to the interfacial water density were found to correlate nicely with the adsorbed conformations of PCEs.

  9. Functional bacterial amyloid increases Pseudomonas biofilm hydrophobicity and stiffness

    DEFF Research Database (Denmark)

    Zeng, Guanghong; Vad, Brian S; Dueholm, Morten S

    2015-01-01

    The success of Pseudomonas species as opportunistic pathogens derives in great part from their ability to form stable biofilms that offer protection against chemical and mechanical attack. The extracellular matrix of biofilms contains numerous biomolecules, and it has recently been discovered...... that in Pseudomonas one of the components includes β-sheet rich amyloid fibrils (functional amyloid) produced by the fap operon. However, the role of the functional amyloid within the biofilm has not yet been investigated in detail. Here we investigate how the fap-based amyloid produced by Pseudomonas affects biofilm...... hydrophobicity and mechanical properties. Using atomic force microscopy imaging and force spectroscopy, we show that the amyloid renders individual cells more resistant to drying and alters their interactions with hydrophobic probes. Importantly, amyloid makes Pseudomonas more hydrophobic and increases biofilm...

  10. Hydrophobic-Core Microcapsules and Their Formation

    Science.gov (United States)

    Calle, Luz M. (Inventor); Li, Wenyan (Inventor); Buhrow, Jerry W. (Inventor); Jolley, Scott T. (Inventor)

    2016-01-01

    Hydrophobic-core microcapsules and methods of their formation are provided. A hydrophobic-core microcapsule may include a shell that encapsulates a hydrophobic substance with a core substance, such as dye, corrosion indicator, corrosion inhibitor, and/or healing agent, dissolved or dispersed therein. The hydrophobic-core microcapsules may be formed from an emulsion having hydrophobic-phase droplets, e.g., containing the core substance and shell-forming compound, dispersed in a hydrophilic phase. The shells of the microcapsules may be capable of being broken down in response to being contacted by an alkali, e.g., produced during corrosion, contacting the shell.

  11. Diameter-dependent hydrophobicity in carbon nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Kyakuno, Haruka, E-mail: h-kyakuno@kanagawa-u.ac.jp [Department of Physics, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji 192-0397 (Japan); Institute of Physics, Faculty of Engineering, Kanagawa University, Yokohama 221-8686 (Japan); Fukasawa, Mamoru; Ichimura, Ryota; Nakai, Yusuke; Maniwa, Yutaka, E-mail: maniwa@phys.se.tmu.ac.jp [Department of Physics, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji 192-0397 (Japan); Matsuda, Kazuyuki [Institute of Physics, Faculty of Engineering, Kanagawa University, Yokohama 221-8686 (Japan); Miyata, Yasumitsu [Department of Physics, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji 192-0397 (Japan); PRESTO, JST, Kawaguchi 332-0012 (Japan); Saito, Takeshi [Nanotube Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8565 (Japan)

    2016-08-14

    Single-wall carbon nanotubes (SWCNTs) are a good model system that provides atomically smooth nanocavities. It has been reported that water-SWCNTs exhibit hydrophobicity depending on the temperature T and the SWCNT diameter D. SWCNTs adsorb water molecules spontaneously in their cylindrical pores around room temperature, whereas they exhibit a hydrophilic-hydrophobic transition or wet-dry transition (WDT) at a critical temperature T{sub wd} ≈ 220-230 K and above a critical diameter D{sub c} ≈ 1.4-1.6 nm. However, details of the WDT phenomenon and its mechanism remain unknown. Here, we report a systematic experimental study involving X-ray diffraction, optical microscopy, and differential scanning calorimetry. It is found that water molecules inside thick SWCNTs (D > D{sub c}) evaporate and condense into ice Ih outside the SWCNTs at T{sub wd} upon cooling, and the ice Ih evaporates and condenses inside the SWCNTs upon heating. On the other hand, residual water trapped inside the SWCNTs below T{sub wd} freezes. Molecular dynamics simulations indicate that upon lowering T, the hydrophobicity of thick SWCNTs increases without any structural transition, while the water inside thin SWCNTs (D < D{sub c}) exhibits a structural transition, forming an ordered ice. This ice has a well-developed hydrogen bonding network adapting to the cylindrical pores of the SWCNTs. Thus, the unusual diameter dependence of the WDT is attributed to the adaptability of the structure of water to the pore dimension and shape.

  12. Computational Modelling of Dapsone Interaction With Dihydropteroate Synthase in Mycobacterium leprae; Insights Into Molecular Basis of Dapsone Resistance in Leprosy.

    Science.gov (United States)

    Chaitanya V, Sundeep; Das, Madhusmita; Bhat, Pritesh; Ebenezer, Mannam

    2015-10-01

    The molecular basis for determination of resistance to anti-leprosy drugs is the presence of point mutations within the genes of Mycobacterium leprae (M. leprae) that encode active drug targets. The downstream structural and functional implications of these point mutations on drug targets were scarcely studied. In this study, we utilized computational tools to develop native and mutant protein models for 5 point mutations at codon positions 53 and 55 in 6-hydroxymethyl-7, 8-dihydropteroate synthase (DHPS) of M. leprae, an active target for dapsone encoded by folp1 gene, that confer resistance to dapsone. Molecular docking was performed to identify variations in dapsone interaction with mutant DHPS in terms of hydrogen bonding, hydrophobic interactions, and energy changes. Schrodinger Suite 2014-3 was used to build homology models and in performing molecular docking. An increase in volume of the binding cavities of mutant structures was noted when compared to native form indicating a weakening in interaction (60.7 Å(3) in native vs. 233.6 Å(3) in Thr53Ala, 659.9 Å(3) in Thr53Ile, 400 Å(3) for Thr53Val, 385 Å(3) for Pro55Arg, and 210 Å(3) for Pro55Leu). This was also reflected by changes in hydrogen bonds and decrease in hydrophobic interactions in the mutant models. The total binding energy (ΔG) decreased significantly in mutant forms when compared to the native form (-51.92 Kcal/mol for native vs. -35.64, -35.24, -46.47, -47.69, and -41.36 Kcal/mol for mutations Thr53Ala, Thr53Ile, Thr53Val, Pro55Arg, and Pro55Leu, respectively. In brief, this analysis provided structural and mechanistic insights to the degree of dapsone resistance contributed by each of these DHPS mutants in leprosy. © 2015 Wiley Periodicals, Inc.

  13. Quantum dynamics modeled by interacting trajectories

    Science.gov (United States)

    Cruz-Rodríguez, L.; Uranga-Piña, L.; Martínez-Mesa, A.; Meier, C.

    2018-03-01

    We present quantum dynamical simulations based on the propagation of interacting trajectories where the effect of the quantum potential is mimicked by effective pseudo-particle interactions. The method is applied to several quantum systems, both for bound and scattering problems. For the bound systems, the quantum ground state density and zero point energy are shown to be perfectly obtained by the interacting trajectories. In the case of time-dependent quantum scattering, the Eckart barrier and uphill ramp are considered, with transmission coefficients in very good agreement with standard quantum calculations. Finally, we show that via wave function synthesis along the trajectories, correlation functions and energy spectra can be obtained based on the dynamics of interacting trajectories.

  14. In silico modelling of drug–polymer interactions for pharmaceutical formulations

    Science.gov (United States)

    Ahmad, Samina; Johnston, Blair F.; Mackay, Simon P.; Schatzlein, Andreas G.; Gellert, Paul; Sengupta, Durba; Uchegbu, Ijeoma F.

    2010-01-01

    Selecting polymers for drug encapsulation in pharmaceutical formulations is usually made after extensive trial and error experiments. To speed up excipient choice procedures, we have explored coarse-grained computer simulations (dissipative particle dynamics (DPD) and coarse-grained molecular dynamics using the MARTINI force field) of polymer–drug interactions to study the encapsulation of prednisolone (log p = 1.6), paracetamol (log p = 0.3) and isoniazid (log p = −1.1) in poly(l-lactic acid) (PLA) controlled release microspheres, as well as the encapsulation of propofol (log p = 4.1) in bioavailability enhancing quaternary ammonium palmitoyl glycol chitosan (GCPQ) micelles. Simulations have been compared with experimental data. DPD simulations, in good correlation with experimental data, correctly revealed that hydrophobic drugs (prednisolone and paracetamol) could be encapsulated within PLA microspheres and predicted the experimentally observed paracetamol encapsulation levels (5–8% of the initial drug level) in 50 mg ml−1 PLA microspheres, but only when initial paracetamol levels exceeded 5 mg ml−1. However, the mesoscale technique was unable to model the hydrophilic drug (isoniazid) encapsulation (4–9% of the initial drug level) which was observed in experiments. Molecular dynamics simulations using the MARTINI force field indicated that the self-assembly of GCPQ is rapid, with propofol residing at the interface between micellar hydrophobic and hydrophilic groups, and that there is a heterogeneous distribution of propofol within the GCPQ micelle population. GCPQ–propofol experiments also revealed a population of relatively empty and drug-filled GCPQ particles. PMID:20519214

  15. Exploring the mechanism of interaction between sulindac and human serum albumin: Spectroscopic and molecular modeling methods

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Xiao-Ping; Hou, Ya-He [Department of Material Engineering, Xuzhou College of Industrial Technology, Xuzhou, Jiangsu 221140 (China); Wang, Li [Department of Chemistry, College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou, Hubei 434023 (China); Zhang, Ye-Zhong, E-mail: zhangfluorescence@126.com [Department of Chemistry, College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou, Hubei 434023 (China); Liu, Yi, E-mail: prof.liuyi@263.net [Department of Chemistry, College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou, Hubei 434023 (China); College of Chemistry and Molecular Sciences and State Key Laboratory of Virology, Wuhan University, Wuhan 430072 (China)

    2013-06-15

    In the present study, a combination of fluorescence, molecular modeling and circular dichroism (CD) approaches had been employed to investigate the interaction between sulindac and human serum albumin (HSA). Results of mechanism discussion demonstrated that the fluorescence quenching of HSA by sulindac was a static quenching procedure. Binding parameters calculated from the modified Stern–Volmer equation showed that sulindac bound to HSA with the binding affinities in the order of 10{sup 5} L mol{sup −1}. The thermodynamic parameters (ΔH=−18.58 kJ mol{sup −1}; ΔS=37.26 J mol{sup −1} K{sup −1}) obtained by the van′t Hoff equation revealed that hydrophobic forces played a leading role in the formation of sulindac–HSA complex, but hydrogen bonds could not be omitted. Site marker competitive experiments revealed a displacement of warfarin by sulindac, which indicated that the binding site of sulindac to HSA located in the sub-domain IIA (Sudlow′s site I). The molecular docking study confirmed the specific binding mode and binding site obtained by fluorescence and site marker competitive experiments. CD and three-dimensional fluorescence spectroscopy were used to investigate the changes of HSA secondary structure and microenvironment in the presence of sulindac. Alterations of HSA conformation were observed with the reduction of α-helix from 60.1% (free HSA) to 57.3%, manifesting a slight unfolding of the polypeptides of protein. -- Highlights: ► The quenching mechanism between sulindac and HSA is a static process. ► The binding of sulindac to HSA takes place in sub-domain IIA (Sudlow′s site I). ► The binding is spontaneous and hydrophobic force plays major role in stabilizing the complex. ► CD and 3-D fluorescence spectra prove the change of the microenvironment and conformation of HSA.

  16. Hydrophobic perfluoro-silane functionalization of porous silicon photoluminescent films and particles

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez, C.; Laplace, P.; Gallach-Pérez, D.; Pellacani, P.; Martín-Palma, R.J. [Departamento de Física Aplicada e Instituto de Ciencia de Materiales Nicolás Cabrera, Universidad Autónoma de Madrid, 28049, Madrid (Spain); Torres-Costa, V. [Departamento de Física Aplicada e Instituto de Ciencia de Materiales Nicolás Cabrera, Universidad Autónoma de Madrid, 28049, Madrid (Spain); Centro de Microanálisis de Materiales, Universidad Autónoma de Madrid, 28049, Madrid (Spain); Ceccone, G. [European Commission, Joint Research Centre, Institute for Health and Consumer Protection, 21020, Ispra (Italy); Manso Silván, M., E-mail: miguel.manso@uam.es [Departamento de Física Aplicada e Instituto de Ciencia de Materiales Nicolás Cabrera, Universidad Autónoma de Madrid, 28049, Madrid (Spain)

    2016-09-01

    Highlights: • Hydrophobic functionalization of porous silicon structures. • Perfluorooctyl group binding confirmed by XPS. • Improved stability face to extreme oxidation conditions. • Perfluorooctyl functionalization compatible with photoluminescence of porous silicon particles. - Abstract: Luminescent structures based on semiconductor quantum dots (QDs) are increasingly used in biomolecular assays, cell tracking systems, and in-vivo diagnostics devices. In this work we have carried out the functionalization of porous silicon (PSi) luminescent structures by a perfluorosilane (Perfluoro-octyltriethoxysilane, PFOS) self assembly. The PFOS surface binding (traced by X-ray photoelectron spectroscopy) and photoluminescence efficiency were analyzed on flat model PSi. Maximal photoluminescence intensity was obtained from PSi layers anodized at 110 mA/cm{sup 2}. Resistance to hydroxylation was assayed in H{sub 2}O{sub 2}:ethanol solutions and evidenced by water contact angle (WCA) measurements. PFOS-functionalized PSi presented systematically higher WCA than untreated PSi. The PFOS functionalization was found to slightly improve the aging of the PSi particles in water giving rise to particles with longer luminescent life. Confirmation of PFOS binding to PSi particles was derived from FTIR spectra and the preservation of luminescence was observed by fluorescence microscopy. Such functionalization opens the possibility of promoting hydrophobic-hydrophobic interactions between biomolecules and fluorescent QD structures, which may enlarge their biomedical applications catalogue.

  17. Modelling microbial interactions and food structure in predictive microbiology

    NARCIS (Netherlands)

    Malakar, P.K.

    2002-01-01

    Keywords: modelling, dynamic models, microbial interactions, diffusion, microgradients, colony growth, predictive microbiology.

    Growth response of microorganisms in foods is a complex process. Innovations in food production and preservation techniques have resulted in adoption of

  18. Influence of hydrophobic modification in alginate-based hydrogels for biomedical applications

    Science.gov (United States)

    Choudhary, Soumitra

    Alginate has been exploited commercially for decades in foods, textiles, paper, pharmaceutical industries, and also as a detoxifier for removing heavy metals. Alginate is also popular in cell encapsulation because of its relatively mild gelation protocol and simple chemistry with which biological active entities can be immobilized. Surface modification of alginate gels has been explored to induce desired cell interactions with the gel matrix. These modifications alter the bulk properties, which strongly determine on how cells feel and response to the three-dimensional microenvironment. However, there is a need to develop strategies to engineer functionalities into bulk alginate hydrogels that not only preserve their inherent qualities but are also less toxic. In this thesis, our main focus was to optimize the mechanical properties of alginate-based hydrogels, and by doing so control the performance of the biomaterials. In the first scheme, we used alginate and hydrophobically modified ethyl hydroxy ethyl cellulose as components in interpenetrating polymer network (IPN) gels. The second network was used to control gelation time and rheological properties. We believe these experiments also may provide insight into the mechanical and structural properties of more complex biopolymer gels and naturally-occurring IPNs. Next, we worked on incorporating a hydrophobic moiety directly into the alginate chain, resulting in materials for extended release of hydrophobic drugs. We successfully synthesized hydrophobically modified alginate (HMA) by attaching octylamine groups onto the alginate backbone by standard carbodiimide based amide coupling reaction. Solubility of several model hydrophobic drugs in dilute HMA solutions was found to be increased by more than an order of magnitude. HMA hydrogels, prepared by crosslinking the alginate chains with calcium ions, were found to exhibit excellent mechanical properties (modulus ˜100 kPa) with release extended upto 5 days. Ability

  19. In-line gas chromatographic apparatus for measuring the hydrophobic micropore volume (HMV) and contaminant transformation in mineral micropores

    International Nuclear Information System (INIS)

    Cheng Hefa; Reinhard, Martin

    2010-01-01

    Desorption of hydrophobic organic compounds from micropores is characteristically slow compared to surface adsorption and partitioning. The slow-desorbing mass of a hydrophobic probe molecule can be used to calculate the hydrophobic micropore volume (HMV) of microporous solids. A gas chromatographic apparatus is described that allows characterization of the sorbed mass with respect to the desorption rate. The method is demonstrated using a dealuminated zeolite and an aquifer sand as the model and reference sorbents, respectively, and trichloroethylene (TCE) as the probe molecule. A glass column packed with the microporous sorbent is coupled directly to a gas chromatograph that is equipped with flame ionization and electron capture detectors. Sorption and desorption of TCE on the sorbent was measured by sampling the influent and effluent of the column using a combination of switching and injection valves. For geosorbents, the HMV is quantified based on Gurvitsch's rule from the mass of TCE desorbed at a rate that is characteristic for micropores. Instrumental requirements, design considerations, hardware details, detector calibration, performance, and data analysis are discussed along with applications. The method is novel and complements traditional vacuum gravimetric and piezometric techniques, which quantify the total pore volume under vacuum conditions. The HMV is more relevant than the total micropore volume for predicting the fate and transport of organic contaminants in the subsurface. Sorption in hydrophobic micropores strongly impacts the mobility of organic contaminants, and their chemical and biological transformations. The apparatus can serve as a tool for characterizing microprous solids and investigating contaminant-solid interactions.

  20. On the intracellular release mechanism of hydrophobic cargo and its relation to the biodegradation behavior of mesoporous silica nanocarriers.

    Science.gov (United States)

    von Haartman, Eva; Lindberg, Desiré; Prabhakar, Neeraj; Rosenholm, Jessica M

    2016-12-01

    The intracellular release mechanism of hydrophobic molecules from surface-functionalized mesoporous silica nanoparticles was studied in relation to the biodegradation behavior of the nanocarrier, with the purpose of determining the dominant release mechanism for the studied drug delivery system. To be able to follow the real-time intracellular release, a hydrophobic fluorescent dye was used as model drug molecule. The in vitro release of the dye was investigated under varying conditions in terms of pH, polarity, protein and lipid content, presence of hydrophobic structures and ultimately, in live cancer cells. Results of investigating the drug delivery system show that the degradation and drug release mechanisms display a clear interdependency in simple aqueous solvents. In pure aqueous media, the cargo release was primarily dependent on the degradation of the nanocarrier, while in complex media, mimicking intracellular conditions, the physicochemical properties of the cargo molecule itself and its interaction with the carrier and/or surrounding media were found to be the main release-governing factors. Since the material degradation was retarded upon loading with hydrophobic guest molecules, the cargo could be efficiently delivered into live cancer cells and released intracellularly without pronounced premature release under extracellular conditions. From a rational design point of view, pinpointing the interdependency between these two processes can be of paramount importance considering future applications and fundamental understanding of the drug delivery system. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. Open Interactivity: A Model for Audience Agency

    Directory of Open Access Journals (Sweden)

    Charlotte Gould

    2018-04-01

    Full Text Available Artists have increasingly acknowledged the role of the audience as collaborators both in the construction of meaning (Bathes, 1977, through subjective experience (Dewey, 1934 and in contributing to the creative act by externalising the work. (Duchamp Lucy Lippard identifies 1966-72 as a period where artists turned increasingly towards the audience, representing a "dematerialization of the art object" (Lippard, 1997 through "Happenings" and "Fluxus" movements. Digital media has facilitated this trajectory, implicit in the interactive computer interface (Manovich, 2005, but interactivity per se may offer no more than a series of choices put forward by the artist (Daniels, 2011. Interactivity represents interplay between artist and audience (Dinka, 1996 and is potentially a process of audience empowerment to offer agency, defined as real and creative choice (Browning, 1964. Public screen installation "Peoples Screen" Guangzhou, linking China to Perth Australia (Sermon & Gould, 2015 offered a partnership between artist and audience to co-create content though playful narratives and active engagement in a drama that unfolds using improvisation and play. Initially visitors enjoy observing the self on the screen but audiences quickly start to interact with the environment and other participants. Immersed in play they lose a sense of the self (Callois, 2011 and enter a virtual third space where possibilities for creativity and direction of play are limitless. The self becomes an avatar where the audience can inhabit "the other" thereby exploring alternative realities through ludic play, promoting tolerance and empathy and developing collective memory.

  2. Modelling interactions in grass-clover mixtures

    NARCIS (Netherlands)

    Nassiri Mahallati, M.

    1998-01-01

    The study described in this thesis focuses on a quantitative understanding of the complex interactions in binary mixtures of perennial ryegrass (Lolium perenne L.) and white clover (Trifolium repens L.) under cutting. The first part of the study describes the dynamics of growth, production

  3. Guided interaction exploration in artifact-centric process models

    NARCIS (Netherlands)

    van Eck, M.L.; Sidorova, N.; van der Aalst, W.M.P.

    2017-01-01

    Artifact-centric process models aim to describe complex processes as a collection of interacting artifacts. Recent development in process mining allow for the discovery of such models. However, the focus is often on the representation of the individual artifacts rather than their interactions. Based

  4. Interactive wood combustion for botanical tree models

    KAUST Repository

    Pirk, Sö ren; Jarząbek, Michał; Hadrich, Torsten; Michels, Dominik L.; Palubicki, Wojciech

    2017-01-01

    We present a novel method for the combustion of botanical tree models. Tree models are represented as connected particles for the branching structure and a polygonal surface mesh for the combustion. Each particle stores biological and physical

  5. Five challenges in modelling interacting strain dynamics

    DEFF Research Database (Denmark)

    Wikramaratna, Paul S; Kurcharski, Adam; Gupta, Sunetra

    2015-01-01

    population models. Next we consider the nature of so-called “strain space”. We describe two key types of host heterogeneities, and explain how models could help generate a better understanding of their effects. Finally, for diseases with many strains, we consider the challenge of modelling how immunity...

  6. Contemporary Ecological Interactions Improve Models of Past Trait Evolution.

    Science.gov (United States)

    Hutchinson, Matthew C; Gaiarsa, Marília P; Stouffer, Daniel B

    2018-02-20

    Despite the fact that natural selection underlies both traits and interactions, evolutionary models often neglect that ecological interactions may, and in many cases do, influence the evolution of traits. Here, we explore the interdependence of ecological interactions and functional traits in the pollination associations of hawkmoths and flowering plants. Specifically, we develop an adaptation of the Ornstein-Uhlenbeck model of trait evolution that allows us to study the influence of plant corolla depth and observed hawkmoth-plant interactions on the evolution of hawkmoth proboscis length. Across diverse modelling scenarios, we find that the inclusion of contemporary interactions can provide a better description of trait evolution than the null expectation. Moreover, we show that the pollination interactions provide more-likely models of hawkmoth trait evolution when interactions are considered at increasingly finescale groups of hawkmoths. Finally, we demonstrate how the results of best-fit modelling approaches can implicitly support the association between interactions and trait evolution that our method explicitly examines. In showing that contemporary interactions can provide insight into the historical evolution of hawkmoth proboscis length, we demonstrate the clear utility of incorporating additional ecological information to models designed to study past trait evolution.

  7. Interacting holographic dark energy models: a general approach

    Science.gov (United States)

    Som, S.; Sil, A.

    2014-08-01

    Dark energy models inspired by the cosmological holographic principle are studied in homogeneous isotropic spacetime with a general choice for the dark energy density . Special choices of the parameters enable us to obtain three different holographic models, including the holographic Ricci dark energy (RDE) model. Effect of interaction between dark matter and dark energy on the dynamics of those models are investigated for different popular forms of interaction. It is found that crossing of phantom divide can be avoided in RDE models for β>0.5 irrespective of the presence of interaction. A choice of α=1 and β=2/3 leads to a varying Λ-like model introducing an IR cutoff length Λ -1/2. It is concluded that among the popular choices an interaction of the form Q∝ Hρ m suits the best in avoiding the coincidence problem in this model.

  8. User Interaction Modeling and Profile Extraction in Interactive Systems: A Groupware Application Case Study †

    Science.gov (United States)

    Tîrnăucă, Cristina; Duque, Rafael; Montaña, José L.

    2017-01-01

    A relevant goal in human–computer interaction is to produce applications that are easy to use and well-adjusted to their users’ needs. To address this problem it is important to know how users interact with the system. This work constitutes a methodological contribution capable of identifying the context of use in which users perform interactions with a groupware application (synchronous or asynchronous) and provides, using machine learning techniques, generative models of how users behave. Additionally, these models are transformed into a text that describes in natural language the main characteristics of the interaction of the users with the system. PMID:28726762

  9. Five challenges in modelling interacting strain dynamics

    Directory of Open Access Journals (Sweden)

    Paul S. Wikramaratna

    2015-03-01

    Full Text Available Population epidemiological models where hosts can be infected sequentially by different strains have the potential to help us understand many important diseases. Researchers have in recent years started to develop and use such models, but the extra layer of complexity from multiple strains brings with it many technical challenges. It is therefore hard to build models which have realistic assumptions yet are tractable. Here we outline some of the main challenges in this area. First we begin with the fundamental question of how to translate from complex small-scale dynamics within a host to useful population models. Next we consider the nature of so-called “strain space”. We describe two key types of host heterogeneities, and explain how models could help generate a better understanding of their effects. Finally, for diseases with many strains, we consider the challenge of modelling how immunity accumulates over multiple exposures.

  10. Supersymmetric models of weak and electromagnetic interactions

    International Nuclear Information System (INIS)

    Egoryan, Eh.; Slavnov, A.A.

    1978-01-01

    Examples of realistic supergauge lepton models based on the SU(2)xU(1) and SU(2)xSU(2)xU(1) groups are considered. These models do not contradict to up-to-date experimental data, give a natural explanation for the Higgs mechanism and predict the existence of heavy leptons. The first model predicts the conservation of parity, the second one predicts parity breaking in atomic processes

  11. Supporting inquiry and modelling with interactive drawings

    NARCIS (Netherlands)

    van Joolingen, Wouter

    2012-01-01

    Creating models is at the heart of any scientific endeavor and therefore should have a place in science curricula. However, creating computer-based models faces resistance in early science education because of the difficulty to create the formal representations required by computational systems. In

  12. Models of πNN interactions

    International Nuclear Information System (INIS)

    Lee, T.S.H.

    1988-01-01

    A πNN model inspired by Quantum Chromodynamics is presented. The model gives an accurate fit to the most recent Arndt NN phase shifts up to 1 GeV and can be applied to study intermediate- and high-energy nuclear reactions. 20 refs., 2 figs

  13. Modeling techniques and fluorescence imaging investigation of the interactions of an anthraquinone derivative with HSA and ctDNA

    Science.gov (United States)

    Fu, Zheng; Cui, Yanrui; Cui, Fengling; Zhang, Guisheng

    2016-01-01

    A new anthraquinone derivative (AORha) was synthesized. Its interactions with human serum albumin (HSA) and calf thymus DNA (ctDNA) were investigated by fluorescence spectroscopy, UV-visible absorption spectroscopy and molecular modeling. Cell viability assay and cell imaging experiment were performed using cervical cancer cells (HepG2 cells). The fluorescence results revealed that the quenching mechanism was static quenching. At different temperatures (290, 300, 310 K), the binding constants (K) and the number of binding sites (n) were determined, respectively. The positive ΔH and ΔS values showed that the binding of AORha with HSA was hydrophobic force, which was identical with the molecular docking result. Studying the fluorescence spectra, UV spectra and molecular modeling also verified that the binding mode of AORha and ctDNA might be intercalative. When HepG2 cells were treated with AORha, the fluorescence became brighter and turned green, which could be used for bioimaging.

  14. Investigations on the interactions of diclofenac sodium with HSA and ctDNA using molecular modeling and multispectroscopic methods

    Science.gov (United States)

    Cui, Yanrui; Hao, Erjun; Hui, Guangquan; Guo, Wei; Cui, Fengling

    2013-06-01

    A tentative study on interaction of diclofenac sodium (DF-Na) with human serum albumin (HSA) and calf thymus DNA (ctDNA) was conducted by using multi-spectroscopic and molecular modeling techniques under simulative physiological conditions. The results of spectroscopic measurements suggested that the quenching mechanisms were static quenching. Three-dimensional fluorescence spectroscopy clearly demonstrated the occurrence of conformational changes of HSA with addition of DF-Na. In addition, competitive studies with ethidium bromide (EB) have shown that DF-Na can bind to ctDNA relatively strong via groove binding. Based on the values of thermodynamic parameters and the results of molecular modeling, it was confirmed that hydrophobic forces and hydrogen bond were the mainly binding forces in DF-Na-HSA and DF-Na-DNA systems. The binding distance between DF-Na and HSA was also determined using the theory of the Förster energy transference.

  15. Interaction and transport of cysteamine (MEA) through membrane models. {sup 15}N-NMR et {sup 1}H-NMR; Interaction et transport de la cysteamine (MEA) a travers des membranes modeles. Etude par {sup 15}N-RMN et {sup 1}H-RMN

    Energy Technology Data Exchange (ETDEWEB)

    Lagoueyte, C.; Subra, G.; Bonnet, P.A.; Chapat, J.P.; Debouzy, J.C.; Fauvelle, F.; Berleur, F.; Roman, V.; Fatome, M.; Fernandez, J.P.

    1995-12-31

    We investigated by {sup 15}N-NMR the interactions of [{sup 15}N]-MEA, a radio-protecting aminothiol, with model membranes (SUVs and LUVs) of egg yolk phosphatidylcholine and phosphatidic acid. We prepared LUVs with a pH gradient between the intravesicular space and the bulk medium. Even though the external pH was low, MEA penetrates into the vesicles. With SUVs, {sup 1}H-NMR revealed that the interactions of unlabeled MEA within the hydrophobic core of the bilayer vary with external pH value. (author). 5 refs.

  16. ADDIE Model Application Promoting Interactive Multimedia

    Science.gov (United States)

    Baharuddin, B.

    2018-02-01

    This paper presents the benefits of interactive learning in a vocational high school, which is developed by Research and Developmet (R&D) method. The questionnaires, documentations, and instrument tests are used to obtain data and it is analyzed by descriptive statistic. The results show the students’ competence is generated up to 80.00 %, and the subject matter aspects of the content is up to 90.00 %. The learning outcomes average is 85. This type media fulfils the proposed objective which can enhance the learning outcome.

  17. Study of the Deformation/Interaction Model: How Interactions Increase the Reaction Barrier

    Directory of Open Access Journals (Sweden)

    Zhiling Liang

    2018-01-01

    Full Text Available The interactions (including weak interactions between dienophiles and dienes play an important role in the Diels-Alder reaction. To elucidate the influence of these interactions on the reactivity, a popular DFT functional and a variational DFT functional corrected with dispersion terms are used to investigate different substituent groups incorporated on the dienophiles and dienes. The bond order is used to track the trajectory of the cycloaddition reaction. The deformation/interaction model is used to obtain the interaction energy from the reactant complex to the inflection point until reaching the saddle point. The interaction energy initially increases with a decrease in the interatomic distance, reaching a maximum value, but then decreases when the dienophiles and dienes come closer. Reduced density gradient and chemical energy component analysis are used to analyse the interaction. Traditional transition state theory and variational transition state theory are used to obtain the reaction rates. The influence of tunneling on the reaction rate is also discussed.

  18. Toward a Simple Molecular Theory of Hydrophobic Hydration.

    Czech Academy of Sciences Publication Activity Database

    Jirsák, Jan; Škvor, J.; Nezbeda, Ivo

    2014-01-01

    Roč. 189, SI (2014), s. 13-19 ISSN 0167-7322 R&D Projects: GA AV ČR IAA200760905 Institutional support: RVO:67985858 Keywords : perturbation theory * primitive models * hydrophobic hydration Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 2.515, year: 2014

  19. Effects of solute--solvent attractive forces on hydrophobic correlations

    International Nuclear Information System (INIS)

    Pratt, L.R.; Chandler, D.

    1980-01-01

    A theory is presented for the effect of slowly varying attractive forces on correlations between nonpolar solutes in dilute aqueous solution. We find that hydrophobic correlations are sensitive to relatively long range slowly varying interactions. Thus, it is possible to make qualitative changes in these correlations by introducing small changes in the attractive forces. Several model calculations are presented to illustrate these facts. The contributions of the Lennard-Jones attractive forces to the computer simulation results of Pangali, Rao, and Berne are calculated. For this case it is found that the potential of mean force between spherical nonpolar solutes is hardly affected by inclusion of attractive forces. However, the osmotic second virial coefficient is dominated by the contributions of the attractive forces. For spherical solutes which provide a reasonable model for the methane molecule, inclusion of attractive forces produces a qualitative change in the methane--methane potential of mean force. The connection between these effects of slowly varying attractive forces and the enthalpic part of Ben-Naim's deltaA/sup H/I is discussed

  20. Modeling of Interactions of Ablated Plumes

    National Research Council Canada - National Science Library

    Povitsky, Alex

    2008-01-01

    Heat transfer modulation between the gas flow and the Thermal Protection Shield (TPS) that occurs because of ejection of under-expanded pyrolysis gases through the cracks in the TPS is studied by numerical modeling...

  1. Some dynamical aspects of interacting quintessence model

    Indian Academy of Sciences (India)

    Binayak S Choudhury

    2018-03-16

    Mar 16, 2018 ... Accelerated expansion of the Universe; quintessence; dynamical system; Friedmann–Lemaitre–. Robertson–Walker ... accepted theoretical model. One of the .... Thus, quintessence loses its self-strength and gives dark matter.

  2. Utilitarian supersymmetric gauge model of particle interactions

    International Nuclear Information System (INIS)

    Ma, Ernest

    2010-01-01

    A remarkabale U(1) gauge extension of the supersymmetric standard model was proposed 8 years ago. It is anomaly free, has no μ term, and conserves baryon and lepton numbers automatically. The phenomenology of a specific version of this model is discussed. In particular, leptoquarks are predicted, with couplings to the heavy singlet neutrinos, the scalar partners of which may be components of dark matter. The Majorana neutrino mass matrix itself may have two zero subdeterminants.

  3. Preliminary model for core/concrete interactions

    International Nuclear Information System (INIS)

    Murfin, W.B.

    1977-08-01

    A preliminary model is described for computing the rate of penetration of concrete by a molten LWR core. Among the phenomena included are convective stirring of the melt by evolved gases, admixture of concrete decomposition products to the melt, chemical reactions, radiative heat loss, and variation of heat transfer coefficients with local pressure. The model is most applicable to a two-phase melt (metallic plus oxidic) having a fairly high metallic content

  4. Vector condensate model of electroweak interactions

    International Nuclear Information System (INIS)

    Cynolter, G.; Pocsik, G.

    1997-01-01

    Motivated by the fact that the Higgs is not seen, a new version of the standard model is proposed where the scalar doublet is replaced by a vector doublet and its neutral member forms a nonvanishing condensate. Gauge fields are coupled to the new vector fields B in a gauge invariant way leading to mass terms for the gauge fields by condensation. The model is presented and some implications are discussed. (K.A.)

  5. Pedagogical Interaction in High School, the Structural and Functional Model of Pedagogical Interaction

    Science.gov (United States)

    Semenova, Larissa A.; Kazantseva, Anastassiya I.; Sergeyeva, Valeriya V.; Raklova, Yekaterina M.; Baiseitova, Zhanar B.

    2016-01-01

    The study covers the problems of pedagogical technologies and their experimental implementation in the learning process. The theoretical aspects of the "student-teacher" interaction are investigated. A structural and functional model of pedagogical interaction is offered, which determines the conditions for improving pedagogical…

  6. Approaches to modelling hydrology and ecosystem interactions

    Science.gov (United States)

    Silberstein, Richard P.

    2014-05-01

    As the pressures of industry, agriculture and mining on groundwater resources increase there is a burgeoning un-met need to be able to capture these multiple, direct and indirect stresses in a formal framework that will enable better assessment of impact scenarios. While there are many catchment hydrological models and there are some models that represent ecological states and change (e.g. FLAMES, Liedloff and Cook, 2007), these have not been linked in any deterministic or substantive way. Without such coupled eco-hydrological models quantitative assessments of impacts from water use intensification on water dependent ecosystems under changing climate are difficult, if not impossible. The concept would include facility for direct and indirect water related stresses that may develop around mining and well operations, climate stresses, such as rainfall and temperature, biological stresses, such as diseases and invasive species, and competition such as encroachment from other competing land uses. Indirect water impacts could be, for example, a change in groundwater conditions has an impact on stream flow regime, and hence aquatic ecosystems. This paper reviews previous work examining models combining ecology and hydrology with a view to developing a conceptual framework linking a biophysically defensable model that combines ecosystem function with hydrology. The objective is to develop a model capable of representing the cumulative impact of multiple stresses on water resources and associated ecosystem function.

  7. Multispectroscopic and molecular modeling approach to investigate the interaction of diclofop-methyl enantiomers with human serum albumin

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Ping; Liu, Donghui; Li, Zhe; Shen, Zhigang; Wang, Peng [Department of Applied Chemistry, China Agricultural University, Beijing 100193 (China); Zhou, Meng [Business School, University of Bedfordshire, Luton LU1 3JU (United Kingdom); Zhou, Zhiqiang [Department of Applied Chemistry, China Agricultural University, Beijing 100193 (China); Zhu, Wentao, E-mail: wentaozhu@cau.edu.cn [Department of Applied Chemistry, China Agricultural University, Beijing 100193 (China)

    2014-11-15

    Pesticides and related environmental contaminants have always been threated to human health due to their intrinsic toxicity. In the context of this contribution, the interaction between diclofop-methyl (DM) enantiomers and human serum albumin (HSA) has been characterized by steady state and three-dimensional fluorescence, molecular modeling, circular dichroism (CD) and ultraviolet–visible (UV–vis) spectroscopy. The binding constants significantly showed the binding was enantioselective and HSA had higher affinity for S-DM. The thermodynamic parameters of the binding reaction (ΔG, ΔH and ΔS) clearly signified that hydrophobic effects and H-bonds contribute to the formation of DM-HSA complex. The alterations of protein secondary structure in the presence of DM enantiomers were confirmed by CD spectroscopy, UV–vis and three-dimensional fluorescence spectroscopy. In addition, both fluorescence probe study and molecular modeling simulation evidenced the binding of DM enantiomers to HSA primarily took place in subdomain IIIA (Sudlow's site II). This investigation highlights the binding mechanism, specific binding sites and binding region of DM enantiomers on human serum albumin at the first time. Besides, such task can provide important insight to the interaction of the physiological protein HSA with chiral aryloxyphenoxypropionate herbicides and give support to the human health risk assessment. - Highlights: • The binding of DM enantiomers to HSA was enantioselective. • HSA had higher affinity for S-DM than R-DM. • Hydrophobic effects and hydrogen bonds were involved in the DM-HSA interaction. • The binding of DM enantiomers to HSA primarily took place in Sudlow's site II. • DM enantiomers could alter the second structure of HSA.

  8. Multispectroscopic and molecular modeling approach to investigate the interaction of diclofop-methyl enantiomers with human serum albumin

    International Nuclear Information System (INIS)

    Zhang, Ping; Liu, Donghui; Li, Zhe; Shen, Zhigang; Wang, Peng; Zhou, Meng; Zhou, Zhiqiang; Zhu, Wentao

    2014-01-01

    Pesticides and related environmental contaminants have always been threated to human health due to their intrinsic toxicity. In the context of this contribution, the interaction between diclofop-methyl (DM) enantiomers and human serum albumin (HSA) has been characterized by steady state and three-dimensional fluorescence, molecular modeling, circular dichroism (CD) and ultraviolet–visible (UV–vis) spectroscopy. The binding constants significantly showed the binding was enantioselective and HSA had higher affinity for S-DM. The thermodynamic parameters of the binding reaction (ΔG, ΔH and ΔS) clearly signified that hydrophobic effects and H-bonds contribute to the formation of DM-HSA complex. The alterations of protein secondary structure in the presence of DM enantiomers were confirmed by CD spectroscopy, UV–vis and three-dimensional fluorescence spectroscopy. In addition, both fluorescence probe study and molecular modeling simulation evidenced the binding of DM enantiomers to HSA primarily took place in subdomain IIIA (Sudlow's site II). This investigation highlights the binding mechanism, specific binding sites and binding region of DM enantiomers on human serum albumin at the first time. Besides, such task can provide important insight to the interaction of the physiological protein HSA with chiral aryloxyphenoxypropionate herbicides and give support to the human health risk assessment. - Highlights: • The binding of DM enantiomers to HSA was enantioselective. • HSA had higher affinity for S-DM than R-DM. • Hydrophobic effects and hydrogen bonds were involved in the DM-HSA interaction. • The binding of DM enantiomers to HSA primarily took place in Sudlow's site II. • DM enantiomers could alter the second structure of HSA

  9. Ferromagnetic interaction model of activity level in workplace communication

    Science.gov (United States)

    Akitomi, Tomoaki; Ara, Koji; Watanabe, Jun-ichiro; Yano, Kazuo

    2013-03-01

    The nature of human-human interaction, specifically, how people synchronize with each other in multiple-participant conversations, is described by a ferromagnetic interaction model of people’s activity levels. We found two microscopic human interaction characteristics from a real-environment face-to-face conversation. The first characteristic is that people quite regularly synchronize their activity level with that of the other participants in a conversation. The second characteristic is that the degree of synchronization increases as the number of participants increases. Based on these microscopic ferromagnetic characteristics, a “conversation activity level” was modeled according to the Ising model. The results of a simulation of activity level based on this model well reproduce macroscopic experimental measurements of activity level. This model will give a new insight into how people interact with each other in a conversation.

  10. Non-perturbative effective interactions in the standard model

    CERN Document Server

    Arbuzov, Boris A

    2014-01-01

    This monograph is devoted to the nonperturbative dynamics in the Standard Model (SM), the basic theory of all, but gravity, fundamental interactions in nature. The Standard Model is devided into two parts: the Quantum chromodynamics (QCD) and the Electro-weak theory (EWT) are well-defined renormalizable theories in which the perturbation theory is valid. However, for the adequate description of the real physics nonperturbative effects are inevitable. This book describes how these nonperturbative effects may be obtained in the framework of spontaneous generation of effective interactions. The well-known example of such effective interaction is provided by the famous Nambu--Jona-Lasinio effective interaction. Also a spontaneous generation of this interaction in the framework of QCD is described and applied to the method for other effective interactions in QCD and EWT. The method is based on N.N. Bogoliubov conception of compensation equations. As a result we then describe the principle feathures of the Standard...

  11. Targeting of the hydrophobic metabolome by pathogens.

    Science.gov (United States)

    Helms, J Bernd; Kaloyanova, Dora V; Strating, Jeroen R P; van Hellemond, Jaap J; van der Schaar, Hilde M; Tielens, Aloysius G M; van Kuppeveld, Frank J M; Brouwers, Jos F

    2015-05-01

    The hydrophobic molecules of the metabolome - also named the lipidome - constitute a major part of the entire metabolome. Novel technologies show the existence of a staggering number of individual lipid species, the biological functions of which are, with the exception of only a few lipid species, unknown. Much can be learned from pathogens that have evolved to take advantage of the complexity of the lipidome to escape the immune system of the host organism and to allow their survival and replication. Different types of pathogens target different lipids as shown in interaction maps, allowing visualization of differences between different types of pathogens. Bacterial and viral pathogens target predominantly structural and signaling lipids to alter the cellular phenotype of the host cell. Fungal and parasitic pathogens have complex lipidomes themselves and target predominantly the release of polyunsaturated fatty acids from the host cell lipidome, resulting in the generation of eicosanoids by either the host cell or the pathogen. Thus, whereas viruses and bacteria induce predominantly alterations in lipid metabolites at the host cell level, eukaryotic pathogens focus on interference with lipid metabolites affecting systemic inflammatory reactions that are part of the immune system. A better understanding of the interplay between host-pathogen interactions will not only help elucidate the fundamental role of lipid species in cellular physiology, but will also aid in the generation of novel therapeutic drugs. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  12. Bayesian network model for identification of pathways by integrating protein interaction with genetic interaction data.

    Science.gov (United States)

    Fu, Changhe; Deng, Su; Jin, Guangxu; Wang, Xinxin; Yu, Zu-Guo

    2017-09-21

    Molecular interaction data at proteomic and genetic levels provide physical and functional insights into a molecular biosystem and are helpful for the construction of pathway structures complementarily. Despite advances in inferring biological pathways using genetic interaction data, there still exists weakness in developed models, such as, activity pathway networks (APN), when integrating the data from proteomic and genetic levels. It is necessary to develop new methods to infer pathway structure by both of interaction data. We utilized probabilistic graphical model to develop a new method that integrates genetic interaction and protein interaction data and infers exquisitely detailed pathway structure. We modeled the pathway network as Bayesian network and applied this model to infer pathways for the coherent subsets of the global genetic interaction profiles, and the available data set of endoplasmic reticulum genes. The protein interaction data were derived from the BioGRID database. Our method can accurately reconstruct known cellular pathway structures, including SWR complex, ER-Associated Degradation (ERAD) pathway, N-Glycan biosynthesis pathway, Elongator complex, Retromer complex, and Urmylation pathway. By comparing N-Glycan biosynthesis pathway and Urmylation pathway identified from our approach with that from APN, we found that our method is able to overcome its weakness (certain edges are inexplicable). According to underlying protein interaction network, we defined a simple scoring function that only adopts genetic interaction information to avoid the balance difficulty in the APN. Using the effective stochastic simulation algorithm, the performance of our proposed method is significantly high. We developed a new method based on Bayesian network to infer detailed pathway structures from interaction data at proteomic and genetic levels. The results indicate that the developed method performs better in predicting signaling pathways than previously

  13. Descriptor Data Bank (DDB): A Cloud Platform for Multiperspective Modeling of Protein-Ligand Interactions.

    Science.gov (United States)

    Ashtawy, Hossam M; Mahapatra, Nihar R

    2018-01-22

    Protein-ligand (PL) interactions play a key role in many life processes such as molecular recognition, molecular binding, signal transmission, and cell metabolism. Examples of interaction forces include hydrogen bonding, hydrophobic effects, steric clashes, electrostatic contacts, and van der Waals attractions. Currently, a large number of hypotheses and perspectives to model these interaction forces are scattered throughout the literature and largely forgotten. Instead, had they been assembled and utilized collectively, they would have substantially improved the accuracy of predicting binding affinity of protein-ligand complexes. In this work, we present Descriptor Data Bank (DDB), a data-driven platform on the cloud for facilitating multiperspective modeling of PL interactions. DDB is an open-access hub for depositing, hosting, executing, and sharing descriptor extraction tools and data for a large number of interaction modeling hypotheses. The platform also implements a machine-learning (ML) toolbox for automatic descriptor filtering and analysis and scoring function (SF) fitting and prediction. The descriptor filtering module is used to filter out irrelevant and/or noisy descriptors and to produce a compact subset from all available features. We seed DDB with 16 diverse descriptor extraction tools developed in-house and collected from the literature. The tools altogether generate over 2700 descriptors that characterize (i) proteins, (ii) ligands, and (iii) protein-ligand complexes. The in-house descriptors we extract are protein-specific which are based on pairwise primary and tertiary alignment of protein structures followed by clustering and trilateration. We built and used DDB's ML library to fit SFs to the in-house descriptors and those collected from the literature. We then evaluated them on several data sets that were constructed to reflect real-world drug screening scenarios. We found that multiperspective SFs that were constructed using a large number

  14. A Statistical Model for Soliton Particle Interaction in Plasmas

    DEFF Research Database (Denmark)

    Dysthe, K. B.; Pécseli, Hans; Truelsen, J.

    1986-01-01

    A statistical model for soliton-particle interaction is presented. A master equation is derived for the time evolution of the particle velocity distribution as induced by resonant interaction with Korteweg-de Vries solitons. The detailed energy balance during the interaction subsequently determines...... the evolution of the soliton amplitude distribution. The analysis applies equally well for weakly nonlinear plasma waves in a strongly magnetized waveguide, or for ion acoustic waves propagating in one-dimensional systems....

  15. New analytically solvable models of relativistic point interactions

    International Nuclear Information System (INIS)

    Gesztesy, F.; Seba, P.

    1987-01-01

    Two new analytically solvable models of relativistic point interactions in one dimension (being natural extensions of the nonrelativistic δ-resp, δ'-interaction) are considered. Their spectral properties in the case of finitely many point interactions as well as in the periodic case are fully analyzed. Moreover the spectrum is explicitely determined in the case of independent, identically distributed random coupling constants and the analog of the Saxon and Huther conjecture concerning gaps in the energy spectrum of such systems is derived

  16. Robust predictions of the interacting boson model

    International Nuclear Information System (INIS)

    Casten, R.F.; Koeln Univ.

    1994-01-01

    While most recognized for its symmetries and algebraic structure, the IBA model has other less-well-known but equally intrinsic properties which give unavoidable, parameter-free predictions. These predictions concern central aspects of low-energy nuclear collective structure. This paper outlines these ''robust'' predictions and compares them with the data

  17. Modeling Group Interactions via Open Data Sources

    Science.gov (United States)

    2011-08-30

    data. The state-of-art search engines are designed to help general query-specific search and not suitable for finding disconnected online groups. The...groups, (2) developing innovative mathematical and statistical models and efficient algorithms that leverage existing search engines and employ

  18. Interactive Character Deformation Using Simplified Elastic Models

    NARCIS (Netherlands)

    Luo, Z.

    2016-01-01

    This thesis describes the results of our research into realistic skin and model deformation methods aimed at the field of character deformation and animation. The main contributions lie in the properties of our deformation scheme. Our approach preserves the volume of the deformed object while

  19. Object interaction competence model v. 2.0

    DEFF Research Database (Denmark)

    Bennedsen, Jens; Schulte, C.

    2013-01-01

    Teaching and learning object oriented programming has to take into account the specific object oriented characteristics of program execution, namely the interaction of objects during runtime. Prior to the research reported in this article, we have developed a competence model for object interaction...

  20. Approximate Solutions of Interactive Dynamic Influence Diagrams Using Model Clustering

    DEFF Research Database (Denmark)

    Zeng, Yifeng; Doshi, Prashant; Qiongyu, Cheng

    2007-01-01

    Interactive dynamic influence diagrams (I-DIDs) offer a transparent and semantically clear representation for the sequential decision-making problem over multiple time steps in the presence of other interacting agents. Solving I-DIDs exactly involves knowing the solutions of possible models...

  1. Bilingual Lexical Interactions in an Unsupervised Neural Network Model

    Science.gov (United States)

    Zhao, Xiaowei; Li, Ping

    2010-01-01

    In this paper we present an unsupervised neural network model of bilingual lexical development and interaction. We focus on how the representational structures of the bilingual lexicons can emerge, develop, and interact with each other as a function of the learning history. The results show that: (1) distinct representations for the two lexicons…

  2. Modelling dynamic human-device interaction in healthcare

    OpenAIRE

    Niezen, Gerrit

    2013-01-01

    Errors are typically blamed on human factors, forgetting that the system should have been designed to take them into account and minimise these problems. In our research we are developing tools to design interactive medical devices using human-in-the-loop modelling. Manual control theory is used to describe and analyse the dynamic aspects of human-device interaction.

  3. Levels of Interaction Provided by Online Distance Education Models

    Science.gov (United States)

    Alhih, Mohammed; Ossiannilsson, Ebba; Berigel, Muhammet

    2017-01-01

    Interaction plays a significant role to foster usability and quality in online education. It is one of the quality standard to reveal the evidence of practice in online distance education models. This research study aims to evaluate levels of interaction in the practices of distance education centres. It is aimed to provide online distance…

  4. HPMA-based block copolymers promote differential drug delivery kinetics for hydrophobic and amphiphilic molecules.

    Science.gov (United States)

    Tomcin, Stephanie; Kelsch, Annette; Staff, Roland H; Landfester, Katharina; Zentel, Rudolf; Mailänder, Volker

    2016-04-15

    We describe a method how polymeric nanoparticles stabilized with (2-hydroxypropyl)methacrylamide (HPMA)-based block copolymers are used as drug delivery systems for a fast release of hydrophobic and a controlled release of an amphiphilic molecule. The versatile method of the miniemulsion solvent-evaporation technique was used to prepare polystyrene (PS) as well as poly-d/l-lactide (PDLLA) nanoparticles. Covalently bound or physically adsorbed fluorescent dyes labeled the particles' core and their block copolymer corona. Confocal laser scanning microscopy (CLSM) in combination with flow cytometry measurements were applied to demonstrate the burst release of a fluorescent hydrophobic drug model without the necessity of nanoparticle uptake. In addition, CLSM studies and quantitative calculations using the image processing program Volocity® show the intracellular detachment of the amphiphilic block copolymer from the particles' core after uptake. Our findings offer the possibility to combine the advantages of a fast release for hydrophobic and a controlled release for an amphiphilic molecule therefore pointing to the possibility to a 'multi-step and multi-site' targeting by one nanocarrier. We describe thoroughly how different components of a nanocarrier end up in cells. This enables different cargos of a nanocarrier having a consecutive release and delivery of distinct components. Most interestingly we demonstrate individual kinetics of distinct components of such a system: first the release of a fluorescent hydrophobic drug model at contact with the cell membrane without the necessity of nanoparticle uptake. Secondly, the intracellular detachment of the amphiphilic block copolymer from the particles' core after uptake occurs. This offers the possibility to combine the advantages of a fast release for a hydrophobic substance at the time of interaction of the nanoparticle with the cell surface and a controlled release for an amphiphilic molecule later on therefore

  5. AIC, BIC, Bayesian evidence against the interacting dark energy model

    Energy Technology Data Exchange (ETDEWEB)

    Szydlowski, Marek [Jagiellonian University, Astronomical Observatory, Krakow (Poland); Jagiellonian University, Mark Kac Complex Systems Research Centre, Krakow (Poland); Krawiec, Adam [Jagiellonian University, Institute of Economics, Finance and Management, Krakow (Poland); Jagiellonian University, Mark Kac Complex Systems Research Centre, Krakow (Poland); Kurek, Aleksandra [Jagiellonian University, Astronomical Observatory, Krakow (Poland); Kamionka, Michal [University of Wroclaw, Astronomical Institute, Wroclaw (Poland)

    2015-01-01

    Recent astronomical observations have indicated that the Universe is in a phase of accelerated expansion. While there are many cosmological models which try to explain this phenomenon, we focus on the interacting ΛCDM model where an interaction between the dark energy and dark matter sectors takes place. This model is compared to its simpler alternative - the ΛCDM model. To choose between these models the likelihood ratio test was applied as well as the model comparison methods (employing Occam's principle): the Akaike information criterion (AIC), the Bayesian information criterion (BIC) and the Bayesian evidence. Using the current astronomical data: type Ia supernova (Union2.1), h(z), baryon acoustic oscillation, the Alcock- Paczynski test, and the cosmic microwave background data, we evaluated both models. The analyses based on the AIC indicated that there is less support for the interacting ΛCDM model when compared to the ΛCDM model, while those based on the BIC indicated that there is strong evidence against it in favor of the ΛCDM model. Given the weak or almost non-existing support for the interacting ΛCDM model and bearing in mind Occam's razor we are inclined to reject this model. (orig.)

  6. AIC, BIC, Bayesian evidence against the interacting dark energy model

    Energy Technology Data Exchange (ETDEWEB)

    Szydłowski, Marek, E-mail: marek.szydlowski@uj.edu.pl [Astronomical Observatory, Jagiellonian University, Orla 171, 30-244, Kraków (Poland); Mark Kac Complex Systems Research Centre, Jagiellonian University, Reymonta 4, 30-059, Kraków (Poland); Krawiec, Adam, E-mail: adam.krawiec@uj.edu.pl [Institute of Economics, Finance and Management, Jagiellonian University, Łojasiewicza 4, 30-348, Kraków (Poland); Mark Kac Complex Systems Research Centre, Jagiellonian University, Reymonta 4, 30-059, Kraków (Poland); Kurek, Aleksandra, E-mail: alex@oa.uj.edu.pl [Astronomical Observatory, Jagiellonian University, Orla 171, 30-244, Kraków (Poland); Kamionka, Michał, E-mail: kamionka@astro.uni.wroc.pl [Astronomical Institute, University of Wrocław, ul. Kopernika 11, 51-622, Wrocław (Poland)

    2015-01-14

    Recent astronomical observations have indicated that the Universe is in a phase of accelerated expansion. While there are many cosmological models which try to explain this phenomenon, we focus on the interacting ΛCDM model where an interaction between the dark energy and dark matter sectors takes place. This model is compared to its simpler alternative—the ΛCDM model. To choose between these models the likelihood ratio test was applied as well as the model comparison methods (employing Occam’s principle): the Akaike information criterion (AIC), the Bayesian information criterion (BIC) and the Bayesian evidence. Using the current astronomical data: type Ia supernova (Union2.1), h(z), baryon acoustic oscillation, the Alcock–Paczynski test, and the cosmic microwave background data, we evaluated both models. The analyses based on the AIC indicated that there is less support for the interacting ΛCDM model when compared to the ΛCDM model, while those based on the BIC indicated that there is strong evidence against it in favor of the ΛCDM model. Given the weak or almost non-existing support for the interacting ΛCDM model and bearing in mind Occam’s razor we are inclined to reject this model.

  7. Quark compound bag (QCB) model and nucleon-nucleon interaction

    International Nuclear Information System (INIS)

    Simonov, Yu.A.

    1983-01-01

    Quark degrees of freedom are treated in the NN system in the framework of the QCB model. The resulting QCB potential is in agreement with experimental data. P-matrix analysis inherent to the QCB model is discussed in detail. Applications of the QCB model are given including the weak NN interaction

  8. AIC, BIC, Bayesian evidence against the interacting dark energy model

    International Nuclear Information System (INIS)

    Szydlowski, Marek; Krawiec, Adam; Kurek, Aleksandra; Kamionka, Michal

    2015-01-01

    Recent astronomical observations have indicated that the Universe is in a phase of accelerated expansion. While there are many cosmological models which try to explain this phenomenon, we focus on the interacting ΛCDM model where an interaction between the dark energy and dark matter sectors takes place. This model is compared to its simpler alternative - the ΛCDM model. To choose between these models the likelihood ratio test was applied as well as the model comparison methods (employing Occam's principle): the Akaike information criterion (AIC), the Bayesian information criterion (BIC) and the Bayesian evidence. Using the current astronomical data: type Ia supernova (Union2.1), h(z), baryon acoustic oscillation, the Alcock- Paczynski test, and the cosmic microwave background data, we evaluated both models. The analyses based on the AIC indicated that there is less support for the interacting ΛCDM model when compared to the ΛCDM model, while those based on the BIC indicated that there is strong evidence against it in favor of the ΛCDM model. Given the weak or almost non-existing support for the interacting ΛCDM model and bearing in mind Occam's razor we are inclined to reject this model. (orig.)

  9. Durability of hydrophobic treatment of concrete

    NARCIS (Netherlands)

    Vries, J. de; Polder, R.B.; Borsje, H.

    1998-01-01

    The subject of this study was the performance of hydrophobic treatment to protect concrete against chloride penetration from de-icing salts. Hydrophobic treatment makes a concrete surface absorb less water and less chloride. Test methods and requirements for commercial products were established. In

  10. Durability of hydrophobic treatment of concrete

    NARCIS (Netherlands)

    Vries, J. de; Polder, R.B.; Borsje, H.

    1998-01-01

    The subject of this study was the performance of hydrophobic treatment to protect concrete against chloride penetration from de-icing salts. Hydrophobic treatment makes a concrete surface absorb less water and less chloride. Several types of tests were carried out to study the performance of

  11. Studying the interaction between three synthesized heterocyclic sulfonamide compounds with hemoglobin by spectroscopy and molecular modeling techniques.

    Science.gov (United States)

    Naeeminejad, Samane; Assaran Darban, Reza; Beigoli, Sima; Saberi, Mohammad Reza; Chamani, Jamshidkhan

    2017-11-01

    The interaction between synthesized heterocyclic benzene sulfonamide compounds, N-(7-benzyl-56-biphenyl-2m-tolyl-7H-pyrrolo[23-d]pyrimidine-4-yl)-benzene sulfonamide (HBS 1 ), N-(7-benzyl-56-biphenyl-2-m-tolyl-7H-pyrrolo[23-d] pyrimidine-4-yl)-4-methyl- benzene sulfonamide (HBS 2 ), and N-(7-benzyl-56-biphenyl-2-m-tolyl-7H-pyrrolo[23-d]pyrimidine-4-yl)-4-chloro-benzene sulfonamide (HBS 3 ) with Hb was studied by fluorescence quenching, zeta potentional, circular dichroism, and molecular modeling techniques. The fluorescence spectroscopy experiments were performed in order to study the conformational changes, possibly due to a discrete reorganization of Trp residues during binding between HBS derivatives and Hb. The variation of the K SV value suggested that hydrophobic and electrostatic interactions were the predominant intermolecular forces stabilizing the complex. The K SV1 ans K SV2 values of HBS derivatives with Hb are .6 × 10 13 and 3 × 10 13  M -1 for Hb-HBS 1 , 1 × 10 13 and 4 × 10 13  M -1 for Hb-HBS 2 , .9 × 10 13 , and 6 × 10 13  M -1 for Hb-HBS 3 , respectively. The molecular distances between Hb and HBS derivatives in binary and ternary systems were estimated according to Förster's theory of dipole-dipole non-radiation energy transfer. The quantitative analysis data of circular dichroism spectra demonstrated that the binding of the three HBS derivatives to Hb induced conformational changes in Hb. Changes in the zeta potential of the Hb-HBS derivatives complexes demonstrated a hydrophobic adsorption of the anionic ligand onto the surface of Hb as well as both electrostatic and hydrophobic adsorption in the case of the complex. The modeling data thus confirmed the experimental results. This study is expected to provide important insight into the interaction of Hb with three HBS derivatives to use in various toxicological and therapeutic processes.

  12. Modelling of energetic molecule-surface interactions

    International Nuclear Information System (INIS)

    Kerford, M.

    2000-09-01

    This thesis contains the results of molecular dynamics simulations of molecule-surface interactions, looking particularly at fullerene molecules and carbon surfaces. Energetic impacts of fullerene molecules on graphite create defect craters. The relationship between the parameters of the impacting molecule and the parameters of the crater axe examined and found to be a function of the energy and velocity of the impacting molecule. Less energetic fullerene molecules can be scattered from a graphite surface and the partitioning of energy after a scattering event is investigated. It is found that a large fraction of the kinetic energy retained after impact is translational energy, with a small fraction of rotational energy and a number of vibrational modes. At impact energies where the surface is not broken and at normal incidence, surface waves axe seen to occur. These waves axe used to develop a method of desorbing molecules from a graphite surface without damage to either the surface or the molecules being desorbed. A number of fullerene molecules are investigated and ways to increase the desorption yield are examined. It is found that this is a successful technique for desorbing large numbers of intact molecules from graphite. This technique could be used for desorbing intact molecules into a gas phase for mass spectrometric analysis. (author)

  13. Study on competitive interaction models in Cayley tree

    International Nuclear Information System (INIS)

    Moreira, J.G.M.A.

    1987-12-01

    We propose two kinds of models in the Cayley tree to simulate Ising models with axial anisotropy in the cubic lattice. The interaction in the direction of the anisotropy is simulated by the interaction along the branches of the tree. The interaction in the planes perpendicular to the anisotropy direction, in the first model, is simulated by interactions between spins in neighbour branches of the same generation arising from same site of the previous generation. In the second model, the simulation of the interaction in the planes are produced by mean field interactions among all spins in sites of the same generation arising from the same site of the previous generations. We study these models in the limit of infinite coordination number. First, we analyse a situation with antiferromagnetic interactions along the branches between first neighbours only, and we find the analogous of a metamagnetic Ising model. In the following, we introduce competitive interactions between first and second neighbours along the branches, to simulate the ANNNI model. We obtain one equation of differences which relates the magnetization of one generation with the magnetization of the two previous generations, to permit a detailed study of the modulated phase region. We note that the wave number of the modulation, for one fixed temperature, changes with the competition parameter to form a devil's staircase with a fractal dimension which increases with the temperature. We discuss the existence of strange atractors, related to a possible caothic phase. Finally, we show the obtained results when we consider interactions along the branches with three neighbours. (author)

  14. Origins of protein denatured state compactness and hydrophobic clustering in aqueous urea: inferences from nonpolar potentials of mean force.

    Science.gov (United States)

    Shimizu, Seishi; Chan, Hue Sun

    2002-12-01

    Free energies of pairwise hydrophobic association are simulated in aqueous solutions of urea at concentrations ranging from 0-8 M. Consistent with the expectation that hydrophobic interactions are weakened by urea, the association of relatively large nonpolar solutes is destabilized by urea. However, the association of two small methane-sized nonpolar solutes in water has the opposite tendency of being slightly strengthened by the addition of urea. Such size effects and the dependence of urea-induced stability changes on the configuration of nonpolar solutes are not predicted by solvent accessible surface area approaches based on energetic parameters derived from bulk-phase solubilities of model compounds. Thus, to understand hydrophobic interactions in proteins, it is not sufficient to rely solely on transfer experiment data that effectively characterize a single nonpolar solute in an aqueous environment but not the solvent-mediated interactions among two or more nonpolar solutes. We find that the m-values for the rate of change of two-methane association free energy with respect to urea concentration is a dramatically nonmonotonic function of the spatial separation between the two methanes, with a distance-dependent profile similar to the corresponding two-methane heat capacity of association in pure water. Our results rationalize the persistence of residual hydrophobic contacts in some proteins at high urea concentrations and explain why the heat capacity signature (DeltaC(P)) of a compact denatured state can be similar to DeltaC(P) values calculated by assuming an open random-coil-like unfolded state. Copyright 2002 Wiley-Liss, Inc.

  15. Interactive Modelling and Simulation of Human Motion

    DEFF Research Database (Denmark)

    Engell-Nørregård, Morten Pol

    menneskers led, der udviser både ikke-konveksitet og flere frihedsgrader • En generel og alsidig model for aktivering af bløde legemer. Modellen kan anvendes som et animations værktøj, men er lige så velegnet til simulering af menneskelige muskler, da den opfylder de grundlæggende fysiske principper......Dansk resumé Denne ph.d.-afhandling beskæftiger sig med modellering og simulation af menneskelig bevægelse. Emnerne i denne afhandling har mindst to ting til fælles. For det første beskæftiger de sig med menneskelig bevægelse. Selv om de udviklede modeller også kan benyttes til andre ting,er det...... primære fokus på at modellere den menneskelige krop. For det andet, beskæftiger de sig alle med simulering som et redskab til at syntetisere bevægelse og dermed skabe animationer. Dette er en vigtigt pointe, da det betyder, at vi ikke kun skaber værktøjer til animatorer, som de kan bruge til at lave sjove...

  16. Interactive Coherence-Based Façade Modeling

    KAUST Repository

    Musialski, Przemyslaw; Wimmer, Michael; Wonka, Peter

    2012-01-01

    We propose a novel interactive framework for modeling building facades from images. Our method is based on the notion of coherence-based editing which allows exploiting partial symmetries across the facade at any level of detail. The proposed

  17. A mathematical model of tumor–immune interactions

    KAUST Repository

    Robertson-Tessi, Mark; El-Kareh, Ardith; Goriely, Alain

    2012-01-01

    the interactions between the cell populations. Decreased access of effector cells to the tumor interior with increasing tumor size is accounted for. The model is applied to tumors with different growth rates and antigenicities to gauge the relative importance

  18. An interactive web-based extranet system model for managing ...

    African Journals Online (AJOL)

    ... objectives for students, lecturers and parents to access and compute results ... The database will serve as repository of students' academic records over a ... Keywords: Extranet-Model, Interactive, Web-Based, Students, Academic, Records ...

  19. The lake foodweb: modelling predation and abiotic/biotic interactions

    National Research Council Canada - National Science Library

    Hakanson, L; Boulion, V.V

    2002-01-01

    .... The model is based on many new approaches of structuring lake foodweb interactions. It uses ordinary differential equations and gives weekly variations in production and biomass for its nine groups of organisms...

  20. Molecular dynamics modeling the synthetic and biological polymers interactions pre-studied via docking

    Science.gov (United States)

    Tsvetkov, Vladimir B.; Serbin, Alexander V.

    2014-06-01

    In previous works we reported the design, synthesis and in vitro evaluations of synthetic anionic polymers modified by alicyclic pendant groups (hydrophobic anchors), as a novel class of inhibitors of the human immunodeficiency virus type 1 ( HIV-1) entry into human cells. Recently, these synthetic polymers interactions with key mediator of HIV-1 entry-fusion, the tri-helix core of the first heptad repeat regions [ HR1]3 of viral envelope protein gp41, were pre-studied via docking in terms of newly formulated algorithm for stepwise approximation from fragments of polymeric backbone and side-group models toward real polymeric chains. In the present article the docking results were verified under molecular dynamics ( MD) modeling. In contrast with limited capabilities of the docking, the MD allowed of using much more large models of the polymeric ligands, considering flexibility of both ligand and target simultaneously. Among the synthesized polymers the dinorbornen anchors containing alternating copolymers of maleic acid were selected as the most representative ligands (possessing the top anti-HIV activity in vitro in correlation with the highest binding energy in the docking). To verify the probability of binding of the polymers with the [HR1]3 in the sites defined via docking, various starting positions of polymer chains were tried. The MD simulations confirmed the main docking-predicted priority for binding sites, and possibilities for axial and belting modes of the ligands-target interactions. Some newly MD-discovered aspects of the ligand's backbone and anchor units dynamic cooperation in binding the viral target clarify mechanisms of the synthetic polymers anti-HIV activity and drug resistance prevention.

  1. Dynamics of Wetting of Ultra Hydrophobic Surfaces

    Science.gov (United States)

    Mohammad Karim, Alireza; Kim, Jeong-Hyun; Rothstein, Jonathan; Kavehpour, Pirouz; Mechanical and Industrial Engineering, University of Massachusetts, Amherst Collaboration

    2013-11-01

    Controlling the surface wettability of hydrophobic and super hydrophobic surfaces has extensive industrial applications ranging from coating, painting and printing technology and waterproof clothing to efficiency increase in power and water plants. This requires enhancing the knowledge about the dynamics of wetting on these hydrophobic surfaces. We have done experimental investigation on the dynamics of wetting on hydrophobic surfaces by looking deeply in to the dependency of the dynamic contact angles both advancing and receding on the velocity of the three-phase boundary (Solid/Liquid/Gas interface) using the Wilhelmy plate method with different ultra-hydrophobic surfaces. Several fluids with different surface tension and viscosity are used to study the effect of physical properties of liquids on the governing laws.

  2. Phase space analysis of some interacting Chaplygin gas models

    Energy Technology Data Exchange (ETDEWEB)

    Khurshudyan, M. [Academy of Sciences of Armenia, Institute for Physical Research, Ashtarak (Armenia); Tomsk State University of Control Systems and Radioelectronics, Laboratory for Theoretical Cosmology, Tomsk (Russian Federation); Tomsk State Pedagogical University, Department of Theoretical Physics, Tomsk (Russian Federation); Myrzakulov, R. [Eurasian National University, Eurasian International Center for Theoretical Physics, Astana (Kazakhstan)

    2017-02-15

    In this paper we discuss a phase space analysis of various interacting Chaplygin gas models in general relativity. Linear and nonlinear sign changeable interactions are considered. For each case appropriate late time attractors of field equations are found. The Chaplygin gas is one of the dark fluids actively considered in modern cosmology due to the fact that it is a joint model of dark energy and dark matter. (orig.)

  3. Weak interaction models with spontaneously broken left-right symmetry

    International Nuclear Information System (INIS)

    Mohapatra, R.H.

    1978-01-01

    The present status of weak interaction models with spontaneously broken left-right symmetry is reviewed. The theoretical basis for asymptotic parity conservation, manifest left-right symmetry in charged current weak interactions, natural parity conservation in neutral currents and CP-violation in the context of SU(2)/sub L/ circled x SU (2)/sub R/ circled x U(1) models are outlined in detail. Various directions for further research in the theoretical and experimental side are indicated

  4. Ethanol Concentration Influences the Mechanisms of Wine Tannin Interactions with Poly(L-proline) in Model Wine.

    Science.gov (United States)

    McRae, Jacqui M; Ziora, Zyta M; Kassara, Stella; Cooper, Matthew A; Smith, Paul A

    2015-05-06

    Changes in ethanol concentration influence red wine astringency, and yet the effect of ethanol on wine tannin-salivary protein interactions is not well understood. Isothermal titration calorimetry (ITC) was used to measure the binding strength between the model salivary protein, poly(L-proline) (PLP) and a range of wine tannins (tannin fractions from a 3- and a 7-year old Cabernet Sauvignon wine) across different ethanol concentrations (5, 10, 15, and 40% v/v). Tannin-PLP interactions were stronger at 5% ethanol than at 40% ethanol. The mechanism of interaction changed for most tannin samples across the wine-like ethanol range (10-15%) from a combination of hydrophobic and hydrogen binding at 10% ethanol to only hydrogen binding at 15% ethanol. These results indicate that ethanol concentration can influence the mechanisms of wine tannin-protein interactions and that the previously reported decrease in wine astringency with increasing alcohol may, in part, relate to a decrease tannin-protein interaction strength.

  5. Modeling microwave/electron-cloud interaction

    International Nuclear Information System (INIS)

    Mattes, M; Sorolla, E; Zimmermann, F

    2013-01-01

    Starting from the separate codes BI-RME and ECLOUD or PyECLOUD, we are developing a novel joint simulation tool, which models the combined effect of a charged particle beam and of microwaves on an electron cloud. Possible applications include the degradation of microwave transmission in telecommunication satellites by electron clouds; the microwave-transmission techniques being used in particle accelerators for the purpose of electroncloud diagnostics; the microwave emission by the electron cloud itself in the presence of a magnetic field; and the possible suppression of electron-cloud formation in an accelerator by injecting microwaves of suitable amplitude and frequency. A few early simulation results are presented. (author)

  6. KN interaction in a constituent quark model

    International Nuclear Information System (INIS)

    Labarsouque, J.; Leandri, J.; Silvestre Brac, B.

    1997-01-01

    The kaon-nucleon s-wave phase shift have been calculated in a quark potential model using the resonating group method. The Hill-Wheeler equation has been solved numerically without any parametrization of the KN relative wave-function. The I = 0 phase shift has been found in agreement with the experimental data. In the I = 1 channel too much repulsion has been obtained., probably due to the lack of medium-range boson exchange type attraction. In a second step, pion and sigma-type exchange have been incorporated in the calculation

  7. FILAMENT INTERACTION MODELED BY FLUX ROPE RECONNECTION

    International Nuclear Information System (INIS)

    Toeroek, T.; Chandra, R.; Pariat, E.; Demoulin, P.; Schmieder, B.; Aulanier, G.; Linton, M. G.; Mandrini, C. H.

    2011-01-01

    Hα observations of solar active region NOAA 10501 on 2003 November 20 revealed a very uncommon dynamic process: during the development of a nearby flare, two adjacent elongated filaments approached each other, merged at their middle sections, and separated again, thereby forming stable configurations with new footpoint connections. The observed dynamic pattern is indicative of 'slingshot' reconnection between two magnetic flux ropes. We test this scenario by means of a three-dimensional zero β magnetohydrodynamic simulation, using a modified version of the coronal flux rope model by Titov and Demoulin as the initial condition for the magnetic field. To this end, a configuration is constructed that contains two flux ropes which are oriented side-by-side and are embedded in an ambient potential field. The choice of the magnetic orientation of the flux ropes and of the topology of the potential field is guided by the observations. Quasi-static boundary flows are then imposed to bring the middle sections of the flux ropes into contact. After sufficient driving, the ropes reconnect and two new flux ropes are formed, which now connect the former adjacent flux rope footpoints of opposite polarity. The corresponding evolution of filament material is modeled by calculating the positions of field line dips at all times. The dips follow the morphological evolution of the flux ropes, in qualitative agreement with the observed filaments.

  8. Variable sound speed in interacting dark energy models

    Science.gov (United States)

    Linton, Mark S.; Pourtsidou, Alkistis; Crittenden, Robert; Maartens, Roy

    2018-04-01

    We consider a self-consistent and physical approach to interacting dark energy models described by a Lagrangian, and identify a new class of models with variable dark energy sound speed. We show that if the interaction between dark energy in the form of quintessence and cold dark matter is purely momentum exchange this generally leads to a dark energy sound speed that deviates from unity. Choosing a specific sub-case, we study its phenomenology by investigating the effects of the interaction on the cosmic microwave background and linear matter power spectrum. We also perform a global fitting of cosmological parameters using CMB data, and compare our findings to ΛCDM.

  9. A novel in situ hydrophobic ion paring (HIP) formulation strategy for clinical product selection of a nanoparticle drug delivery system.

    Science.gov (United States)

    Song, Young Ho; Shin, Eyoung; Wang, Hong; Nolan, Jim; Low, Susan; Parsons, Donald; Zale, Stephen; Ashton, Susan; Ashford, Marianne; Ali, Mir; Thrasher, Daniel; Boylan, Nicholas; Troiano, Greg

    2016-05-10

    The present studies were aimed at formulating AZD2811-loaded polylactic acid-polyethylene glycol (PLA-PEG) nanoparticles with adjustable release rates without altering the chemical structures of the polymer or active pharmaceutical ingredient (API). This was accomplished through the use of a hydrophobic ion pairing approach. A series of AZD2811-containing nanoparticles with a variety of hydrophobic counterions including oleic acid, 1-hydroxy-2-naphthoic acid, cholic acid, deoxycholic acid, dioctylsulfosuccinic acid, and pamoic acid is described. The hydrophobicity of AZD2811 was increased through formation of ion pairs with these hydrophobic counterions, producing nanoparticles with exceptionally high drug loading-up to five fold higher encapsulation efficiency and drug loading compared to nanoparticles made without hydrophobic ion pairs. Furthermore, the rate at which the drug was released from the nanoparticles could be controlled by employing counterions with various hydrophobicities and structures, resulting in release half-lives ranging from about 2 to 120h using the same polymer, nanoparticle size, and nanoemulsion process. Process recipe variables affecting drug load and release rate were identified, including pH and molarity of quench buffer. Ion pair formation between AZD2811 and pamoic acid as a model counterion was investigated using solubility enhancement as well as nuclear magnetic resonance spectroscopy to demonstrate solution-state interactions. Further evidence for an ion pairing mechanism of controlled release was provided through the measurement of API and counterion release profiles using high-performance liquid chromatography, which had stoichiometric relationships. Finally, Raman spectra of an AZD2811-pamoate salt compared well with those of the formulated nanoparticles, while single components (AZD2811, pamoic acid) alone did not. A library of AZD2811 batches was created for analytical and preclinical characterization. Dramatically improved

  10. Dynamical system analysis of interacting models

    Science.gov (United States)

    Carneiro, S.; Borges, H. A.

    2018-01-01

    We perform a dynamical system analysis of a cosmological model with linear dependence between the vacuum density and the Hubble parameter, with constant-rate creation of dark matter. We show that the de Sitter spacetime is an asymptotically stable critical point, future limit of any expanding solution. Our analysis also shows that the Minkowski spacetime is an unstable critical point, which eventually collapses to a singularity. In this way, such a prescription for the vacuum decay not only predicts the correct future de Sitter limit, but also forbids the existence of a stable Minkowski universe. We also study the effect of matter creation on the growth of structures and their peculiar velocities, showing that it is inside the current errors of redshift space distortions observations.

  11. Pattern formation of a nonlocal, anisotropic interaction model

    KAUST Repository

    Burger, Martin

    2017-11-24

    We consider a class of interacting particle models with anisotropic, repulsive–attractive interaction forces whose orientations depend on an underlying tensor field. An example of this class of models is the so-called Kücken–Champod model describing the formation of fingerprint patterns. This class of models can be regarded as a generalization of a gradient flow of a nonlocal interaction potential which has a local repulsion and a long-range attraction structure. In contrast to isotropic interaction models the anisotropic forces in our class of models cannot be derived from a potential. The underlying tensor field introduces an anisotropy leading to complex patterns which do not occur in isotropic models. This anisotropy is characterized by one parameter in the model. We study the variation of this parameter, describing the transition between the isotropic and the anisotropic model, analytically and numerically. We analyze the equilibria of the corresponding mean-field partial differential equation and investigate pattern formation numerically in two dimensions by studying the dependence of the parameters in the model on the resulting patterns.

  12. Pattern formation of a nonlocal, anisotropic interaction model

    KAUST Repository

    Burger, Martin; Dü ring, Bertram; Kreusser, Lisa Maria; Markowich, Peter A.; Schö nlieb, Carola-Bibiane

    2017-01-01

    We consider a class of interacting particle models with anisotropic, repulsive–attractive interaction forces whose orientations depend on an underlying tensor field. An example of this class of models is the so-called Kücken–Champod model describing the formation of fingerprint patterns. This class of models can be regarded as a generalization of a gradient flow of a nonlocal interaction potential which has a local repulsion and a long-range attraction structure. In contrast to isotropic interaction models the anisotropic forces in our class of models cannot be derived from a potential. The underlying tensor field introduces an anisotropy leading to complex patterns which do not occur in isotropic models. This anisotropy is characterized by one parameter in the model. We study the variation of this parameter, describing the transition between the isotropic and the anisotropic model, analytically and numerically. We analyze the equilibria of the corresponding mean-field partial differential equation and investigate pattern formation numerically in two dimensions by studying the dependence of the parameters in the model on the resulting patterns.

  13. Element-specific density profiles in interacting biomembrane models

    International Nuclear Information System (INIS)

    Schneck, Emanuel; Rodriguez-Loureiro, Ignacio; Bertinetti, Luca; Gochev, Georgi; Marin, Egor; Novikov, Dmitri; Konovalov, Oleg

    2017-01-01

    Surface interactions involving biomembranes, such as cell–cell interactions or membrane contacts inside cells play important roles in numerous biological processes. Structural insight into the interacting surfaces is a prerequisite to understand the interaction characteristics as well as the underlying physical mechanisms. Here, we work with simplified planar experimental models of membrane surfaces, composed of lipids and lipopolymers. Their interaction is quantified in terms of pressure–distance curves using ellipsometry at controlled dehydrating (interaction) pressures. For selected pressures, their internal structure is investigated by standing-wave x-ray fluorescence (SWXF). This technique yields specific density profiles of the chemical elements P and S belonging to lipid headgroups and polymer chains, as well as counter-ion profiles for charged surfaces. (paper)

  14. Solution properties of hydrophobically modified

    Directory of Open Access Journals (Sweden)

    A.M. Al-Sabagh

    2016-12-01

    Full Text Available We tested nine hydrophobically modified polyacrylamides with molecular weights situated between 1.58 and 0.89 × 106 g/mol for enhanced oil recovery applications. Their solution properties were investigated in the distilled water, brine solution, formation water and sea water. Their critical association concentrations were determined from the relationship between their concentrations and the corresponding apparent viscosities (ηapp at 30 °C at shear rate 6 s−1. They were between 0.4 and 0.5 g/dl. The brine solutions of 0.5 g/dl of HM-PAMs were investigated at different conditions regarding their apparent viscosities. Such conditions were mono and divalent cations, temperature ranging from 30 to 90 °C, the shear rate ranging from 6 to 30 s−1 and the aging time for 45 days. The surface and interfacial tensions for the HM-PAMs were measured for concentration range from 0.01 to 1 g/dl brine solutions at 30 °C and their emulsification efficiencies were investigated for 7 days. The discrepancy in the properties and efficiencies of the tested copolymers was discussed in the light of their chemical structure.

  15. Modeling the Effect of a Hydrophobic Concrete Admixture on Chloride Ingress: Contractors Supplemental Report for CPC Project F09-AR05A

    Science.gov (United States)

    2017-12-01

    diffusion, moisture transport, temperature variation and chemical reactions occurring inside cementitious materials to assist civil engineers predicting...coefficient does not incorporate the hidden effect of chemical reactions or boundary conditions (Marchand 2009). Also, only diffusion coefficients of...and chemical activity gradients. Also, the model focuses on the dissolution/precipitation chemical reactions due to the high reactivity of the paste

  16. Impact of bacterial activity on turnover of insoluble hydrophobic substrates (phenanthrene and pyrene)—Model simulations for prediction of bioremediation success

    DEFF Research Database (Denmark)

    Rein, Arno; Adam, Iris K.U.; Miltner, Anja

    2016-01-01

    Many attempts for bioremediation of polycyclic aromatic hydrocarbon (PAH) contaminated sites failed in the past, but the reasons for this failure are not well understood. Here we apply and improve a model for integrated assessment of mass transfer, biodegradation and residual concentrations...

  17. Species Coexistence in Nitrifying Chemostats: A Model of Microbial Interactions

    Directory of Open Access Journals (Sweden)

    Maxime Dumont

    2016-12-01

    Full Text Available In a previous study, the two nitrifying functions (ammonia oxidizing bacteria (AOB or nitrite-oxidizing bacteria (NOB of a nitrification reactor—operated continuously over 525 days with varying inputs—were assigned using a mathematical modeling approach together with the monitoring of bacterial phylotypes. Based on these theoretical identifications, we develop here a chemostat model that does not explicitly include only the resources’ dynamics (different forms of soluble nitrogen but also explicitly takes into account microbial inter- and intra-species interactions for the four dominant phylotypes detected in the chemostat. A comparison of the models obtained with and without interactions has shown that such interactions permit the coexistence of two competing ammonium-oxidizing bacteria and two competing nitrite-oxidizing bacteria in competition for ammonium and nitrite, respectively. These interactions are analyzed and discussed.

  18. Study on the interaction between tabersonine and human serum albumin by optical spectroscopy and molecular modeling methods

    Energy Technology Data Exchange (ETDEWEB)

    Jiang Hua; Chen, Rongrong [Department of Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632 (China); Pu Hanlin, E-mail: tphl@jnu.edu.cn [Department of Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632 (China)

    2012-03-15

    The mechanism of interaction between tabersonine (TAB) and human serum albumin (HSA) was investigated by the methods of fluorescence spectroscopy, UV-vis absorption spectroscopy and molecular modeling under simulative physiological conditions. Results obtained from analysis of fluorescence spectrum and fluorescence intensity indicated that TAB has a strong ability to quench the intrinsic fluorescence of HSA through a static quenching procedure. The binding site number n and apparent binding constant K{sub a}, corresponding thermodynamic parameters {Delta}G, {Delta}H and {Delta}S at different temperatures were calculated. The distance r between donor (human serum albumin) and acceptor (tabersonine) was obtained according to the Foerster theory of non-radiation energy transfer. The effect of common ions on binding constant was also investigated. The synchronous fluorescence and three-dimensional fluorescence spectra were used to investigate the structural change of HSA molecules with addition of TAB. Furthermore, the study of molecular modeling indicated that TAB could bind to the site I of HSA and hydrophobic interaction was the major acting force, which was in agreement with the binding mode study. - Highlights: Black-Right-Pointing-Pointer Fluorescence study of the mechanism of interaction between tabersonine and HSA. Black-Right-Pointing-Pointer The binding parameters and thermodynamic parameters were calculated. Black-Right-Pointing-Pointer The distance r was obtained and common ions effects was investigated. Black-Right-Pointing-Pointer Conformation of HSA and its molecular modeling was analyzed.

  19. Towards a Revised Monte Carlo Neutral Particle Surface Interaction Model

    International Nuclear Information System (INIS)

    Stotler, D.P.

    2005-01-01

    The components of the neutral- and plasma-surface interaction model used in the Monte Carlo neutral transport code DEGAS 2 are reviewed. The idealized surfaces and processes handled by that model are inadequate for accurately simulating neutral transport behavior in present day and future fusion devices. We identify some of the physical processes missing from the model, such as mixed materials and implanted hydrogen, and make some suggestions for improving the model

  20. Spatially balanced topological interaction grants optimal cohesion in flocking models.

    Science.gov (United States)

    Camperi, Marcelo; Cavagna, Andrea; Giardina, Irene; Parisi, Giorgio; Silvestri, Edmondo

    2012-12-06

    Models of self-propelled particles (SPPs) are an indispensable tool to investigate collective animal behaviour. Originally, SPP models were proposed with metric interactions, where each individual coordinates with neighbours within a fixed metric radius. However, recent experiments on bird flocks indicate that interactions are topological: each individual interacts with a fixed number of neighbours, irrespective of their distance. It has been argued that topological interactions are more robust than metric ones against external perturbations, a significant evolutionary advantage for systems under constant predatory pressure. Here, we test this hypothesis by comparing the stability of metric versus topological SPP models in three dimensions. We show that topological models are more stable than metric ones. We also show that a significantly better stability is achieved when neighbours are selected according to a spatially balanced topological rule, namely when interacting neighbours are evenly distributed in angle around the focal individual. Finally, we find that the minimal number of interacting neighbours needed to achieve fully stable cohesion in a spatially balanced model is compatible with the value observed in field experiments on starling flocks.

  1. MODELING OF THE TRACK AND ROLLING STOCK INTERACTION

    Directory of Open Access Journals (Sweden)

    N. V. Khalipova

    2013-09-01

    Full Text Available Purpose. Interaction of system’s elements of "carriage–track" modelling requires consideration of various criteria, it also requires analysis of many uncertainty and randomness factors’ influence on the basic parameters to ensure optimal or rational parameters of the system. The researching of interactions’ process requires new theoretical approaches to formulation of objectives, based on a generalization of existing modeling approaches. The purpose of this work is development of interaction models between track and rolling stock based on multiple structures of objects. Methodology. Dedicated and formed the main evaluation criteria of dynamic interaction between track and rolling stock optimization - quality assurance and safety of transportation process, improving of their efficiency and reducing of prime cost’s. Based on vector optimization methods, proposed model of rolling stock and track’s elements interaction. For the synthesis of the model used mathematical machine of multiple objects structures. Findings. Generalized approaches to modeling in the interaction of rolling stock and track for different structural elements of the system under different exploitation conditions. This theoretical approach demonstrated on the examples of modeling of passenger and freight cars with track under different exploitation conditions. Originality. Proposed theoretical approach to the problem of track and rolling stock interaction, based on a synthesis of existing models by using of multiple objects structures. Practical value. Using of proposed model allows to structure key data and rational parameters of rolling stock and track interaction’s modeling and to formulate optimal and rational parameters of the system, to determine the effective exploitation parameters and measurement system for rational use of infrastructure.

  2. Structure effect on the interaction of phenylurea herbicides with model biomembrane as an environmental mobility parameter.

    Science.gov (United States)

    Librando, Vito; Forte, Stefano; Sarpietro, Maria G

    2004-01-15

    During recent years, intensive use of herbicides has raised increasing concern mainly due to their massive pollution of the environment. As these herbicides are directly or indirectly toxic to a wide range of organisms, their potential for contaminating soil, surface water, and groundwater makes these xenobiotics of special interest from a health and environmental point of view. Knowledge of the mechanisms by which they exert their toxic effects is becoming a need. Because of the herbicides' lipophilicity, a possible site of interaction in the cell is represented by biomembranes. The interaction of four herbicides, difenoxuron, diuron, linuron, and metoxuron, with model membranes constituted of dimyristoylphosphatidylcholine multilamellar vesicles was investigated by the differential scanning calorimetry technique. The aim was to study the effects exerted by an increasing amount of the examined compounds on thermotropic behavior of the model phospholipid membranes and to correlate the obtained results with structural features of the herbicides due to their environmental mobility. Among the herbicides studied, linuron is the most effective in perturbing the ordinate structure of vesicles forming phospholipids, whereas metoxuron is the least effective and the others exert an intermediate effect. Linuron exerts its effect both on the transition temperature of the gel to the liquid crystalline phase and on the enthalpy change. Difenoxuron, diuron, and metoxuron cause a change in the transition temperature but have an insignificant effect on the enthalpy change. The calorimetric results, correlated with the structural features of the herbicides, are consistent with their partition coefficient, log K(ow), suggesting that the more hydrophobic compound character causes a greater liposolubility and consequential cellular absorption with more effectiveness on the membrane order.

  3. Optimization of mathematical models for soil structure interaction

    International Nuclear Information System (INIS)

    Vallenas, J.M.; Wong, C.K.; Wong, D.L.

    1993-01-01

    Accounting for soil-structure interaction in the design and analysis of major structures for DOE facilities can involve significant costs in terms of modeling and computer time. Using computer programs like SASSI for modeling major structures, especially buried structures, requires the use of models with a large number of soil-structure interaction nodes. The computer time requirements (and costs) increase as a function of the number of interaction nodes to the third power. The added computer and labor cost for data manipulation and post-processing can further increase the total cost. This paper provides a methodology to significantly reduce the number of interaction nodes. This is achieved by selectively increasing the thickness of soil layers modeled based on the need for the mathematical model to capture as input only those frequencies that can actually be transmitted by the soil media. The authors have rarely found that a model needs to capture frequencies as high as 33 Hz. Typically coarser meshes (and a lesser number of interaction nodes) are adequate

  4. Impact of bacterial activity on turnover of insoluble hydrophobic substrates (phenanthrene and pyrene)-Model simulations for prediction of bioremediation success.

    Science.gov (United States)

    Rein, Arno; Adam, Iris K U; Miltner, Anja; Brumme, Katja; Kästner, Matthias; Trapp, Stefan

    2016-04-05

    Many attempts for bioremediation of polycyclic aromatic hydrocarbon (PAH) contaminated sites failed in the past, but the reasons for this failure are not well understood. Here we apply and improve a model for integrated assessment of mass transfer, biodegradation and residual concentrations for predicting the success of remediation actions. First, we provide growth parameters for Mycobacterium rutilum and Mycobacterium pallens growing on phenanthrene (PHE) or pyrene (PYR) degraded the PAH completely at all investigated concentrations. Maximum metabolic rates vmax and growth rates μ were similar for the substrates PHE and PYR and for both strains. The investigated Mycobacterium species were not superior in PHE degradation to strains investigated earlier with this method. Real-world degradation scenario simulations including diffusive flux to the microbial cells indicate: that (i) bioaugmentation only has a small, short-lived effect; (ii) Increasing sorption shifts the remaining PAH to the adsorbed/sequestered PAH pool; (iii) mobilizing by solvents or surfactants resulted in a significant decrease of the sequestered PAH, and (iv) co-metabolization e.g. by compost addition can contribute significantly to the reduction of PAH, because active biomass is maintained at a high level by the compost. The model therefore is a valuable contribution to the assessment of potential remediation action at PAH-polluted sites. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Coarse-grain modelling of protein-protein interactions

    NARCIS (Netherlands)

    Baaden, Marc; Marrink, Siewert J.

    2013-01-01

    Here, we review recent advances towards the modelling of protein-protein interactions (PPI) at the coarse-grained (CG) level, a technique that is now widely used to understand protein affinity, aggregation and self-assembly behaviour. PPI models of soluble proteins and membrane proteins are

  6. Interactive Coherence-Based Façade Modeling

    KAUST Repository

    Musialski, Przemyslaw

    2012-05-01

    We propose a novel interactive framework for modeling building facades from images. Our method is based on the notion of coherence-based editing which allows exploiting partial symmetries across the facade at any level of detail. The proposed workflow mixes manual interaction with automatic splitting and grouping operations based on unsupervised cluster analysis. In contrast to previous work, our approach leads to detailed 3d geometric models with up to several thousand regions per facade. We compare our modeling scheme to others and evaluate our approach in a user study with an experienced user and several novice users.

  7. Energy economy in the actomyosin interaction: lessons from simple models.

    Science.gov (United States)

    Lehman, Steven L

    2010-01-01

    The energy economy of the actomyosin interaction in skeletal muscle is both scientifically fascinating and practically important. This chapter demonstrates how simple cross-bridge models have guided research regarding the energy economy of skeletal muscle. Parameter variation on a very simple two-state strain-dependent model shows that early events in the actomyosin interaction strongly influence energy efficiency, and late events determine maximum shortening velocity. Addition of a weakly-bound state preceding force production allows weak coupling of cross-bridge mechanics and ATP turnover, so that a simple three-state model can simulate the velocity-dependence of ATP turnover. Consideration of the limitations of this model leads to a review of recent evidence regarding the relationship between ligand binding states, conformational states, and macromolecular structures of myosin cross-bridges. Investigation of the fine structure of the actomyosin interaction during the working stroke continues to inform fundamental research regarding the energy economy of striated muscle.

  8. Nanoscale encapsulation: the structure of cations in hydrophobic microporous aluminosilicates

    International Nuclear Information System (INIS)

    Wasserman, S.R.; Yuchs, S.E.; Giaquinta, D.; Soderholm, L.; Song, Kang.

    1996-01-01

    Hydrophobic microporous aluminosilicates, created by organic surface modification of inherently hydrophilic materials such as zeolites and clays, are currently being investigated as storage media for hazardous cations. Use of organic monolayers to modify the surface of an aluminosilicate after introducing an ion into the zeolite/clay reduces the interaction of water with the material. Resulting systems are about 20 times more resistant to leaching of stored ion. XAS spectra from the encapsulated ion demonstrate that byproducts from the organic modifier can complex with the stored cation. This complexation can result in a decreased affinity of the cation for the aluminosilicate matrix. Changing the organic modifier eliminates this problem. XAS spectra also indicate that the reactivity and speciation of the encapsulated ion may change upon application of the hydrophobic layer

  9. Meson exchange current (MEC) models in neutrino interaction generators

    International Nuclear Information System (INIS)

    Katori, Teppei

    2015-01-01

    Understanding of the so-called 2 particle-2 hole (2p-2h) effect is an urgent program in neutrino interaction physics for current and future oscillation experiments. Such processes are believed to be responsible for the event excesses observed by recent neutrino experiments. The 2p-2h effect is dominated by the meson exchange current (MEC), and is accompanied by a 2-nucleon emission from the primary vertex, instead of a single nucleon emission from the charged-current quasi-elastic (CCQE) interaction. Current and future high resolution experiments can potentially nail down this effect. For this reason, there are world wide efforts to model and implement this process in neutrino interaction simulations. In these proceedings, I would like to describe how this channel is modeled in neutrino interaction generators

  10. Modeling strategic interaction with application to environmental engineering

    Energy Technology Data Exchange (ETDEWEB)

    Dagnino, A.

    1987-01-01

    The main purpose of this thesis is to develop practical decision models for use in the analysis of complex strategic interaction situations. Following the presentation of the different bargain in models that have been developed previously, an algorithm that formally defines, models, and analyzes the cooperation present in strategic interaction is given. In addition to other valuable information, the algorithm predicts the compromise solutions to complex disputes and how a given decision maker can select a strategy to reach a preferable solution. To model misconceptions of decision makers involved in strategic interaction situations, a cooperative hypergame model is developed. Then a computerized algorithm that handles preference information of decision makers involved in strategic interaction is presented. This model allows one to perform exhaustive sensitivity analyses in an efficient and quick manner. Following this, practical decision algorithms useful for mediators seeking for joint solutions are presented. These mediation models allow the study and development of compromise zones among decision makers taking part in a dispute.

  11. Model-Mapped RPA for Determining the Effective Coulomb Interaction

    Science.gov (United States)

    Sakakibara, Hirofumi; Jang, Seung Woo; Kino, Hiori; Han, Myung Joon; Kuroki, Kazuhiko; Kotani, Takao

    2017-04-01

    We present a new method to obtain a model Hamiltonian from first-principles calculations. The effective interaction contained in the model is determined on the basis of random phase approximation (RPA). In contrast to previous methods such as projected RPA and constrained RPA (cRPA), the new method named "model-mapped RPA" takes into account the long-range part of the polarization effect to determine the effective interaction in the model. After discussing the problems of cRPA, we present the formulation of the model-mapped RPA, together with a numerical test for the single-band Hubbard model of HgBa2CuO4.

  12. Models for genotype by environment interaction estimation on halomorphic soil

    Directory of Open Access Journals (Sweden)

    Dimitrijević Miodrag

    2006-01-01

    Full Text Available In genotype by environment interaction estimation, as well as, in total trial variability anal­ysis several models are in use. The most often used are Analysis of variance, Eberhart and Russell model and AMMI model. Each of the models has its own specificities, in the way of sources of varia­tion comprehension and treatment. It is known that agriculturally less productive environments increase errors, dimmish reaction differences between genotypes and decrease repeatability of conditions during years. A sample consisting on six bread wheat varieties was studied in three veg­etation periods on halomorphic soil, solonetz type in Banat (vil. Kumane. Genotype by environ­ment interaction was quantified using ANOVA, Eberhart and Russell model and AMMI model. The results were compared not only on pure solonetz soil (control, but also on two level of ameliora­tion (25 and 50t/ha phosphor-gypsum.

  13. Literature review of models on tire-pavement interaction noise

    Science.gov (United States)

    Li, Tan; Burdisso, Ricardo; Sandu, Corina

    2018-04-01

    Tire-pavement interaction noise (TPIN) becomes dominant at speeds above 40 km/h for passenger vehicles and 70 km/h for trucks. Several models have been developed to describe and predict the TPIN. However, these models do not fully reveal the physical mechanisms or predict TPIN accurately. It is well known that all the models have both strengths and weaknesses, and different models fit different investigation purposes or conditions. The numerous papers that present these models are widely scattered among thousands of journals, and it is difficult to get the complete picture of the status of research in this area. This review article aims at presenting the history and current state of TPIN models systematically, making it easier to identify and distribute the key knowledge and opinions, and providing insight into the future research trend in this field. In this work, over 2000 references related to TPIN were collected, and 74 models were reviewed from nearly 200 selected references; these were categorized into deterministic models (37), statistical models (18), and hybrid models (19). The sections explaining the models are self-contained with key principles, equations, and illustrations included. The deterministic models were divided into three sub-categories: conventional physics models, finite element and boundary element models, and computational fluid dynamics models; the statistical models were divided into three sub-categories: traditional regression models, principal component analysis models, and fuzzy curve-fitting models; the hybrid models were divided into three sub-categories: tire-pavement interface models, mechanism separation models, and noise propagation models. At the end of each category of models, a summary table is presented to compare these models with the key information extracted. Readers may refer to these tables to find models of their interest. The strengths and weaknesses of the models in different categories were then analyzed. Finally

  14. Including lateral interactions into microkinetic models of catalytic reactions

    DEFF Research Database (Denmark)

    Hellman, Anders; Honkala, Johanna Karoliina

    2007-01-01

    In many catalytic reactions lateral interactions between adsorbates are believed to have a strong influence on the reaction rates. We apply a microkinetic model to explore the effect of lateral interactions and how to efficiently take them into account in a simple catalytic reaction. Three differ...... different approximations are investigated: site, mean-field, and quasichemical approximations. The obtained results are compared to accurate Monte Carlo numbers. In the end, we apply the approximations to a real catalytic reaction, namely, ammonia synthesis....

  15. Smilansky-Solomyak model with a delta '-interaction

    Czech Academy of Sciences Publication Activity Database

    Exner, Pavel; Lipovský, J.

    2018-01-01

    Roč. 382, č. 18 (2018), s. 1207-1213 ISSN 0375-9601 R&D Projects: GA ČR GA17-01706S Institutional support: RVO:61389005 Keywords : Smilansky-Solomyak model * delta '-interaction * spectral theory Subject RIV: BE - Theoretical Physics OBOR OECD: Atomic, molecular and chemical physics ( physics of atoms and molecules including collision, interaction with radiation, magnetic resonances, Mössbauer effect) Impact factor: 1.772, year: 2016

  16. NON-LINEAR MODELING OF THE RHIC INTERACTION REGIONS

    International Nuclear Information System (INIS)

    TOMAS, R.; FISCHER, W.; JAIN, A.; LUO, Y.; PILAT, F.

    2004-01-01

    For RHIC's collision lattices the dominant sources of transverse non-linearities are located in the interaction regions. The field quality is available for most of the magnets in the interaction regions from the magnetic measurements, or from extrapolations of these measurements. We discuss the implementation of these measurements in the MADX models of the Blue and the Yellow rings and their impact on beam stability

  17. General quadrupole shapes in the Interacting Boson Model

    International Nuclear Information System (INIS)

    Leviatan, A.

    1990-01-01

    Characteristic attributes of nuclear quadrupole shapes are investigated within the algebraic framework of the Interacting Boson Model. For each shape the Hamiltonian is resolved into intrinsic and collective parts, normal modes are identified and intrinsic states are constructed and used to estimate transition matrix elements. Special emphasis is paid to new features (e.g. rigid triaxiality and coexisting deformed shapes) that emerge in the presence of the three-body interactions. 27 refs

  18. Multinucleon Ejection Model for Two Body Current Neutrino Interactions

    Energy Technology Data Exchange (ETDEWEB)

    Sobczyk, Jan T.; /Fermilab

    2012-06-01

    A model is proposed to describe nucleons ejected from a nucleus as a result of two-body-current neutrino interactions. The model can be easily implemented in Monte Carlo neutrino event generators. Various possibilities to measure the two-body-current contribution are discussed. The model can help identify genuine charge current quasielastic events and allow for a better determination of the systematic error on neutrino energy reconstruction in neutrino oscillation experiments.

  19. Modeling of ultrafast THz interactions in molecular crystals

    DEFF Research Database (Denmark)

    Pedersen, Pernille Klarskov; Clark, Stewart J.; Jepsen, Peter Uhd

    2014-01-01

    In this paper we present a numerical study of terahertz pulses interacting with crystals of cesium iodide. We model the molecular dynamics of the cesium iodide crystals with the Density Functional Theory software CASTEP, where ultrafast terahertz pulses are implemented to the CASTEP software...... to interact with molecular crystals. We investigate the molecular dynamics of cesium iodide crystals when interacting with realistic terahertz pulses of field strengths from 0 to 50 MV/cm. We find nonlinearities in the response of the CsI crystals at field strengths higher than 10 MV/cm....

  20. Lagrangian model of conformal invariant interacting quantum field theory

    International Nuclear Information System (INIS)

    Lukierski, J.

    1976-01-01

    A Lagrangian model of conformal invariant interacting quantum field theory is presented. The interacting Lagrangian and free Lagrangian are derived replacing the canonical field phi by the field operator PHIsub(d)sup(c) and introducing the conformal-invariant interaction Lagrangian. It is suggested that in the conformal-invariant QFT with the dimensionality αsub(B) obtained from the bootstrep equation, the normalization constant c of the propagator and the coupling parametery do not necessarily need to satisfy the relation xsub(B) = phi 2 c 3

  1. Real and financial interacting markets: A behavioral macro-model

    International Nuclear Information System (INIS)

    Naimzada, Ahmad; Pireddu, Marina

    2015-01-01

    Highlights: •We propose a model in which the real sector and the stock market interact. •In the stock market there are optimistic and pessimistic fundamentalists. •We detect the mechanisms through which instabilities get transmitted between markets. •In order to perform such analysis, we introduce the “interaction degree approach”. •We show the effects of increasing the interaction degree between the two markets. -- Abstract: In the present paper we propose a model in which the real side of the economy, described via a Keynesian good market approach, interacts with the stock market with heterogeneous speculators, i.e., optimistic and pessimistic fundamentalists, that respectively overestimate and underestimate the reference value due to a belief bias. Agents may switch between optimism and pessimism according to which behavior is more profitable. To the best of our knowledge, this is the first contribution considering both real and financial interacting markets and an evolutionary selection process for which an analytical study is performed. Indeed, employing analytical and numerical tools, we detect the mechanisms and the channels through which the stability of the isolated real and financial sectors leads to instability for the two interacting markets. In order to perform such analysis, we introduce the “interaction degree approach”, which allows us to study the complete three-dimensional system by decomposing it into two subsystems, i.e., the isolated financial and real markets, easier to analyze, that are then linked through a parameter describing the interaction degree between the two markets. We derive the stability conditions both for the isolated markets and for the whole system with interacting markets. Next, we show how to apply the interaction degree approach to our model. Among the various scenarios we are led to analyze, the most interesting one is that in which the isolated markets are stable, but their interaction is destabilizing

  2. Non-perturbative effective interactions in the standard model

    Energy Technology Data Exchange (ETDEWEB)

    Arbuzov, Boris A. [Moscow Lomonosov State Univ. (Russian Federation). Skobeltsyn Inst. of Nuclear Physics

    2014-07-01

    This monograph is devoted to the nonperturbative dynamics in the Standard Model (SM), the basic theory of allfundamental interactions in natureexcept gravity. The Standard Model is divided into two parts: the quantum chromodynamics (QCD) and the electro-weak theory (EWT) are well-defined renormalizable theories in which the perturbation theory is valid. However, for the adequate description of the real physics nonperturbative effects are inevitable. This book describes how these nonperturbative effects may be obtained in the framework of spontaneous generation of effective interactions. The well-known example of such effective interaction is provided by the famous Nambu-Jona-Lasinio effective interaction. Also a spontaneous generation of this interaction in the framework of QCD is described and applied to the method for other effective interactions in QCD and EWT. The method is based on N.N. Bogolyubov's conception of compensation equations. As a result we then describe the principal features of the Standard Model, e.g. Higgs sector, and significant nonperturbative effects including recent results obtained at LHC and TEVATRON.

  3. Rhizosphere hydrophobicity: A positive trait in the competition for water.

    Science.gov (United States)

    Zeppenfeld, Thorsten; Balkenhol, Niko; Kóvacs, Kristóf; Carminati, Andrea

    2017-01-01

    The ability to acquire water from the soil is a major driver in interspecific plant competition and it depends on several root functional traits. One of these traits is the excretion of gel-like compounds (mucilage) that modify physical soil properties. Mucilage secreted by roots becomes hydrophobic upon drying, impedes the rewetting of the soil close to the root, the so called rhizosphere, and reduces water availability to plants. The function of rhizosphere hydrophobicity is not easily understandable when looking at a single plant, but it may constitute a competitive advantage at the ecosystem level. We hypothesize that by making the top soil hydrophobic, deep-rooted plants avoid competititon with shallow-rooted plants. To test this hypothesis we used an individual-based model to simulate water uptake and growth of two virtual plant species, one deep-rooted plant capable of making the soil hydrophobic and a shallow-rooted plant. We ran scenarios with different precipitation regimes ranging from dry to wet (350, 700, and 1400 mm total annual precipitation) and from high to low precipitation frequencies (1, 7, and 14 days). Plant species abundance and biomass were chosen as indicators for competitiveness of plant species. At constant precipitation frequency mucilage hydrophobicity lead to a benefit in biomass and abundance of the tap-rooted population. Under wet conditions this effect diminished and tap-rooted plants were less productive. Without this trait both species coexisted. The effect of root exudation trait remained constant under different precipitation frequencies. This study shows that mucilage secretion is a competitive trait for the acquisition of water. This advantage is achieved by the modification of the soil hydraulic properties and specifically by inducing water repellency in soil regions which are shared with other species.

  4. Rhizosphere hydrophobicity: A positive trait in the competition for water.

    Directory of Open Access Journals (Sweden)

    Thorsten Zeppenfeld

    Full Text Available The ability to acquire water from the soil is a major driver in interspecific plant competition and it depends on several root functional traits. One of these traits is the excretion of gel-like compounds (mucilage that modify physical soil properties. Mucilage secreted by roots becomes hydrophobic upon drying, impedes the rewetting of the soil close to the root, the so called rhizosphere, and reduces water availability to plants. The function of rhizosphere hydrophobicity is not easily understandable when looking at a single plant, but it may constitute a competitive advantage at the ecosystem level. We hypothesize that by making the top soil hydrophobic, deep-rooted plants avoid competititon with shallow-rooted plants. To test this hypothesis we used an individual-based model to simulate water uptake and growth of two virtual plant species, one deep-rooted plant capable of making the soil hydrophobic and a shallow-rooted plant. We ran scenarios with different precipitation regimes ranging from dry to wet (350, 700, and 1400 mm total annual precipitation and from high to low precipitation frequencies (1, 7, and 14 days. Plant species abundance and biomass were chosen as indicators for competitiveness of plant species. At constant precipitation frequency mucilage hydrophobicity lead to a benefit in biomass and abundance of the tap-rooted population. Under wet conditions this effect diminished and tap-rooted plants were less productive. Without this trait both species coexisted. The effect of root exudation trait remained constant under different precipitation frequencies. This study shows that mucilage secretion is a competitive trait for the acquisition of water. This advantage is achieved by the modification of the soil hydraulic properties and specifically by inducing water repellency in soil regions which are shared with other species.

  5. Physical model and calculation code for fuel coolant interactions

    International Nuclear Information System (INIS)

    Goldammer, H.; Kottowski, H.

    1976-01-01

    A physical model is proposed to describe fuel coolant interactions in shock-tube geometry. According to the experimental results, an interaction model which divides each cycle into three phases is proposed. The first phase is the fuel-coolant-contact, the second one is the ejection and recently of the coolant, and the third phase is the impact and fragmentation. Physical background of these phases are illustrated in the first part of this paper. Mathematical expressions of the model are exposed in the second part. A principal feature of the computational method is the consistent application of the fourier-equation throughout the whole interaction process. The results of some calculations, performed for different conditions are compiled in attached figures. (Aoki, K.)

  6. Heat-resistant hydrophobic-oleophobic coatings

    OpenAIRE

    Uyanik, Mehmet; Arpac, Ertugrul; Schmidt, Helmut K.; Akarsu, Murat; Sayilkan, Funda; Sayilkan, Hikmet

    2006-01-01

    Thermally and chemically durable hydrophobic oleophobic coatings, containing different ceramic particles such as SiO2, SiC, Al 2O3, which can be alternative instead of Teflon, have been developed and applied on the aluminum substrates by spin-coating method. Polyimides, which are high-thermal resistant heteroaromatic polymers, were synthesized, and fluor oligomers were added to these polymers to obtain hydrophobic-oleophobic properties. After coating, Al surface was subjected to Taber-abrasio...

  7. Hydrophobic polymers modification of mesoporous silica with large pore size for drug release

    Energy Technology Data Exchange (ETDEWEB)

    Zhu Shenmin, E-mail: smzhu@sjtu.edu.c [Shanghai Jiao Tong University, State Key Lab of Metal Matrix Composites (China); Zhang Di; Yang Na [Fudan University, Ministry of Education, Key Lab of Molecular Engineering of Polymers (China)

    2009-04-15

    Mesostructure cellular foam (MCF) materials were modified with hydrophobic polyisoprene (PI) through free radical polymerization in the pores network, and the resulting materials (MCF-PI) were investigated as matrices for drug storage. The successful synthesis of PI inside MCF was characterized by Fourier transform infrared (FT-IR), hydrogen nuclear magnetic resonance ({sup 1}H NMR), X-ray diffraction patterns (XRD) and nitrogen adsorption/desorption measurements. It was interesting to find the resultant system held a relatively large pore size (19.5 nm) and pore volume (1.02 cm{sup 3} g{sup -1}), which would benefit for drug storage. Ibuprofen (IBU) and vancomycin were selected as model drugs and loaded onto unmodified MCF and modified MCF (MCF-PI). The adsorption capacities of these model drugs on MCF-PI were observed increase as compared to that of on pure MCF, due to the trap effects induced by polyisoprene chains inside the pores. The delivery system of MCF-PI was found to be more favorable for the adsorption of IBU (31 wt%, IBU/silica), possibly attributing to the hydrophobic interaction between IBU and PI formed on the internal surface of MCF matrix. The release of drug through the porous network was investigated by measuring uptake and release of IBU.

  8. Order and correlation contributions to the entropy of hydrophobic solvation

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Maoyuan; Besford, Quinn Alexander; Mulvaney, Thomas; Gray-Weale, Angus, E-mail: gusgw@gusgw.net [School of Chemistry, The University of Melbourne, Victoria 3010 (Australia)

    2015-03-21

    The entropy of hydrophobic solvation has been explained as the result of ordered solvation structures, of hydrogen bonds, of the small size of the water molecule, of dispersion forces, and of solvent density fluctuations. We report a new approach to the calculation of the entropy of hydrophobic solvation, along with tests of and comparisons to several other methods. The methods are assessed in the light of the available thermodynamic and spectroscopic information on the effects of temperature on hydrophobic solvation. Five model hydrophobes in SPC/E water give benchmark solvation entropies via Widom’s test-particle insertion method, and other methods and models are tested against these particle-insertion results. Entropies associated with distributions of tetrahedral order, of electric field, and of solvent dipole orientations are examined. We find these contributions are small compared to the benchmark particle-insertion entropy. Competitive with or better than other theories in accuracy, but with no free parameters, is the new estimate of the entropy contributed by correlations between dipole moments. Dipole correlations account for most of the hydrophobic solvation entropy for all models studied and capture the distinctive temperature dependence seen in thermodynamic and spectroscopic experiments. Entropies based on pair and many-body correlations in number density approach the correct magnitudes but fail to describe temperature and size dependences, respectively. Hydrogen-bond definitions and free energies that best reproduce entropies from simulations are reported, but it is difficult to choose one hydrogen bond model that fits a variety of experiments. The use of information theory, scaled-particle theory, and related methods is discussed briefly. Our results provide a test of the Frank-Evans hypothesis that the negative solvation entropy is due to structured water near the solute, complement the spectroscopic detection of that solvation structure by

  9. Adsorption of Hydrophobically Modified Polyelectrolytes on Hydrophobic Substrates Adsorption de polyélectrolytes modifiés hydrophobiquement sur les substrats hydrophobes

    Directory of Open Access Journals (Sweden)

    Mays J. W.

    2006-12-01

    Full Text Available A series of diblock copolymers, poly (tert-butyl styrene-sodium poly (styrene sulfonate with different molecular weight and percentage of sulfonation have been used to study the effect of polymer structure on its adsorption behavior onto hydrophobically modified silicon wafers. The percentage of the hydrophobic block varies from 3. 6-8. 9%. Previous studies show that salt concentration is very important for the adsorption of such polyelectrolytes onto silica surfaces. Octadecyltriethoxysilane (OTE has been used to modify the silicon wafer which changes the water contact angle from 50° on unmodified silica to 100° to 120°. On this hydrophobic surface, we found that the adsorption of these slightly hydrophobically modified polyelectrolytes is close to the 4/23rd power of salt concentration predicted by a recent model. The grafting density is also consistent with a dependence on the length of the hydrophobic block to the -12/23rd power, and the length of the polyelectrolyte block to the -6/23rd power, predicted by this model. Une série de copolymères à diblocs poly (tert-butyle styrène-sodium (sulfonate de polystyrène de masses moléculaires et pourcentages de sulfonation différents ont été utilisés pour étudier les effets de la structure du polymère sur son pouvoir d'adsorption sur des surfaces de silicium modifiées hydrophobiquement. Le pourcentage du bloc hydrophobe varie de 3,6 à 8,9%. Les études antérieures montrent que la concentration saline est très importante pour l'adsorption de ces polyélectrolytes sur les surfaces de silice. Nous avons utilisé l'octadecyltriéthoxysilane (OTE pour modifier la surface de silicium qui change l'angle de contact de l'eau de 50° sur la silice non modifiée à une valeur comprise entre 100° et 120° sur la silice modifiée. Sur cette surface hydrophobe, nous constatons que l'adsorption de ces polyélectrolytes légèrement modifiés hydrophobiquement est proche de la loi puissance 4

  10. Hybrid modelling of soil-structure interaction for embedded structures

    International Nuclear Information System (INIS)

    Gupta, S.; Penzien, J.

    1981-01-01

    The basic methods currently being used for the analysis of soil-structure interaction fail to properly model three-dimensional embedded structures with flexible foundations. A hybrid model for the analysis of soil-structure interaction is developed in this investigation which takes advantage of the desirable features of both the finite element and substructure methods and which minimizes their undesirable features. The hybrid model is obtained by partitioning the total soil-structure system into a nearfield and a far-field with a smooth hemispherical interface. The near-field consists of the structure and a finite region of soil immediately surrounding its base. The entire near-field may be modelled in three-dimensional form using the finite element method; thus, taking advantage of its ability to model irregular geometries, and the non-linear soil behavior in the immediate vicinity of the structure. (orig./WL)

  11. Probabilistic models of population evolution scaling limits, genealogies and interactions

    CERN Document Server

    Pardoux, Étienne

    2016-01-01

    This expository book presents the mathematical description of evolutionary models of populations subject to interactions (e.g. competition) within the population. The author includes both models of finite populations, and limiting models as the size of the population tends to infinity. The size of the population is described as a random function of time and of the initial population (the ancestors at time 0). The genealogical tree of such a population is given. Most models imply that the population is bound to go extinct in finite time. It is explained when the interaction is strong enough so that the extinction time remains finite, when the ancestral population at time 0 goes to infinity. The material could be used for teaching stochastic processes, together with their applications. Étienne Pardoux is Professor at Aix-Marseille University, working in the field of Stochastic Analysis, stochastic partial differential equations, and probabilistic models in evolutionary biology and population genetics. He obtai...

  12. Ecosystem management via interacting models of political and ecological processes

    Directory of Open Access Journals (Sweden)

    Haas, T. C.

    2004-01-01

    Full Text Available The decision to implement environmental protection options is a political one. Political realities may cause a country to not heed the most persuasive scientific analysis of an ecosystem's future health. A predictive understanding of the political processes that result in ecosystem management decisions may help guide ecosystem management policymaking. To this end, this article develops a stochastic, temporal model of how political processes influence and are influenced by ecosystem processes. This model is realized in a system of interacting influence diagrams that model the decision making of a country's political bodies. These decisions interact with a model of the ecosystem enclosed by the country. As an example, a model for Cheetah (Acinonyx jubatus management in Kenya is constructed and fitted to decision and ecological data.

  13. Fish skin bacteria: Colonial and cellular hydrophobicity.

    Science.gov (United States)

    Sar, N; Rosenberg, E

    1987-05-01

    Bacteria were desorbed from the skin of healthy, fast-swimming fish by several procedures, including brief exposure to sonic oscillation and treatment with nontoxic surface active agents. The surface properties of these bacteria were studied by measuring their adhesion to hexadecane, as well as by a newly developed, simple method for studying the hydrophobicity of bacterial lawns. This method, referred to as the "Direction of Spreading" (DOS) method, consists of recording the direction to which a water drop spreads when introduced at the border between bacterial lawns and other surfaces. Of the 13 fish skin isolates examined, two strains were as hydrophobic as polystyrene by the DOS method. Suspended cells of one of these strains adhered strongly to hexadecane (84%), whereas cells of the other strain adhered poorly (13%). Another strain which was almost as hydrophobic as polystyrene by the DOS method did not adhere to hexadecane at all. Similarly, lawns of three other strains were more hydrophobic than glass by the DOS method, but cell suspensions prepared from these colonies showed little or no adhesion to hexadecane. The high colonial but relatively low cellular hydrophobicity could be due to a hydrophobic slime that is removed during the suspension and washing procedures. The possibility that specific bacteria assist in fish locomotion by changing the surface properties of the fish skin and by producing drag-reducing polymers is discussed.

  14. [Analytic methods for seed models with genotype x environment interactions].

    Science.gov (United States)

    Zhu, J

    1996-01-01

    Genetic models with genotype effect (G) and genotype x environment interaction effect (GE) are proposed for analyzing generation means of seed quantitative traits in crops. The total genetic effect (G) is partitioned into seed direct genetic effect (G0), cytoplasm genetic of effect (C), and maternal plant genetic effect (Gm). Seed direct genetic effect (G0) can be further partitioned into direct additive (A) and direct dominance (D) genetic components. Maternal genetic effect (Gm) can also be partitioned into maternal additive (Am) and maternal dominance (Dm) genetic components. The total genotype x environment interaction effect (GE) can also be partitioned into direct genetic by environment interaction effect (G0E), cytoplasm genetic by environment interaction effect (CE), and maternal genetic by environment interaction effect (GmE). G0E can be partitioned into direct additive by environment interaction (AE) and direct dominance by environment interaction (DE) genetic components. GmE can also be partitioned into maternal additive by environment interaction (AmE) and maternal dominance by environment interaction (DmE) genetic components. Partitions of genetic components are listed for parent, F1, F2 and backcrosses. A set of parents, their reciprocal F1 and F2 seeds is applicable for efficient analysis of seed quantitative traits. MINQUE(0/1) method can be used for estimating variance and covariance components. Unbiased estimation for covariance components between two traits can also be obtained by the MINQUE(0/1) method. Random genetic effects in seed models are predictable by the Adjusted Unbiased Prediction (AUP) approach with MINQUE(0/1) method. The jackknife procedure is suggested for estimation of sampling variances of estimated variance and covariance components and of predicted genetic effects, which can be further used in a t-test for parameter. Unbiasedness and efficiency for estimating variance components and predicting genetic effects are tested by

  15. Modelling the interaction between flooding events and economic growth

    Directory of Open Access Journals (Sweden)

    J. Grames

    2015-06-01

    Full Text Available Socio-hydrology describes the interaction between the socio-economy and water. Recent models analyze the interplay of community risk-coping culture, flooding damage and economic growth (Di Baldassarre et al., 2013; Viglione et al., 2014. These models descriptively explain the feedbacks between socio-economic development and natural disasters like floods. Contrary to these descriptive models, our approach develops an optimization model, where the intertemporal decision of an economic agent interacts with the hydrological system. In order to build this first economic growth model describing the interaction between the consumption and investment decisions of an economic agent and the occurrence of flooding events, we transform an existing descriptive stochastic model into an optimal deterministic model. The intermediate step is to formulate and simulate a descriptive deterministic model. We develop a periodic water function to approximate the former discrete stochastic time series of rainfall events. Due to the non-autonomous exogenous periodic rainfall function the long-term path of consumption and investment will be periodic.

  16. Random regression models for detection of gene by environment interaction

    Directory of Open Access Journals (Sweden)

    Meuwissen Theo HE

    2007-02-01

    Full Text Available Abstract Two random regression models, where the effect of a putative QTL was regressed on an environmental gradient, are described. The first model estimates the correlation between intercept and slope of the random regression, while the other model restricts this correlation to 1 or -1, which is expected under a bi-allelic QTL model. The random regression models were compared to a model assuming no gene by environment interactions. The comparison was done with regards to the models ability to detect QTL, to position them accurately and to detect possible QTL by environment interactions. A simulation study based on a granddaughter design was conducted, and QTL were assumed, either by assigning an effect independent of the environment or as a linear function of a simulated environmental gradient. It was concluded that the random regression models were suitable for detection of QTL effects, in the presence and absence of interactions with environmental gradients. Fixing the correlation between intercept and slope of the random regression had a positive effect on power when the QTL effects re-ranked between environments.

  17. A two-level solvable model involving competing pairing interactions

    International Nuclear Information System (INIS)

    Dussel, G.G.; Maqueda, E.E.; Perazzo, R.P.J.; Evans, J.A.

    1986-01-01

    A model is considered consisting of nucleons moving in two non-degenerate l-shells and interacting through two pairing residual interactions with (S, T) = (1, 0) and (0, 1). These, together with the single particle hamiltonian induce mutually destructive correlations, giving rise to various collective pictures that can be discussed as representing a two-dimensional space of phases. The model is solved exactly using an O(8)xO(8) group theoretical classification scheme. The transfer of correlated pairs and quartets is also discussed. (orig.)

  18. Impact of a Hydrophobic Sphere onto a Bath

    Science.gov (United States)

    Harris, Daniel M.; Edmonds, John; Galeano-Rios, Carlos A.; Milewski, Paul A.

    2017-11-01

    Small hydrophobic particles impacting a water surface can rebound completely from the interface (Lee & Kim, Langmuir, 2008). In the present work, we focus on the bouncing dynamics of millimetric hydrophobic spheres impacting the surface of a quiescent water bath. Particular attention is given to the dependence of the normal coefficient of restitution and contact time on the impact velocity and the radius and density of the sphere. Our experimental observations are compared to the predictions of a fluid model derived from linearized Navier-Stokes under the assumption of a high Reynolds number regime (Galeano-Rios et al., JFM, in press). In the model, the motions of the sphere and the fluid interface are found by imposing the natural geometric and kinematic compatibility conditions. Future directions will be discussed. C.A.G.-R. and P.A.M. gratefully acknowledge support through the EPSRC project EP/N018176/1.

  19. Hydrophobicity study of kaolinite from La Unión, Antioquia

    Directory of Open Access Journals (Sweden)

    Liliana M. Usuga-Manco

    2015-07-01

    Full Text Available In this research three methodologies to convert the hydrophilic surface of kaolinite into a hydrophobic surface are proposed, this condition is required to recover this mineral by means of froth flotation. Taking into account the anisotropy, zeta potential and complex surface electrical properties of the kaolinite, three surface chemical treatments based on the interacting and absorption of anionic collectors onto the mineral surface, causing an increase in the contact angle and thus increased hydrophobicity of kaolinite were applied. The methodologies proposed were interactions of kaolinite particles with: sodium dodecyl sulfate solutions with concentration 1x10-3M, 1x10-4M, 1x10-5M; sodium dodecyl sulfate solutions 1x10-3M, 1x10-4M, 1x10-5M with further interaction with kerosene solutions 127000 ppm; and oleic acid solutions 1x10-3M, 1x10-4M, 1x10-5M, each one with a five minutes of interaction. The experimental results obtained by zeta potential and contact angle of the kaolinite before and after applying chemical treatments indicate that larger the chain length of the collector and its concentration, bigger the contact angle and so, more hydrophobic the surface (edge or face. In order to optimize, control and understand this solid-liquid interaction phenomenon is suggested to find out about the hydrophobization mechanism of kaolinite with oleic acid and its percentage of hydrophobization.

  20. Effect of three body interaction in the Hamiltonian of the interacting bosons model

    International Nuclear Information System (INIS)

    Nunes, C.A.A.

    1987-01-01

    The interacting boson model algebra is analysed on the basis of group theory. Through the topological properties of the groups a geometry is associated and the fundamental state of the nucleus is obtained. Calculations were carried out for 102 Ru and 168 Er. (A.C.A.S.) [pt

  1. A model of mechanical interactions between heart and lungs.

    Science.gov (United States)

    Fontecave Jallon, Julie; Abdulhay, Enas; Calabrese, Pascale; Baconnier, Pierre; Gumery, Pierre-Yves

    2009-12-13

    To study the mechanical interactions between heart, lungs and thorax, we propose a mathematical model combining a ventilatory neuromuscular model and a model of the cardiovascular system, as described by Smith et al. (Smith, Chase, Nokes, Shaw & Wake 2004 Med. Eng. Phys.26, 131-139. (doi:10.1016/j.medengphy.2003.10.001)). The respiratory model has been adapted from Thibault et al. (Thibault, Heyer, Benchetrit & Baconnier 2002 Acta Biotheor. 50, 269-279. (doi:10.1023/A:1022616701863)); using a Liénard oscillator, it allows the activity of the respiratory centres, the respiratory muscles and rib cage internal mechanics to be simulated. The minimal haemodynamic system model of Smith includes the heart, as well as the pulmonary and systemic circulation systems. These two modules interact mechanically by means of the pleural pressure, calculated in the mechanical respiratory system, and the intrathoracic blood volume, calculated in the cardiovascular model. The simulation by the proposed model provides results, first, close to experimental data, second, in agreement with the literature results and, finally, highlighting the presence of mechanical cardiorespiratory interactions.

  2. Heat transfer modelling of pulsed laser-tissue interaction

    Science.gov (United States)

    Urzova, J.; Jelinek, M.

    2018-03-01

    Due to their attributes, the application of medical lasers is on the rise in numerous medical fields. From a biomedical point of view, the most interesting applications are the thermal interactions and the photoablative interactions, which effectively remove tissue without excessive heat damage to the remaining tissue. The objective of this work is to create a theoretical model for heat transfer in the tissue following its interaction with the laser beam to predict heat transfer during medical laser surgery procedures. The dimensions of the ablated crater (shape and ablation depth) were determined by computed tomography imaging. COMSOL Multiphysics software was used for temperature modelling. The parameters of tissue and blood, such as density, specific heat capacity, thermal conductivity and diffusivity, were calculated from the chemical ratio. The parameters of laser-tissue interaction, such as absorption and reflection coefficients, were experimentally determined. The parameters of the laser beam were power density, repetition frequency, pulse length and spot dimensions. Heat spreading after laser interaction with tissue was captured using a Fluke thermal camera. The model was verified for adipose tissue, skeletal muscle tissue and heart muscle tissue.

  3. Animal models of gene-environment interactions in schizophrenia.

    Science.gov (United States)

    Ayhan, Yavuz; Sawa, Akira; Ross, Christopher A; Pletnikov, Mikhail V

    2009-12-07

    The pathogenesis of schizophrenia and related mental illnesses likely involves multiple interactions between susceptibility genes of small effects and environmental factors. Gene-environment interactions occur across different stages of neurodevelopment to produce heterogeneous clinical and pathological manifestations of the disease. The main obstacle for mechanistic studies of gene-environment interplay has been the paucity of appropriate experimental systems for elucidating the molecular pathways that mediate gene-environment interactions relevant to schizophrenia. Recent advances in psychiatric genetics and a plethora of experimental data from animal studies allow us to suggest a new approach to gene-environment interactions in schizophrenia. We propose that animal models based on identified genetic mutations and measurable environment factors will help advance studies of the molecular mechanisms of gene-environment interplay.

  4. Interactive modelling with stakeholders in two cases in flood management

    Science.gov (United States)

    Leskens, Johannes; Brugnach, Marcela

    2013-04-01

    New policies on flood management called Multi-Level Safety (MLS), demand for an integral and collaborative approach. The goal of MLS is to minimize flood risks by a coherent package of protection measures, crisis management and flood resilience measures. To achieve this, various stakeholders, such as water boards, municipalities and provinces, have to collaborate in composing these measures. Besides the many advances this integral and collaborative approach gives, the decision-making environment becomes also more complex. Participants have to consider more criteria than they used to do and have to take a wide network of participants into account, all with specific perspectives, cultures and preferences. In response, sophisticated models are developed to support decision-makers in grasping this complexity. These models provide predictions of flood events and offer the opportunity to test the effectiveness of various measures under different criteria. Recent model advances in computation speed and model flexibility allow stakeholders to directly interact with a hydrological hydraulic model during meetings. Besides a better understanding of the decision content, these interactive models are supposed to support the incorporation of stakeholder knowledge in modelling and to support mutual understanding of different perspectives of stakeholders To explore the support of interactive modelling in integral and collaborate policies, such as MLS, we tested a prototype of an interactive flood model (3Di) with respect to a conventional model (Sobek) in two cases. The two cases included the designing of flood protection measures in Amsterdam and a flood event exercise in Delft. These case studies yielded two main results. First, we observed that in the exploration phase of a decision-making process, stakeholders participated actively in interactive modelling sessions. This increased the technical understanding of complex problems and the insight in the effectiveness of various

  5. Model of Collective Fish Behavior with Hydrodynamic Interactions

    Science.gov (United States)

    Filella, Audrey; Nadal, François; Sire, Clément; Kanso, Eva; Eloy, Christophe

    2018-05-01

    Fish schooling is often modeled with self-propelled particles subject to phenomenological behavioral rules. Although fish are known to sense and exploit flow features, these models usually neglect hydrodynamics. Here, we propose a novel model that couples behavioral rules with far-field hydrodynamic interactions. We show that (1) a new "collective turning" phase emerges, (2) on average, individuals swim faster thanks to the fluid, and (3) the flow enhances behavioral noise. The results of this model suggest that hydrodynamic effects should be considered to fully understand the collective dynamics of fish.

  6. Interactive Rapid Dose Assessment Model (IRDAM): user's guide

    International Nuclear Information System (INIS)

    Poeton, R.W.; Moeller, M.P.; Laughlin, G.J.; Desrosiers, A.E.

    1983-05-01

    As part of the continuing emphasis on emergency preparedness the US Nuclear Regulatory Commission (NRC) sponsored the development of a rapid dose assessment system by Pacific Northwest Laboratory (PNL). This system, the Interactive Rapid Dose Assessment Model (IRDAM) is a micro-computer based program for rapidly assessing the radiological impact of accidents at nuclear power plants. This User's Guide provides instruction in the setup and operation of the equipment necessary to run IRDAM. Instructions are also given on how to load the magnetic disks and access the interactive part of the program. Two other companion volumes to this one provide additional information on IRDAM. Reactor Accident Assessment Methods (NUREG/CR-3012, Volume 2) describes the technical bases for IRDAM including methods, models and assumptions used in calculations. Scenarios for Comparing Dose Assessment Models (NUREG/CR-3012, Volume 3) provides the results of calculations made by IRDAM and other models for specific accident scenarios

  7. Weakly hydrated surfaces and the binding interactions of small biological solutes.

    Science.gov (United States)

    Brady, John W; Tavagnacco, Letizia; Ehrlich, Laurent; Chen, Mo; Schnupf, Udo; Himmel, Michael E; Saboungi, Marie-Louise; Cesàro, Attilio

    2012-04-01

    Extended planar hydrophobic surfaces, such as are found in the side chains of the amino acids histidine, phenylalanine, tyrosine, and tryptophan, exhibit an affinity for the weakly hydrated faces of glucopyranose. In addition, molecular species such as these, including indole, caffeine, and imidazole, exhibit a weak tendency to pair together by hydrophobic stacking in aqueous solution. These interactions can be partially understood in terms of recent models for the hydration of extended hydrophobic faces and should provide insight into the architecture of sugar-binding sites in proteins.

  8. An exotic k-essence interpretation of interactive cosmological models

    Energy Technology Data Exchange (ETDEWEB)

    Forte, Monica [Universidad de Buenos Aires, Departamento de Fisica, Facultad de ciencias Exactas y Naturales, Buenos Aires (Argentina)

    2016-01-15

    We define a generalization of scalar fields with non-canonical kinetic term which we call exotic k-essence or, briefly, exotik. These fields are generated by the global description of cosmological models with two interactive fluids in the dark sector and under certain conditions they correspond to usual k-essences. The formalism is applied to the cases of constant potential and of inverse square potential and also we develop the purely exotik version for the modified holographic Ricci type (MHR) of dark energy, where the equations of state are not constant. With the kinetic function F = 1 + mx and the inverse square potential we recover, through the interaction term, the identification between k-essences and quintessences of an exponential potential, already known for Friedmann-Robertson-Walker and Bianchi type I geometries. Worked examples are shown that include the self-interacting MHR and also models with crossing of the phantom divide line (PDL). (orig.)

  9. One-dimensional Ising model with multispin interactions

    Science.gov (United States)

    Turban, Loïc

    2016-09-01

    We study the spin-1/2 Ising chain with multispin interactions K involving the product of m successive spins, for general values of m. Using a change of spin variables the zero-field partition function of a finite chain is obtained for free and periodic boundary conditions and we calculate the two-spin correlation function. When placed in an external field H the system is shown to be self-dual. Using another change of spin variables the one-dimensional Ising model with multispin interactions in a field is mapped onto a zero-field rectangular Ising model with first-neighbour interactions K and H. The 2D system, with size m × N/m, has the topology of a cylinder with helical BC. In the thermodynamic limit N/m\\to ∞ , m\\to ∞ , a 2D critical singularity develops on the self-duality line, \\sinh 2K\\sinh 2H=1.

  10. An exotic k-essence interpretation of interactive cosmological models

    International Nuclear Information System (INIS)

    Forte, Monica

    2016-01-01

    We define a generalization of scalar fields with non-canonical kinetic term which we call exotic k-essence or, briefly, exotik. These fields are generated by the global description of cosmological models with two interactive fluids in the dark sector and under certain conditions they correspond to usual k-essences. The formalism is applied to the cases of constant potential and of inverse square potential and also we develop the purely exotik version for the modified holographic Ricci type (MHR) of dark energy, where the equations of state are not constant. With the kinetic function F = 1 + mx and the inverse square potential we recover, through the interaction term, the identification between k-essences and quintessences of an exponential potential, already known for Friedmann-Robertson-Walker and Bianchi type I geometries. Worked examples are shown that include the self-interacting MHR and also models with crossing of the phantom divide line (PDL). (orig.)

  11. A more general interacting model of holographic dark energy

    International Nuclear Information System (INIS)

    Yu Fei; Zhang Jingfei; Lu Jianbo; Wang Wei; Gui Yuanxing

    2010-01-01

    So far, there have been no theories or observational data that deny the presence of interaction between dark energy and dark matter. We extend naturally the holographic dark energy (HDE) model, proposed by Granda and Oliveros, in which the dark energy density includes not only the square of the Hubble scale, but also the time derivative of the Hubble scale to the case with interaction and the analytic forms for the cosmic parameters are obtained under the specific boundary conditions. The various behaviors concerning the cosmic expansion depend on the introduced numerical parameters which are also constrained. The more general interacting model inherits the features of the previous ones of HDE, keeping the consistency of the theory.

  12. Non-invasive high throughput approach for protein hydrophobicity determination based on surface tension.

    Science.gov (United States)

    Amrhein, Sven; Bauer, Katharina Christin; Galm, Lara; Hubbuch, Jürgen

    2015-12-01

    The surface hydrophobicity of a protein is an important factor for its interactions in solution and thus the outcome of its production process. Yet most of the methods are not able to evaluate the influence of these hydrophobic interactions under natural conditions. In the present work we have established a high resolution stalagmometric method for surface tension determination on a liquid handling station, which can cope with accuracy as well as high throughput requirements. Surface tensions could be derived with a low sample consumption (800 μL) and a high reproducibility (content. The protein influence on the solutions' surface tension was correlated to the hydrophobicity of lysozyme, human lysozyme, BSA, and α-lactalbumin. Differences in proteins' hydrophobic character depending on pH and species could be resolved. Within this work we have developed a pH dependent hydrophobicity ranking, which was found to be in good agreement with literature. For the studied pH range of 3-9 lysozyme from chicken egg white was identified to be the most hydrophilic. α-lactalbumin at pH 3 exhibited the most pronounced hydrophobic character. The stalagmometric method occurred to outclass the widely used spectrophotometric method with bromophenol blue sodium salt as it gave reasonable results without restrictions on pH and protein species. © 2015 Wiley Periodicals, Inc.

  13. Molecular origin of urea driven hydrophobic polymer collapse and unfolding depending on side chain chemistry.

    Science.gov (United States)

    Nayar, Divya; Folberth, Angelina; van der Vegt, Nico F A

    2017-07-19

    Osmolytes affect hydrophobic collapse and protein folding equilibria. The underlying mechanisms are, however, not well understood. We report large-scale conformational sampling of two hydrophobic polymers with secondary and tertiary amide side chains using extensive molecular dynamics simulations. The calculated free energy of unfolding increases with urea for the secondary amide, yet decreases for the tertiary amide, in agreement with experiment. The underlying mechanism is rooted in opposing entropic driving forces: while urea screens the hydrophobic macromolecular interface and drives unfolding of the tertiary amide, urea's concomitant loss in configurational entropy drives collapse of the secondary amide. Only at sufficiently high urea concentrations bivalent urea hydrogen bonding interactions with the secondary amide lead to further stabilisation of its collapsed state. The observations provide a new angle on the interplay between side chain chemistry, urea hydrogen bonding, and the role of urea in attenuating or strengthening the hydrophobic effect.

  14. Interacting Quintessence Dark Energy Models in Lyra Manifold

    International Nuclear Information System (INIS)

    Khurshudyan, M.; Myrzakulov, R.; Sadeghi, J.; Farahani, H.; Pasqua, Antonio

    2014-01-01

    We consider two-component dark energy models in Lyra manifold. The first component is assumed to be a quintessence field while the second component may be a viscous polytropic gas, a viscous Van der Waals gas, or a viscous modified Chaplygin gas. We also consider the possibility of interaction between components. By using the numerical analysis, we study some cosmological parameters of the models and compare them with observational data.

  15. Phase diagram for the Kuramoto model with van Hemmen interactions.

    Science.gov (United States)

    Kloumann, Isabel M; Lizarraga, Ian M; Strogatz, Steven H

    2014-01-01

    We consider a Kuramoto model of coupled oscillators that includes quenched random interactions of the type used by van Hemmen in his model of spin glasses. The phase diagram is obtained analytically for the case of zero noise and a Lorentzian distribution of the oscillators' natural frequencies. Depending on the size of the attractive and random coupling terms, the system displays four states: complete incoherence, partial synchronization, partial antiphase synchronization, and a mix of antiphase and ordinary synchronization.

  16. Cognitive Emotional Regulation Model in Human-Robot Interaction

    OpenAIRE

    Liu, Xin; Xie, Lun; Liu, Anqi; Li, Dan

    2015-01-01

    This paper integrated Gross cognitive process into the HMM (hidden Markov model) emotional regulation method and implemented human-robot emotional interaction with facial expressions and behaviors. Here, energy was the psychological driving force of emotional transition in the cognitive emotional model. The input facial expression was translated into external energy by expression-emotion mapping. Robot’s next emotional state was determined by the cognitive energy (the stimulus after cognition...

  17. Configuration mixing in the sdg interacting boson model

    International Nuclear Information System (INIS)

    Bouldjedri, A; Van Isacker, P; Zerguine, S

    2005-01-01

    A wavefunction analysis of the strong-coupling limits of the sdg interacting boson model is presented. The analysis is carried out for two-boson states and allows us to characterize the boson configuration mixing in the different limits. Based on these results and those of a shell-model analysis of the sdg IBM, qualitative conclusions are drawn about the range of applicability of each limit

  18. Configuration mixing in the sdg interacting boson model

    Energy Technology Data Exchange (ETDEWEB)

    Bouldjedri, A [Department of Physics, Faculty of Science, University of Batna, Avenue Boukhelouf M El Hadi, 05000 Batna (Algeria); Van Isacker, P [GANIL, BP 55027, F-14076 Caen cedex 5 (France); Zerguine, S [Department of Physics, Faculty of Science, University of Batna, Avenue Boukhelouf M El Hadi, 05000 Batna (Algeria)

    2005-11-01

    A wavefunction analysis of the strong-coupling limits of the sdg interacting boson model is presented. The analysis is carried out for two-boson states and allows us to characterize the boson configuration mixing in the different limits. Based on these results and those of a shell-model analysis of the sdg IBM, qualitative conclusions are drawn about the range of applicability of each limit.

  19. The sdg interacting-boson model applied to 168Er

    Science.gov (United States)

    Yoshinaga, N.; Akiyama, Y.; Arima, A.

    1986-03-01

    The sdg interacting-boson model is applied to 168Er. Energy levels and E2 transitions are calculated. This model is shown to solve the problem of anharmonicity regarding the excitation energy of the first Kπ=4+ band relative to that of the first Kπ=2+ one. The level scheme including the Kπ=3+ band is well reproduced and the calculated B(E2)'s are consistent with the experimental data.

  20. Sensitivity analysis of physiochemical interaction model: which pair ...

    African Journals Online (AJOL)

    ... of two model parameters at a time on the solution trajectory of physiochemical interaction over a time interval. Our aim is to use this powerful mathematical technique to select the important pair of parameters of this physical process which is cost-effective. Keywords: Passivation Rate, Sensitivity Analysis, ODE23, ODE45 ...

  1. Weak interactions physics: from its birth to the eletroweak model

    International Nuclear Information System (INIS)

    Lopes, J.L.

    1987-01-01

    A review of the evolution of weak interaction physics from its beginning (Fermi-Majorana-Perrin) to the eletroweak model (Glashow-Weinberg-Salam). Contributions from Brazilian physicists are specially mentioned as well as the first prediction of electroweak-unification, of the neutral intermediate vector Z 0 and the first approximate value of the mass of the W-bosons. (Author) [pt

  2. Framework for Modelling Multiple Input Complex Aggregations for Interactive Installations

    DEFF Research Database (Denmark)

    Padfield, Nicolas; Andreasen, Troels

    2012-01-01

    on fuzzy logic and provides a method for variably balancing interaction and user input with the intention of the artist or director. An experimental design is presented, demonstrating an intuitive interface for parametric modelling of a complex aggregation function. The aggregation function unifies...

  3. The Frenkel-Kontorova model with nonconvex interparticle interactions

    International Nuclear Information System (INIS)

    Marianer, S.; Bishop, A.R.; Pouget, J.

    1987-01-01

    A study is presented of the ground state and excitations of the Frenkel-Kontorova model with nonconvex interparticle interactions, emphasizing the special effects of the nonconvexity on the ground state and on the excitations. This study has been limited to nonconvexity with two competing length scales. 10 refs., 3 figs

  4. An Online Interactive Competition Model for E-Learning System ...

    African Journals Online (AJOL)

    An Online Interactive Competition Model for E-Learning System. ... A working prototype of the system was developed using MySQL Database Management System (DBMS), PHP as the scripting language and Apache as the web server. The system was tested and the results were presented graphically in this paper.

  5. Representing climate, disturbance, and vegetation interactions in landscape models

    Science.gov (United States)

    Robert E. Keane; Donald McKenzie; Donald A. Falk; Erica A.H. Smithwick; Carol Miller; Lara-Karena B. Kellogg

    2015-01-01

    The prospect of rapidly changing climates over the next century calls for methods to predict their effects on myriad, interactive ecosystem processes. Spatially explicit models that simulate ecosystem dynamics at fine (plant, stand) to coarse (regional, global) scales are indispensable tools for meeting this challenge under a variety of possible futures. A special...

  6. Interactive Model-Centric Systems Engineering (IMCSE) Phase 5

    Science.gov (United States)

    2018-02-28

    Interactive Model-Centric Systems Engineering (IMCSE) Phase 5 Technical Report SERC-2018-TR-104 Feb 28, 2018 Principal Investigator...Date February 28, 2018 Copyright © 2018 Stevens Institute of Technology, Systems Engineering ...Research Center The Systems Engineering Research Center (SERC) is a federally funded University Affiliated Research Center managed by Stevens

  7. Kinetic models in spin chemistry. 1. The hyperfine interaction

    DEFF Research Database (Denmark)

    Mojaza, M.; Pedersen, J. B.

    2012-01-01

    Kinetic models for quantum systems are quite popular due to their simplicity, although they are difficult to justify. We show that the transformation from quantum to kinetic description can be done exactly for the hyperfine interaction of one nuclei with arbitrary spin; more spins are described w...... induced enhancement of the reaction yield. (C) 2012 Elsevier B.V. All rights reserved....

  8. Gnotobiotic mouse model's contribution to understanding host-pathogen interactions

    Czech Academy of Sciences Publication Activity Database

    Kubelková, K.; Benuchová, M.; Kozáková, Hana; Šinkora, Marek; Kročová, Z.; Pejchal, J.; Macela, A.

    2016-01-01

    Roč. 73, č. 20 (2016), s. 3961-3969 ISSN 1420-682X R&D Projects: GA ČR GA15-02274S Institutional support: RVO:61388971 Keywords : Germ- free model * Gnotobiology * Host-pathogen interaction Subject RIV: EC - Immunology Impact factor: 5.788, year: 2016

  9. Intrinsic states in the sdg interacting boson model

    International Nuclear Information System (INIS)

    Yoshinaga, N.

    1986-01-01

    We give the intrinsic states explicitly in the boson representation in the framework of the sdg interacting boson model. Although they are only valid in the large-N limit, they are useful to estimate various physical quantities in well deformed nuclei. One can compare these results with those predicted in the IBM1 or in the IBM2. (orig.)

  10. Intrinsic states in the sdg interacting boson model

    Energy Technology Data Exchange (ETDEWEB)

    Yoshinaga, N.

    1986-08-04

    We give the intrinsic states explicitly in the boson representation in the framework of the sdg interacting boson model. Although they are only valid in the large-N limit, they are useful to estimate various physical quantities in well deformed nuclei. One can compare these results with those predicted in the IBM1 or in the IBM2.

  11. Geometry of coexistence in the interacting boson model

    International Nuclear Information System (INIS)

    Van Isacker, P.; Frank, A.; Vargas, C.E.

    2004-01-01

    The Interacting Boson Model (IBM) with configuration mixing is applied to describe the phenomenon of coexistence in nuclei. The analysis suggests that the IBM with configuration mixing, used in conjunction with a (matrix) coherent-state method, may be a reliable tool for the study of geometric aspects of shape coexistence in nuclei

  12. Interactive Model-Centric Systems Engineering (IMCSE) Phase Two

    Science.gov (United States)

    2015-02-28

    109 Backend Implementation...as cell-phone GPS data offers unprecedented tracking of commuting, mobility , and navigation patterns within the urban environment. And yet many...Task 4 develops a service API to collect and query results across model executions. Task 5 implements the backend components to interact 160 Forio

  13. The independent molecular interaction sites model. Pt. 1

    International Nuclear Information System (INIS)

    Naumann, K.H.; Lippert, E.

    1981-01-01

    A new reference system for the treatment of molecular fluids within the framework of thermodynamic perturbation theory is presented. The basic ingredient of our approach is a potential transformation which allows us to view molecular liquids and gases as mixtures of formally independent molecular interaction sites (IMIS model). Some relations between out method and the RAM theory are discussed. (orig.)

  14. Interactive computer graphics for bio-stereochemical modelling

    Indian Academy of Sciences (India)

    Proc, Indian Acad. Sci., Vol. 87 A (Chem. Sci.), No. 4, April 1978, pp. 95-113, (e) printed in India. Interactive computer graphics for bio-stereochemical modelling. ROBERT REIN, SHLOMONIR, KAREN HAYDOCK and. ROBERTD MACELROY. Department of Experimental Pathology, Roswell Park Memorial Institute,. 666 Elm ...

  15. Modeling attacker-defender interactions in information networks.

    Energy Technology Data Exchange (ETDEWEB)

    Collins, Michael Joseph

    2010-09-01

    The simplest conceptual model of cybersecurity implicitly views attackers and defenders as acting in isolation from one another: an attacker seeks to penetrate or disrupt a system that has been protected to a given level, while a defender attempts to thwart particular attacks. Such a model also views all non-malicious parties as having the same goal of preventing all attacks. But in fact, attackers and defenders are interacting parts of the same system, and different defenders have their own individual interests: defenders may be willing to accept some risk of successful attack if the cost of defense is too high. We have used game theory to develop models of how non-cooperative but non-malicious players in a network interact when there is a substantial cost associated with effective defensive measures. Although game theory has been applied in this area before, we have introduced some novel aspects of player behavior in our work, including: (1) A model of how players attempt to avoid the costs of defense and force others to assume these costs; (2) A model of how players interact when the cost of defending one node can be shared by other nodes; and (3) A model of the incentives for a defender to choose less expensive, but less effective, defensive actions.

  16. Feed forward neural networks modeling for K-P interactions

    International Nuclear Information System (INIS)

    El-Bakry, M.Y.

    2003-01-01

    Artificial intelligence techniques involving neural networks became vital modeling tools where model dynamics are difficult to track with conventional techniques. The paper make use of the feed forward neural networks (FFNN) to model the charged multiplicity distribution of K-P interactions at high energies. The FFNN was trained using experimental data for the multiplicity distributions at different lab momenta. Results of the FFNN model were compared to that generated using the parton two fireball model and the experimental data. The proposed FFNN model results showed good fitting to the experimental data. The neural network model performance was also tested at non-trained space and was found to be in good agreement with the experimental data

  17. Interaction of Flavonoids from Woodwardia unigemmata with Bovine Serum Albumin (BSA): Application of Spectroscopic Techniques and Molecular Modeling Methods.

    Science.gov (United States)

    Ma, Rui; Pan, Hong; Shen, Tao; Li, Peng; Chen, Yanan; Li, Zhenyu; Di, Xiaxia; Wang, Shuqi

    2017-08-09

    Phytochemical investigation on the methanol extract of Woodwardia unigemmata resulted in the isolation of seven flavonoids, including one new flavonol acylglycoside ( 1 ). The structures of these compounds were elucidated on the basis of extensive spectroscopic analysis and comparison of literature data. The multidrug resistance (MDR) reversing activity was evaluated for the isolated compounds using doxorubicin-resistant K562/A02 cells model. Compound 6 showed comparable MDR reversing effect to verapamil. Furthermore, the interaction between compounds and bovine serum albumin (BSA) was investigated by spectroscopic methods, including steady-state fluorescence, synchronous fluorescence, circular dichroism (CD) spectroscopies, and molecular docking approach. The experimental results indicated that the seven flavonoids bind to BSA by static quenching mechanisms. The negative ΔH and ΔS values indicated that van der Waals interactions and hydrogen bonds contributed in the binding of compounds 2 - 6 to BSA. In the case of compounds 1 and 7 systems, the hydrophobic interactions play a major role. The binding of compounds to BSA causes slight changes in the secondary structure of BSA. There are two binding sites of compound 6 on BSA and site I is the main site according to the molecular docking studies and the site marker competitive binding assay.

  18. Entropic formulation for the protein folding process: Hydrophobic stability correlates with folding rates

    Science.gov (United States)

    Dal Molin, J. P.; Caliri, A.

    2018-01-01

    Here we focus on the conformational search for the native structure when it is ruled by the hydrophobic effect and steric specificities coming from amino acids. Our main tool of investigation is a 3D lattice model provided by a ten-letter alphabet, the stereochemical model. This minimalist model was conceived for Monte Carlo (MC) simulations when one keeps in mind the kinetic behavior of protein-like chains in solution. We have three central goals here. The first one is to characterize the folding time (τ) by two distinct sampling methods, so we present two sets of 103 MC simulations for a fast protein-like sequence. The resulting sets of characteristic folding times, τ and τq were obtained by the application of the standard Metropolis algorithm (MA), as well as by an enhanced algorithm (Mq A). The finding for τq shows two things: (i) the chain-solvent hydrophobic interactions {hk } plus a set of inter-residues steric constraints {ci,j } are able to emulate the conformational search for the native structure. For each one of the 103MC performed simulations, the target is always found within a finite time window; (ii) the ratio τq / τ ≅ 1 / 10 suggests that the effect of local thermal fluctuations, encompassed by the Tsallis weight, provides to the chain an innate efficiency to escape from energetic and steric traps. We performed additional MC simulations with variations of our design rule to attest this first result, both algorithms the MA and the Mq A were applied to a restricted set of targets, a physical insight is provided. Our second finding was obtained by a set of 600 independent MC simulations, only performed with the Mq A applied to an extended set of 200 representative targets, our native structures. The results show how structural patterns should modulate τq, which cover four orders of magnitude; this finding is our second goal. The third, and last result, was obtained with a special kind of simulation performed with the purpose to explore a

  19. Baryons and baryonic matter in four-fermion interaction models

    International Nuclear Information System (INIS)

    Urlichs, K.

    2007-01-01

    In this work we discuss baryons and baryonic matter in simple four-fermion interaction theories, the Gross-Neveu model and the Nambu-Jona-Lasinio model in 1+1 and 2+1 space-time dimensions. These models are designed as toy models for dynamical symmetry breaking in strong interaction physics. Pointlike interactions (''four-fermion'' interactions) between quarks replace the full gluon mediated interaction of quantum chromodynamics. We consider the limit of a large number of fermion flavors, where a mean field approach becomes exact. This method is formulated in the language of relativistic many particle theory and is equivalent to the Hartree-Fock approximation. In 1+1 dimensions, we generalize known results on the ground state to the case where chiral symmetry is broken explicitly by a bare mass term. For the Gross-Neveu model, we derive an exact self-consistent solution for the finite density ground state, consisting of a one-dimensional array of equally spaced potential wells, a baryon crystal. For the Nambu- Jona-Lasinio model we apply the derivative expansion technique to calculate the total energy in powers of derivatives of the mean field. In a picture akin to the Skyrme model of nuclear physics, the baryon emerges as a topological soliton. The solution for both the single baryon and dense baryonic matter is given in a systematic expansion in powers of the pion mass. The solution of the Hartree-Fock problem is more complicated in 2+1 dimensions. In the massless Gross-Neveu model we derive an exact self-consistent solution by extending the baryon crystal of the 1+1 dimensional model, maintaining translational invariance in one spatial direction. This one-dimensional configuration is energetically degenerate to the translationally invariant solution, a hint in favor of a possible translational symmetry breakdown by more general geometrical structures. In the Nambu-Jona-Lasinio model, topological soliton configurations induce a finite baryon number. In contrast

  20. Baryons and baryonic matter in four-fermion interaction models

    Energy Technology Data Exchange (ETDEWEB)

    Urlichs, K.

    2007-02-23

    In this work we discuss baryons and baryonic matter in simple four-fermion interaction theories, the Gross-Neveu model and the Nambu-Jona-Lasinio model in 1+1 and 2+1 space-time dimensions. These models are designed as toy models for dynamical symmetry breaking in strong interaction physics. Pointlike interactions (''four-fermion'' interactions) between quarks replace the full gluon mediated interaction of quantum chromodynamics. We consider the limit of a large number of fermion flavors, where a mean field approach becomes exact. This method is formulated in the language of relativistic many particle theory and is equivalent to the Hartree-Fock approximation. In 1+1 dimensions, we generalize known results on the ground state to the case where chiral symmetry is broken explicitly by a bare mass term. For the Gross-Neveu model, we derive an exact self-consistent solution for the finite density ground state, consisting of a one-dimensional array of equally spaced potential wells, a baryon crystal. For the Nambu- Jona-Lasinio model we apply the derivative expansion technique to calculate the total energy in powers of derivatives of the mean field. In a picture akin to the Skyrme model of nuclear physics, the baryon emerges as a topological soliton. The solution for both the single baryon and dense baryonic matter is given in a systematic expansion in powers of the pion mass. The solution of the Hartree-Fock problem is more complicated in 2+1 dimensions. In the massless Gross-Neveu model we derive an exact self-consistent solution by extending the baryon crystal of the 1+1 dimensional model, maintaining translational invariance in one spatial direction. This one-dimensional configuration is energetically degenerate to the translationally invariant solution, a hint in favor of a possible translational symmetry breakdown by more general geometrical structures. In the Nambu-Jona-Lasinio model, topological soliton configurations induce a finite baryon

  1. Systems pharmacology - Towards the modeling of network interactions.

    Science.gov (United States)

    Danhof, Meindert

    2016-10-30

    Mechanism-based pharmacokinetic and pharmacodynamics (PKPD) and disease system (DS) models have been introduced in drug discovery and development research, to predict in a quantitative manner the effect of drug treatment in vivo in health and disease. This requires consideration of several fundamental properties of biological systems behavior including: hysteresis, non-linearity, variability, interdependency, convergence, resilience, and multi-stationarity. Classical physiology-based PKPD models consider linear transduction pathways, connecting processes on the causal path between drug administration and effect, as the basis of drug action. Depending on the drug and its biological target, such models may contain expressions to characterize i) the disposition and the target site distribution kinetics of the drug under investigation, ii) the kinetics of target binding and activation and iii) the kinetics of transduction. When connected to physiology-based DS models, PKPD models can characterize the effect on disease progression in a mechanistic manner. These models have been found useful to characterize hysteresis and non-linearity, yet they fail to explain the effects of the other fundamental properties of biological systems behavior. Recently systems pharmacology has been introduced as novel approach to predict in vivo drug effects, in which biological networks rather than single transduction pathways are considered as the basis of drug action and disease progression. These models contain expressions to characterize the functional interactions within a biological network. Such interactions are relevant when drugs act at multiple targets in the network or when homeostatic feedback mechanisms are operative. As a result systems pharmacology models are particularly useful to describe complex patterns of drug action (i.e. synergy, oscillatory behavior) and disease progression (i.e. episodic disorders). In this contribution it is shown how physiology-based PKPD and

  2. A unitarized meson model including color Coulomb interaction

    International Nuclear Information System (INIS)

    Metzger, Kees.

    1990-01-01

    Ch. 1 gives a general introduction into the problem field of the thesis. It discusses in how far the internal structure of mesons is understood theoretically and which models exist. It discusses from a phenomenological point of view the problem of confinement indicates how quark models of mesons may provide insight in this phenomenon. In ch. 2 the formal theory of scattering in a system with confinement is given. It is shown how a coupled channel (CC) description and the work of other authors fit into this general framework. Explicit examples and arguments are given to support the CC treatment of such a system. In ch. 3 the full coupled-channel model as is employed in this thesis is presented. On the basis of arguments from the former chapters and the observed regularities in the experimental data, the choices underlying the model are supported. In this model confinement is described with a mass-dependent harmonic-oscillator potential and the presence of open (meson-meson) channels plays an essential role. In ch. 4 the unitarized model is applied to light scalar meson resonances. In this regime the contribution of the open channels is considerable. It is demonstrated that the model parameters as used for the description of the pseudo-scalar and vector mesons, unchanged can be used for the description of these mesons. Ch. 5 treats the color-Coulomb interaction. There the effect of the Coulomb interaction is studied in simple models without decay. The results of incorporating the color-Coulomb interaction into the full CC model are given in ch.6. Ch. 7 discusses the results of the previous chapters and the present status of the model. (author). 182 refs.; 16 figs.; 33 tabs

  3. Hysteretic Models Considering Axial-Shear-Flexure Interaction

    Science.gov (United States)

    Ceresa, Paola; Negrisoli, Giorgio

    2017-10-01

    Most of the existing numerical models implemented in finite element (FE) software, at the current state of the art, are not capable to describe, with enough reliability, the interaction between axial, shear and flexural actions under cyclic loading (e.g. seismic actions), neglecting crucial effects for predicting the nature of the collapse of reinforced concrete (RC) structural elements. Just a few existing 3D volume models or fibre beam models can lead to a quite accurate response, but they are still computationally inefficient for typical applications in earthquake engineering and also characterized by very complex formulation. Thus, discrete models with lumped plasticity hinges may be the preferred choice for modelling the hysteretic behaviour due to cyclic loading conditions, in particular with reference to its implementation in a commercial software package. These considerations lead to this research work focused on the development of a model for RC beam-column elements able to consider degradation effects and interaction between the actions under cyclic loading conditions. In order to develop a model for a general 3D discrete hinge element able to take into account the axial-shear-flexural interaction, it is necessary to provide an implementation which involves a corrector-predictor iterative scheme. Furthermore, a reliable constitutive model based on damage plasticity theory is formulated and implemented for its numerical validation. Aim of this research work is to provide the formulation of a numerical model, which will allow implementation within a FE software package for nonlinear cyclic analysis of RC structural members. The developed model accounts for stiffness degradation effect and stiffness recovery for loading reversal.

  4. Heating and reduction affect the reaction with tannins of wine protein fractions differing in hydrophobicity.

    Science.gov (United States)

    Marangon, Matteo; Vincenzi, Simone; Lucchetta, Marco; Curioni, Andrea

    2010-02-15

    During the storage, bottled white wines can manifest haziness due to the insolubilisation of the grape proteins that may 'survive' in the fermentation process. Although the exact mechanism of this occurrence is not fully understood, proteins and tannins are considered two of the key factors involved in wine hazing, since their aggregation leads to the formation of insoluble particles. To better understand this complex interaction, proteins and tannins from the same unfined Pinot grigio wine were separated. Wine proteins were then fractionated by hydrophobic interaction chromatography (HIC). A significant correlation between hydrophobicity of the wine protein fractions and the haze formed after reacting with wine tannins was found, with the most reactive fractions revealing (by SDS-PAGE and RP-HPLC analyses) the predominant presence of thaumatin-like proteins. Moreover, the effects of both protein heating and disulfide bonds reduction (with dithiotreithol) on haze formation in the presence of tannins were assessed. These treatments generally resulted in an improved reactivity with tannins, and this phenomenon was related to both the surface hydrophobicity and composition of the protein fractions. Therefore, haze formation in wines seems to be related to hydrophobic interactions occurring among proteins and tannins. These interactions should occur on hydrophobic tannin-binding sites, whose exposition on the proteins can depend on both protein heating and reduction. Copyright 2009 Elsevier B.V. All rights reserved.

  5. Adsorption of hydrophobin on different self-assembled monolayers: the role of the hydrophobic dipole and the electric dipole.

    Science.gov (United States)

    Peng, Chunwang; Liu, Jie; Zhao, Daohui; Zhou, Jian

    2014-09-30

    In this work, the adsorptions of hydrophobin (HFBI) on four different self-assembled monolayers (SAMs) (i.e., CH3-SAM, OH-SAM, COOH-SAM, and NH2-SAM) were investigated by parallel tempering Monte Carlo and molecular dynamics simulations. Simulation results indicate that the orientation of HFBI adsorbed on neutral surfaces is dominated by a hydrophobic dipole. HFBI adsorbs on the hydrophobic CH3-SAM through its hydrophobic patch and adopts a nearly vertical hydrophobic dipole relative to the surface, while it is nearly horizontal when adsorbed on the hydrophilic OH-SAM. For charged SAM surfaces, HFBI adopts a nearly vertical electric dipole relative to the surface. HFBI has the narrowest orientation distribution on the CH3-SAM, and thus can form an ordered monolayer and reverse the wettability of the surface. For HFBI adsorption on charged SAMs, the adsorption strength weakens as the surface charge density increases. Compared with those on other SAMs, a larger area of the hydrophobic patch is exposed to the solution when HFBI adsorbs on the NH2-SAM. This leads to an increase of the hydrophobicity of the surface, which is consistent with the experimental results. The binding of HFBI to the CH3-SAM is mainly through hydrophobic interactions, while it is mediated through a hydration water layer near the surface for the OH-SAM. For the charged SAM surfaces, the adsorption is mainly induced by electrostatic interactions between the charged surfaces and the oppositely charged residues. The effect of a hydrophobic dipole on protein adsorption onto hydrophobic surfaces is similar to that of an electric dipole for charged surfaces. Therefore, the hydrophobic dipole may be applied to predict the probable orientations of protein adsorbed on hydrophobic surfaces.

  6. Semantic Interaction for Sensemaking: Inferring Analytical Reasoning for Model Steering.

    Science.gov (United States)

    Endert, A; Fiaux, P; North, C

    2012-12-01

    Visual analytic tools aim to support the cognitively demanding task of sensemaking. Their success often depends on the ability to leverage capabilities of mathematical models, visualization, and human intuition through flexible, usable, and expressive interactions. Spatially clustering data is one effective metaphor for users to explore similarity and relationships between information, adjusting the weighting of dimensions or characteristics of the dataset to observe the change in the spatial layout. Semantic interaction is an approach to user interaction in such spatializations that couples these parametric modifications of the clustering model with users' analytic operations on the data (e.g., direct document movement in the spatialization, highlighting text, search, etc.). In this paper, we present results of a user study exploring the ability of semantic interaction in a visual analytic prototype, ForceSPIRE, to support sensemaking. We found that semantic interaction captures the analytical reasoning of the user through keyword weighting, and aids the user in co-creating a spatialization based on the user's reasoning and intuition.

  7. Incorporating Context Dependency of Species Interactions in Species Distribution Models.

    Science.gov (United States)

    Lany, Nina K; Zarnetske, Phoebe L; Gouhier, Tarik C; Menge, Bruce A

    2017-07-01

    Species distribution models typically use correlative approaches that characterize the species-environment relationship using occurrence or abundance data for a single species. However, species distributions are determined by both abiotic conditions and biotic interactions with other species in the community. Therefore, climate change is expected to impact species through direct effects on their physiology and indirect effects propagated through their resources, predators, competitors, or mutualists. Furthermore, the sign and strength of species interactions can change according to abiotic conditions, resulting in context-dependent species interactions that may change across space or with climate change. Here, we incorporated the context dependency of species interactions into a dynamic species distribution model. We developed a multi-species model that uses a time-series of observational survey data to evaluate how abiotic conditions and species interactions affect the dynamics of three rocky intertidal species. The model further distinguishes between the direct effects of abiotic conditions on abundance and the indirect effects propagated through interactions with other species. We apply the model to keystone predation by the sea star Pisaster ochraceus on the mussel Mytilus californianus and the barnacle Balanus glandula in the rocky intertidal zone of the Pacific coast, USA. Our method indicated that biotic interactions between P. ochraceus and B. glandula affected B. glandula dynamics across >1000 km of coastline. Consistent with patterns from keystone predation, the growth rate of B. glandula varied according to the abundance of P. ochraceus in the previous year. The data and the model did not indicate that the strength of keystone predation by P. ochraceus varied with a mean annual upwelling index. Balanus glandula cover increased following years with high phytoplankton abundance measured as mean annual chlorophyll-a. M. californianus exhibited the same

  8. Reexploration of interacting holographic dark energy model. Cases of interaction term excluding the Hubble parameter

    Energy Technology Data Exchange (ETDEWEB)

    Li, Hai-Li; Zhang, Jing-Fei; Feng, Lu [Northeastern University, Department of Physics, College of Sciences, Shenyang (China); Zhang, Xin [Northeastern University, Department of Physics, College of Sciences, Shenyang (China); Peking University, Center for High Energy Physics, Beijing (China)

    2017-12-15

    In this paper, we make a deep analysis for the five typical interacting holographic dark energy models with the interaction terms Q = 3βH{sub 0}ρ{sub de}, Q = 3βH{sub 0}ρ{sub c}, Q = 3βH{sub 0}(ρ{sub de} + ρ{sub c}), Q = 3βH{sub 0}√(ρ{sub de}ρ{sub c}), and Q = 3βH{sub 0}(ρ{sub de}ρ{sub c})/(ρ{sub de}+ρ{sub c}), respectively. We obtain observational constraints on these models by using the type Ia supernova data (the Joint Light-Curve Analysis sample), the cosmic microwave background data (Planck 2015 distance priors), the baryon acoustic oscillations data, and the direct measurement of the Hubble constant. We find that the values of χ{sub min}{sup 2} for all the five models are almost equal (around 699), indicating that the current observational data equally favor these IHDE models. In addition, a comparison with the cases of an interaction term involving the Hubble parameter H is also made. (orig.)

  9. Pathways to dewetting in hydrophobic confinement.

    Science.gov (United States)

    Remsing, Richard C; Xi, Erte; Vembanur, Srivathsan; Sharma, Sumit; Debenedetti, Pablo G; Garde, Shekhar; Patel, Amish J

    2015-07-07

    Liquid water can become metastable with respect to its vapor in hydrophobic confinement. The resulting dewetting transitions are often impeded by large kinetic barriers. According to macroscopic theory, such barriers arise from the free energy required to nucleate a critical vapor tube that spans the region between two hydrophobic surfaces--tubes with smaller radii collapse, whereas larger ones grow to dry the entire confined region. Using extensive molecular simulations of water between two nanoscopic hydrophobic surfaces, in conjunction with advanced sampling techniques, here we show that for intersurface separations that thermodynamically favor dewetting, the barrier to dewetting does not correspond to the formation of a (classical) critical vapor tube. Instead, it corresponds to an abrupt transition from an isolated cavity adjacent to one of the confining surfaces to a gap-spanning vapor tube that is already larger than the critical vapor tube anticipated by macroscopic theory. Correspondingly, the barrier to dewetting is also smaller than the classical expectation. We show that the peculiar nature of water density fluctuations adjacent to extended hydrophobic surfaces--namely, the enhanced likelihood of observing low-density fluctuations relative to Gaussian statistics--facilitates this nonclassical behavior. By stabilizing isolated cavities relative to vapor tubes, enhanced water density fluctuations thus stabilize novel pathways, which circumvent the classical barriers and offer diminished resistance to dewetting. Our results thus suggest a key role for fluctuations in speeding up the kinetics of numerous phenomena ranging from Cassie-Wenzel transitions on superhydrophobic surfaces, to hydrophobically driven biomolecular folding and assembly.

  10. Evaporation rate of water in hydrophobic confinement.

    Science.gov (United States)

    Sharma, Sumit; Debenedetti, Pablo G

    2012-03-20

    The drying of hydrophobic cavities is believed to play an important role in biophysical phenomena such as the folding of globular proteins, the opening and closing of ligand-gated ion channels, and ligand binding to hydrophobic pockets. We use forward flux sampling, a molecular simulation technique, to compute the rate of capillary evaporation of water confined between two hydrophobic surfaces separated by nanoscopic gaps, as a function of gap, surface size, and temperature. Over the range of conditions investigated (gaps between 9 and 14 Å and surface areas between 1 and 9 nm(2)), the free energy barrier to evaporation scales linearly with the gap between hydrophobic surfaces, suggesting that line tension makes the predominant contribution to the free energy barrier. The exponential dependence of the evaporation rate on the gap between confining surfaces causes a 10 order-of-magnitude decrease in the rate when the gap increases from 9 to 14 Å. The computed free energy barriers are of the order of 50 kT and are predominantly enthalpic. Evaporation rates per unit area are found to be two orders of magnitude faster in confinement by the larger (9 nm(2)) than by the smaller (1 nm(2)) surfaces considered here, at otherwise identical conditions. We show that this rate enhancement is a consequence of the dependence of hydrophobic hydration on the size of solvated objects. For sufficiently large surfaces, the critical nucleus for the evaporation process is a gap-spanning vapor tube.

  11. Mechanical Interaction in Pressurized Pipe Systems: Experiments and Numerical Models

    Directory of Open Access Journals (Sweden)

    Mariana Simão

    2015-11-01

    Full Text Available The dynamic interaction between the unsteady flow occurrence and the resulting vibration of the pipe are analyzed based on experiments and numerical models. Waterhammer, structural dynamic and fluid–structure interaction (FSI are the main subjects dealt with in this study. Firstly, a 1D model is developed based on the method of characteristics (MOC using specific damping coefficients for initial components associated with rheological pipe material behavior, structural and fluid deformation, and type of anchored structural supports. Secondly a 3D coupled complex model based on Computational Fluid Dynamics (CFD, using a Finite Element Method (FEM, is also applied to predict and distinguish the FSI events. Herein, a specific hydrodynamic model of viscosity to replicate the operation of a valve was also developed to minimize the number of mesh elements and the complexity of the system. The importance of integrated analysis of fluid–structure interaction, especially in non-rigidity anchored pipe systems, is equally emphasized. The developed models are validated through experimental tests.

  12. A model of interacting strings and the Hagedorn phase transition

    International Nuclear Information System (INIS)

    Lizzi, F.; Senda, I.

    1990-03-01

    In this letter we introduce a model of interacting string in which the usual ideal gas approximations are not made. The model is constructed in analogy with nucleation models, the formation of droplets in a supersaturate gas. We consider the strings to be interacting and their number not fixed. The equilibrium configuration is the one for which the time derivatives of the number of strings in the various energies vanishes. We evaluate numerically the equilibrium configurations for various values of the energy density. We find that a density of order one in planck units there is a sharp transition, from a 'gas' phase in which there are many strings, all in the massless or first few excited states, to a 'liquid' phase in which all strings have coalesced into one (or few) highly excited string. (author). 14 refs, 4 figs

  13. ANNIE - INTERACTIVE PROCESSING OF DATA BASES FOR HYDROLOGIC MODELS.

    Science.gov (United States)

    Lumb, Alan M.; Kittle, John L.

    1985-01-01

    ANNIE is a data storage and retrieval system that was developed to reduce the time and effort required to calibrate, verify, and apply watershed models that continuously simulate water quantity and quality. Watershed models have three categories of input: parameters to describe segments of a drainage area, linkage of the segments, and time-series data. Additional goals for ANNIE include the development of software that is easily implemented on minicomputers and some microcomputers and software that has no special requirements for interactive display terminals. Another goal is for the user interaction to be based on the experience of the user so that ANNIE is helpful to the inexperienced user and yet efficient and brief for the experienced user. Finally, the code should be designed so that additional hydrologic models can easily be added to ANNIE.

  14. Modeling molecular boiling points using computed interaction energies.

    Science.gov (United States)

    Peterangelo, Stephen C; Seybold, Paul G

    2017-12-20

    The noncovalent van der Waals interactions between molecules in liquids are typically described in textbooks as occurring between the total molecular dipoles (permanent, induced, or transient) of the molecules. This notion was tested by examining the boiling points of 67 halogenated hydrocarbon liquids using quantum chemically calculated molecular dipole moments, ionization potentials, and polarizabilities obtained from semi-empirical (AM1 and PM3) and ab initio Hartree-Fock [HF 6-31G(d), HF 6-311G(d,p)], and density functional theory [B3LYP/6-311G(d,p)] methods. The calculated interaction energies and an empirical measure of hydrogen bonding were employed to model the boiling points of the halocarbons. It was found that only terms related to London dispersion energies and hydrogen bonding proved significant in the regression analyses, and the performances of the models generally improved at higher levels of quantum chemical computation. An empirical estimate for the molecular polarizabilities was also tested, and the best models for the boiling points were obtained using either this empirical polarizability itself or the polarizabilities calculated at the B3LYP/6-311G(d,p) level, along with the hydrogen-bonding parameter. The results suggest that the cohesive forces are more appropriately described as resulting from highly localized interactions rather than interactions between the global molecular dipoles.

  15. Multi-physics fluid-structure interaction modelling software

    CSIR Research Space (South Africa)

    Malan, AG

    2008-11-01

    Full Text Available -structure interaction modelling software AG MALAN AND O OXTOBY CSIR Defence, Peace, Safety and Security, PO Box 395, Pretoria, 0001 Email: amalan@csir.co.za – www.csir.co.za Internationally leading aerospace company Airbus sponsored key components... of the development of the CSIR fl uid-structure interaction (FSI) software. Below are extracts from their evaluation of the devel- oped technology: “The fi eld of FSI covers a massive range of engineering problems, each with their own multi-parameter, individual...

  16. Mathematical models and methods of localized interaction theory

    CERN Document Server

    Bunimovich, AI

    1995-01-01

    The interaction of the environment with a moving body is called "localized" if it has been found or assumed that the force or/and thermal influence of the environment on each body surface point is independent and can be determined by the local geometrical and kinematical characteristics of this point as well as by the parameters of the environment and body-environment interactions which are the same for the whole surface of contact.Such models are widespread in aerodynamics and gas dynamics, covering supersonic and hypersonic flows, and rarefied gas flows. They describe the influence of light

  17. Heavy-ion interactions in relativistic mean-field models

    International Nuclear Information System (INIS)

    Rashdan, M.

    1996-01-01

    The interaction potential between spherical nuclei and the elastic scattering cross section are calculated within relativistic mean-field (linear and non-linear) models, using a generalized relativistic local density approximation. The nuclear densities are calculated self-consistently from the solution of the relativistic mean-field equations. It is found that both the linear and non-linear models predict the characteristic switching-over phenomenon of the heavy-ion nuclear potential, where the potential gets attraction with increasing energy up to some value where it reverses this behaviour. The non-linear NLC model predicts a deeper potential than the linear LW model. The elastic scattering cross section calculated within the non-linear NLC model is in better agreement with experiments than that calculated within the linear LW model. (orig.)

  18. In-line gas chromatographic apparatus for measuring the hydrophobic micropore volume (HMV) and contaminant transformation in mineral micropores.

    Science.gov (United States)

    Cheng, Hefa; Reinhard, Martin

    2010-07-15

    Desorption of hydrophobic organic compounds from micropores is characteristically slow compared to surface adsorption and partitioning. The slow-desorbing mass of a hydrophobic probe molecule can be used to calculate the hydrophobic micropore volume (HMV) of microporous solids. A gas chromatographic apparatus is described that allows characterization of the sorbed mass with respect to the desorption rate. The method is demonstrated using a dealuminated zeolite and an aquifer sand as the model and reference sorbents, respectively, and trichloroethylene (TCE) as the probe molecule. A glass column packed with the microporous sorbent is coupled directly to a gas chromatograph that is equipped with flame ionization and electron capture detectors. Sorption and desorption of TCE on the sorbent was measured by sampling the influent and effluent of the column using a combination of switching and injection valves. For geosorbents, the HMV is quantified based on Gurvitsch's rule from the mass of TCE desorbed at a rate that is characteristic for micropores. Instrumental requirements, design considerations, hardware details, detector calibration, performance, and data analysis are discussed along with applications. The method is novel and complements traditional vacuum gravimetric and piezometric techniques, which quantify the total pore volume under vacuum conditions. The HMV is more relevant than the total micropore volume for predicting the fate and transport of organic contaminants in the subsurface. Sorption in hydrophobic micropores strongly impacts the mobility of organic contaminants, and their chemical and biological transformations. The apparatus can serve as a tool for characterizing microporous solids and investigating contaminant-solid interactions. 2010 Elsevier B.V. All rights reserved.

  19. In-line gas chromatographic apparatus for measuring the hydrophobic micropore volume (HMV) and contaminant transformation in mineral micropores

    Energy Technology Data Exchange (ETDEWEB)

    Cheng Hefa [State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640 (China); Reinhard, Martin, E-mail: reinhard@stanford.edu [Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305-4020 (United States)

    2010-07-15

    Desorption of hydrophobic organic compounds from micropores is characteristically slow compared to surface adsorption and partitioning. The slow-desorbing mass of a hydrophobic probe molecule can be used to calculate the hydrophobic micropore volume (HMV) of microporous solids. A gas chromatographic apparatus is described that allows characterization of the sorbed mass with respect to the desorption rate. The method is demonstrated using a dealuminated zeolite and an aquifer sand as the model and reference sorbents, respectively, and trichloroethylene (TCE) as the probe molecule. A glass column packed with the microporous sorbent is coupled directly to a gas chromatograph that is equipped with flame ionization and electron capture detectors. Sorption and desorption of TCE on the sorbent was measured by sampling the influent and effluent of the column using a combination of switching and injection valves. For geosorbents, the HMV is quantified based on Gurvitsch's rule from the mass of TCE desorbed at a rate that is characteristic for micropores. Instrumental requirements, design considerations, hardware details, detector calibration, performance, and data analysis are discussed along with applications. The method is novel and complements traditional vacuum gravimetric and piezometric techniques, which quantify the total pore volume under vacuum conditions. The HMV is more relevant than the total micropore volume for predicting the fate and transport of organic contaminants in the subsurface. Sorption in hydrophobic micropores strongly impacts the mobility of organic contaminants, and their chemical and biological transformations. The apparatus can serve as a tool for characterizing microprous solids and investigating contaminant-solid interactions.

  20. Modelling transient energy release from molten fuel coolant interaction debris

    International Nuclear Information System (INIS)

    Fletcher, D.F.

    1984-05-01

    A simple model of transient energy release in a Molten Fuel Coolant Interaction is presented. A distributed heat transfer model is used to examine the effect of heat transfer coefficient, time available for rapid energy heat transfer and particle size on transient energy release. The debris is assumed to have an Upper Limit Lognormal distribution. Model predictions are compared with results from the SUW series of experiments which used thermite-generated uranium dioxide molybdenum melts released below the surface of a pool of water. Uncertainties in the physical principles involved in the calculation of energy transfer rates are discussed. (author)

  1. A model of interaction between anticorruption authority and corruption groups

    International Nuclear Information System (INIS)

    Neverova, Elena G.; Malafeyef, Oleg A.

    2015-01-01

    The paper provides a model of interaction between anticorruption unit and corruption groups. The main policy functions of the anticorruption unit involve reducing corrupt practices in some entities through an optimal approach to resource allocation and effective anticorruption policy. We develop a model based on Markov decision-making process and use Howard’s policy-improvement algorithm for solving an optimal decision strategy. We examine the assumption that corruption groups retaliate against the anticorruption authority to protect themselves. This model was implemented through stochastic game

  2. Stability of a spatial model of social interactions

    International Nuclear Information System (INIS)

    Bragard, Jean; Mossay, Pascal

    2016-01-01

    We study a spatial model of social interactions. Though the properties of the spatial equilibrium have been largely discussed in the existing literature, the stability of equilibrium remains an unaddressed issue. Our aim is to fill up this gap by introducing dynamics in the model and by determining the stability of equilibrium. First we derive a variational equation useful for the stability analysis. This allows to study the corresponding eigenvalue problem. While odd modes are shown to be always stable, there is a single even mode of which stability depends on the model parameters. Finally various numerical simulations illustrate our theoretical results.

  3. Fuel compliance model for pellet-cladding mechanical interaction

    International Nuclear Information System (INIS)

    Shah, V.N.; Carlson, E.R.

    1985-01-01

    This paper describes two aspects of fuel pellet deformation that play significant roles in determining maximum cladding hoop strains during pellet-cladding mechanical interaction: compliance of fragmented fuel pellets and influence of the pellet end-face design on the transmission of axial compressive force in the fuel stack. The latter aspect affects cladding ridge formation and explains several related observations that cannot be explained by the hourglassing model. An empirical model, called the fuel compliance model and representing the above aspects of fuel deformation, has been developed using the results from two Halden experiments and incorporated into the FRAP-T6 fuel performance code

  4. Interacting ghost dark energy models with variable G and Λ

    Science.gov (United States)

    Sadeghi, J.; Khurshudyan, M.; Movsisyan, A.; Farahani, H.

    2013-12-01

    In this paper we consider several phenomenological models of variable Λ. Model of a flat Universe with variable Λ and G is accepted. It is well known, that varying G and Λ gives rise to modified field equations and modified conservation laws, which gives rise to many different manipulations and assumptions in literature. We will consider two component fluid, which parameters will enter to Λ. Interaction between fluids with energy densities ρ1 and ρ2 assumed as Q = 3Hb(ρ1+ρ2). We have numerical analyze of important cosmological parameters like EoS parameter of the composed fluid and deceleration parameter q of the model.

  5. Modelling of pellet-cladding interaction in PWR's

    International Nuclear Information System (INIS)

    Esteves, A.M.; Silva, A.T. e.

    1992-01-01

    The pellet-cladding interaction that can occur in a PWR fuel rod design is modelled with the computer codes FRAPCON-1 and ANSYS. The fuel performance code FRAPCON-1 analyses the fuel rod irradiation behavior and generates the initial conditions for the localized fuel rod thermal and mechanical modelling in two and three-dimensional finite elements with ANSYS. In the mechanical modelling, a pellet fragment is placed in the fuel rod gap. Two types of fuel rod cladding materials are considered: Zircaloy and austenitic stainless steel. (author)

  6. A model of interaction between anticorruption authority and corruption groups

    Energy Technology Data Exchange (ETDEWEB)

    Neverova, Elena G.; Malafeyef, Oleg A. [Saint-Petersburg State University, Saint-Petersburg, Russia, 35, Universitetskii prospekt, Petrodvorets, 198504 Email:elenaneverowa@gmail.com, malafeyevoa@mail.ru (Russian Federation)

    2015-03-10

    The paper provides a model of interaction between anticorruption unit and corruption groups. The main policy functions of the anticorruption unit involve reducing corrupt practices in some entities through an optimal approach to resource allocation and effective anticorruption policy. We develop a model based on Markov decision-making process and use Howard’s policy-improvement algorithm for solving an optimal decision strategy. We examine the assumption that corruption groups retaliate against the anticorruption authority to protect themselves. This model was implemented through stochastic game.

  7. Survey of composite particle models of electroweak interaction

    International Nuclear Information System (INIS)

    Suzuki, Mahiko.

    1992-05-01

    Models of composite weak bosons, the top-condensate model of electroweak interaction and related models we surveyed. Composite weak bosons must be tightly bound with a high compositeness scale in order to generate approximate puge symmetry dynamically. However, naturalness argument suggests that the compositeness scale is low at least in toy models. In the top-condensate model, where a composite Higgs doublet is formed with a very high scale, the prediction of the model is insensitive to details of the model and almost model-independent Actually, the numerical prediction of the t-quark and Higgs boson masses does not test compositeness of the Higgs boson nor condensation of the t-quark field. To illustrate the point, a composite t R -quark model is discussed which leads to the same numerical prediction as the top-condensate model. However, different constraints an imposed on the structure of the Higgs sector, depending on which particles are composite. The attempt to account the large t-b mass splitting by the high compositeness scale of the top-condensate model is reinterpreted in terms of fine tuning of more than one vacuum expectation value. It is difficult to lower, without a fourth generation, the t-quark mass in the composite particle models in general because the Yukawa coupling of the i-quark to the Higgs boson, t2 /4π = 0.1 for m t = 200 GeV, is too small for a coupling of a composite particle

  8. A Bone-Implant Interaction Mouse Model for Evaluating Molecular Mechanism of Biomaterials/Bone Interaction.

    Science.gov (United States)

    Liu, Wenlong; Dan, Xiuli; Wang, Ting; Lu, William W; Pan, Haobo

    2016-11-01

    The development of an optimal animal model that could provide fast assessments of the interaction between bone and orthopedic implants is essential for both preclinical and theoretical researches in the design of novel biomaterials. Compared with other animal models, mice have superiority in accessing the well-developed transgenic modification techniques (e.g., cell tracing, knockoff, knockin, and so on), which serve as powerful tools in studying molecular mechanisms. In this study, we introduced the establishment of a mouse model, which was specifically tailored for the assessment of bone-implant interaction in a load-bearing bone marrow microenvironment and could potentially allow the molecular mechanism study of biomaterials by using transgenic technologies. The detailed microsurgery procedures for developing a bone defect (Φ = 0.8 mm) at the metaphysis region of the mouse femur were recorded. According to our results, the osteoconductive and osseointegrative properties of a well-studied 45S5 bioactive glass were confirmed by utilizing our mouse model, verifying the reliability of this model. The feasibility and reliability of the present model were further checked by using other materials as objects of study. Furthermore, our results indicated that this animal model provided a more homogeneous tissue-implant interacting surface than the rat at the early stage of implantation and this is quite meaningful for conducting quantitative analysis. The availability of transgenic techniques to mechanism study of biomaterials was further testified by establishing our model on Nestin-GFP transgenic mice. Intriguingly, the distribution of Nestin + cells was demonstrated to be recruited to the surface of 45S5 glass as early as 3 days postsurgery, indicating that Nestin + lineage stem cells may participate in the subsequent regeneration process. In summary, the bone-implant interaction mouse model could serve as a potential candidate to evaluate the early stage tissue

  9. The hadronic standard model for strong and electroweak interactions

    International Nuclear Information System (INIS)

    Raczka, R.

    1993-01-01

    We propose a new model for strong and electro-weak interactions. First, we review various QCD predictions for hadron-hadron and lepton-hadron processes. We indicate that the present formulation of strong interactions in the frame work of Quantum Chromodynamics encounters serious conceptual and numerical difficulties in a reliable description of hadron-hadron and lepton-hadron interactions. Next we propose to replace the strong sector of Standard Model based on unobserved quarks and gluons by the strong sector based on the set of the observed baryons and mesons determined by the spontaneously broken SU(6) gauge field theory model. We analyse various properties of this model such as asymptotic freedom, Reggeization of gauge bosons and fundamental fermions, baryon-baryon and meson-baryon high energy scattering, generation of Λ-polarization in inclusive processes and others. Finally we extend this model by electro-weak sector. We demonstrate a remarkable lepton and hadron anomaly cancellation and we analyse a series of important lepton-hadron and hadron-hadron processes such as e + + e - → hadrons, e + + e - → W + + W - , e + + e - → p + anti-p, e + p → e + p and p + anti-p → p + anti-p processes. We obtained a series of interesting new predictions in this model especially for processes with polarized particles. We estimated the value of the strong coupling constant α(M z ) and we predicted the top baryon mass M Λ t ≅ 240 GeV. Since in our model the proton, neutron, Λ-particles, vector mesons like ρ, ω, φ, J/ψ ect. and leptons are elementary most of experimentally analysed lepton-hadron and hadron-hadron processes in LEP1, LEP2, LEAR, HERA, HERMES, LHC and SSC experiments may be relatively easily analysed in our model. (author). 252 refs, 65 figs, 1 tab

  10. Controllable picoliter pipetting using hydrophobic microfluidic valves

    Science.gov (United States)

    Zhang, M.; Huang, J.; Qian, X.; Mi, S.; Wang, X.

    2017-06-01

    A picoliter pipetting technique using the microfluidic method is presented. Utilizing the hydrophobic self-assembled monolayer films patterned in microchannels as pressure-controlled valves, a small volume of liquid can be separated by a designed channel trap and then ejected from the channel end at a higher pressure. The liquid trap section is composed of a T-shaped channel junction and a hydrophobic patch. The liquid volume can be precisely controlled by varying the distance of the hydrophobic patch from the T-junction. By this means, liquid less than 100 pl can be separated and pipetted. The developed device is potentially useful for sample dispensing in biological, medical, and chemical applications.

  11. Biosurfactant-enhanced bioremediation of hydrophobic pollutants

    Energy Technology Data Exchange (ETDEWEB)

    Cameotra, S.S.; Makkar, R.S. [Inst. of Microbial Technology, Chandigarh (India)

    2010-01-15

    Biosurfactants are surface-active compounds synthesized by a wide variety of microorganisms. They are molecules that have both hydrophobic and - philic domains and are capable of lowering the surface tension and the interfacial tension of the growth medium. Biosurfactants possess different chemical structures-lipopeptides, glycolipids, neutral lipids, and fatty acids. They are nontoxic biomolecules that are biodegradable. Biosurfactants also exhibit strong emulsification of hydrophobic compounds and form stable emulsions. Polycyclic aromatic hydrocarbons (PAHs), crude on sludge, and pesticides call be toxic, mutagenic, and carcinogenic compounds that pollute the environment. They are released into the environment as a result of oil spillage and by-products of coal treatment processes. The low water solubility of these compounds limits their availability to microorganisms, which is a potential problem for bioremediation of contaminated sites. Microbially produced surfactants enhance the bioavailability of these hydrophobic compounds for bioremediation. Therefore, biosurfactant-enhanced solubility of pollutants has potential hioremediation applications.

  12. Effect of Alcohol on Interaction of Model Biological Membrane with Steroids

    Science.gov (United States)

    Pinna, Marco; Mura, Manuela; Famili, Marjan; Zhou, Yuhua; Zvelindovsky, Andrei

    2014-03-01

    The effect of alcohol in the lipid bilayer changes the gel-phase structure of the lipid bilayer. Interactions between the alcohol molecules and the lipid bilayer were investigated using molecular dynamics. Alcohols such as ethanol and methanol are often used in drug delivery application. Ethanol is used to dissolve hydrophobic steroidal drugs such as Beclamethasone dipropionate, Fluticasone propionate and Prednisone. All the systems considered were equilibrated at 310K and ran for 100ns in the presence of dimyristoylphosphatidylcholine (DMPC) lipid bilayer. In addition the simulations were performed to investigate the behaviour of anti-asthma drugs such as Beclamethasone dipropionate in the water environment and 2.5% of ethanol.

  13. Experimental investigations and modelling of sodium-concrete interaction

    International Nuclear Information System (INIS)

    Schultheiss, G.F.; Deeg, H.J.

    1990-01-01

    The use of sodium as a coolant in liquid metal fast breeder reactors, fusion reactors, and solar plants requires special consideration of its chemical reactivity and related safety problems in the case of sodium leckage. On contact between hot sodium and concrete an interaction takes place resulting in energy release and hydrogen generation, which may contribute to containment loading by pressurization in a hypothetical accident situation. For this reason, sodium-concrete interactions were investigated experimentally and theoretically. The experiments revealed important effects of quartzitic material within the concrete and of the sodium temperature on the interaction mechanisms, the energy release and the consequent hydrogen production. The numerical model shows good agreement with the experimental results. (orig.) [de

  14. Computational Modeling of Arc-Slag Interaction in DC Furnaces

    Science.gov (United States)

    Reynolds, Quinn G.

    2017-02-01

    The plasma arc is central to the operation of the direct-current arc furnace, a unit operation commonly used in high-temperature processing of both primary ores and recycled metals. The arc is a high-velocity, high-temperature jet of ionized gas created and sustained by interactions among the thermal, momentum, and electromagnetic fields resulting from the passage of electric current. In addition to being the primary source of thermal energy, the arc jet also couples mechanically with the bath of molten process material within the furnace, causing substantial splashing and stirring in the region in which it impinges. The arc's interaction with the molten bath inside the furnace is studied through use of a multiphase, multiphysics computational magnetohydrodynamic model developed in the OpenFOAM® framework. Results from the computational solver are compared with empirical correlations that account for arc-slag interaction effects.

  15. Bayesian Genomic Prediction with Genotype × Environment Interaction Kernel Models

    Science.gov (United States)

    Cuevas, Jaime; Crossa, José; Montesinos-López, Osval A.; Burgueño, Juan; Pérez-Rodríguez, Paulino; de los Campos, Gustavo

    2016-01-01

    The phenomenon of genotype × environment (G × E) interaction in plant breeding decreases selection accuracy, thereby negatively affecting genetic gains. Several genomic prediction models incorporating G × E have been recently developed and used in genomic selection of plant breeding programs. Genomic prediction models for assessing multi-environment G × E interaction are extensions of a single-environment model, and have advantages and limitations. In this study, we propose two multi-environment Bayesian genomic models: the first model considers genetic effects (u) that can be assessed by the Kronecker product of variance–covariance matrices of genetic correlations between environments and genomic kernels through markers under two linear kernel methods, linear (genomic best linear unbiased predictors, GBLUP) and Gaussian (Gaussian kernel, GK). The other model has the same genetic component as the first model (u) plus an extra component, f, that captures random effects between environments that were not captured by the random effects u. We used five CIMMYT data sets (one maize and four wheat) that were previously used in different studies. Results show that models with G × E always have superior prediction ability than single-environment models, and the higher prediction ability of multi-environment models with u and f over the multi-environment model with only u occurred 85% of the time with GBLUP and 45% of the time with GK across the five data sets. The latter result indicated that including the random effect f is still beneficial for increasing prediction ability after adjusting by the random effect u. PMID:27793970

  16. Bayesian Genomic Prediction with Genotype × Environment Interaction Kernel Models

    Directory of Open Access Journals (Sweden)

    Jaime Cuevas

    2017-01-01

    Full Text Available The phenomenon of genotype × environment (G × E interaction in plant breeding decreases selection accuracy, thereby negatively affecting genetic gains. Several genomic prediction models incorporating G × E have been recently developed and used in genomic selection of plant breeding programs. Genomic prediction models for assessing multi-environment G × E interaction are extensions of a single-environment model, and have advantages and limitations. In this study, we propose two multi-environment Bayesian genomic models: the first model considers genetic effects ( u that can be assessed by the Kronecker product of variance–covariance matrices of genetic correlations between environments and genomic kernels through markers under two linear kernel methods, linear (genomic best linear unbiased predictors, GBLUP and Gaussian (Gaussian kernel, GK. The other model has the same genetic component as the first model ( u plus an extra component, f, that captures random effects between environments that were not captured by the random effects u . We used five CIMMYT data sets (one maize and four wheat that were previously used in different studies. Results show that models with G × E always have superior prediction ability than single-environment models, and the higher prediction ability of multi-environment models with u   and   f over the multi-environment model with only u occurred 85% of the time with GBLUP and 45% of the time with GK across the five data sets. The latter result indicated that including the random effect f is still beneficial for increasing prediction ability after adjusting by the random effect u .

  17. Bayesian Genomic Prediction with Genotype × Environment Interaction Kernel Models.

    Science.gov (United States)

    Cuevas, Jaime; Crossa, José; Montesinos-López, Osval A; Burgueño, Juan; Pérez-Rodríguez, Paulino; de Los Campos, Gustavo

    2017-01-05

    The phenomenon of genotype × environment (G × E) interaction in plant breeding decreases selection accuracy, thereby negatively affecting genetic gains. Several genomic prediction models incorporating G × E have been recently developed and used in genomic selection of plant breeding programs. Genomic prediction models for assessing multi-environment G × E interaction are extensions of a single-environment model, and have advantages and limitations. In this study, we propose two multi-environment Bayesian genomic models: the first model considers genetic effects [Formula: see text] that can be assessed by the Kronecker product of variance-covariance matrices of genetic correlations between environments and genomic kernels through markers under two linear kernel methods, linear (genomic best linear unbiased predictors, GBLUP) and Gaussian (Gaussian kernel, GK). The other model has the same genetic component as the first model [Formula: see text] plus an extra component, F: , that captures random effects between environments that were not captured by the random effects [Formula: see text] We used five CIMMYT data sets (one maize and four wheat) that were previously used in different studies. Results show that models with G × E always have superior prediction ability than single-environment models, and the higher prediction ability of multi-environment models with [Formula: see text] over the multi-environment model with only u occurred 85% of the time with GBLUP and 45% of the time with GK across the five data sets. The latter result indicated that including the random effect f is still beneficial for increasing prediction ability after adjusting by the random effect [Formula: see text]. Copyright © 2017 Cuevas et al.

  18. Analysis and application of opinion model with multiple topic interactions.

    Science.gov (United States)

    Xiong, Fei; Liu, Yun; Wang, Liang; Wang, Ximeng

    2017-08-01

    To reveal heterogeneous behaviors of opinion evolution in different scenarios, we propose an opinion model with topic interactions. Individual opinions and topic features are represented by a multidimensional vector. We measure an agent's action towards a specific topic by the product of opinion and topic feature. When pairs of agents interact for a topic, their actions are introduced to opinion updates with bounded confidence. Simulation results show that a transition from a disordered state to a consensus state occurs at a critical point of the tolerance threshold, which depends on the opinion dimension. The critical point increases as the dimension of opinions increases. Multiple topics promote opinion interactions and lead to the formation of macroscopic opinion clusters. In addition, more topics accelerate the evolutionary process and weaken the effect of network topology. We use two sets of large-scale real data to evaluate the model, and the results prove its effectiveness in characterizing a real evolutionary process. Our model achieves high performance in individual action prediction and even outperforms state-of-the-art methods. Meanwhile, our model has much smaller computational complexity. This paper provides a demonstration for possible practical applications of theoretical opinion dynamics.

  19. Modeling fluid-rock interaction at Yucca Mountain, Nevada

    International Nuclear Information System (INIS)

    Viani, B.E.; Bruton, C.J.

    1992-08-01

    Volcanic rocks at Yucca Mountain, Nevada aie being assessed for their suitability as a potential repository for high-level nuclear waste. Recent progress in modeling fluid-rock interactions, in particular the mineralogical and chemical changes that may accompany waste disposal at Yucca Mountain, will be reviewed in this publication. In Part 1 of this publication, ''Geochemical Modeling of Clinoptilolite-Water Interactions,'' solid-solution and cation-exchange models for the zeolite clinoptilolite are developed and compared to experimental and field observations. At Yucca Mountain, clinoptilolite which is found lining fractures and as a major component of zeolitized tuffs, is expected to play an important role in sequestering radionuclides that may escape from a potential nuclear waste repository. The solid-solution and ion-exchange models were evaluated by comparing predicted stabilities and exchangeable cation distributions of clinoptilolites with: (1) published binary exchange data; (2) compositions of coexisting clinoptilolites and formation waters at Yucca Mountain; (3) experimental sorption isotherms of Cs and Sr on zeolitized tuff, and (4) high temperature experimental data. Good agreement was found between predictions and expertmental data, especially for binary exchange and Cs and Sr sorption on clinoptilolite. Part 2 of this publication, ''Geochemical Simulation of Fluid-Rock Interactions at Yucca Mountain,'' describes preliminary numerical simulations of fluid-rock interactions at Yucca Mountain. The solid-solution model developed in the first part of the paper is used to evaluate the stability and composition of clinciptilolite and other minerals in the host rock under ambient conditions and after waste emplacement

  20. Numerical Cerebrospinal System Modeling in Fluid-Structure Interaction.

    Science.gov (United States)

    Garnotel, Simon; Salmon, Stéphanie; Balédent, Olivier

    2018-01-01

    Cerebrospinal fluid (CSF) stroke volume in the aqueduct is widely used to evaluate CSF dynamics disorders. In a healthy population, aqueduct stroke volume represents around 10% of the spinal stroke volume while intracranial subarachnoid space stroke volume represents 90%. The amplitude of the CSF oscillations through the different compartments of the cerebrospinal system is a function of the geometry and the compliances of each compartment, but we suspect that it could also be impacted be the cardiac cycle frequency. To study this CSF distribution, we have developed a numerical model of the cerebrospinal system taking into account cerebral ventricles, intracranial subarachnoid spaces, spinal canal and brain tissue in fluid-structure interactions. A numerical fluid-structure interaction model is implemented using a finite-element method library to model the cerebrospinal system and its interaction with the brain based on fluid mechanics equations and linear elasticity equations coupled in a monolithic formulation. The model geometry, simplified in a first approach, is designed in accordance with realistic volume ratios of the different compartments: a thin tube is used to mimic the high flow resistance of the aqueduct. CSF velocity and pressure and brain displacements are obtained as simulation results, and CSF flow and stroke volume are calculated from these results. Simulation results show a significant variability of aqueduct stroke volume and intracranial subarachnoid space stroke volume in the physiological range of cardiac frequencies. Fluid-structure interactions are numerous in the cerebrospinal system and difficult to understand in the rigid skull. The presented model highlights significant variations of stroke volumes under cardiac frequency variations only.

  1. Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water

    Energy Technology Data Exchange (ETDEWEB)

    Riback, Joshua A.; Bowman, Micayla A.; Zmyslowski, Adam M.; Knoverek, Catherine R.; Jumper, John M.; Hinshaw, James R.; Kaye, Emily B.; Freed, Karl F.; Clark, Patricia L.; Sosnick, Tobin R.

    2017-10-12

    A substantial fraction of the proteome is intrinsically disordered, and even well-folded proteins adopt non-native geometries during synthesis, folding, transport, and turnover. Characterization of intrinsically disordered proteins (IDPs) is challenging, in part because of a lack of accurate physical models and the difficulty of interpreting experimental results. We have developed a general method to extract the dimensions and solvent quality (self-interactions) of IDPs from a single small-angle x-ray scattering measurement. We applied this procedure to a variety of IDPs and found that even IDPs with low net charge and high hydrophobicity remain highly expanded in water, contrary to the general expectation that protein-like sequences collapse in water. Our results suggest that the unfolded state of most foldable sequences is expanded; we conjecture that this property was selected by evolution to minimize misfolding and aggregation.

  2. Antimycotic activity of fengycin C biosurfactant and its interaction with phosphatidylcholine model membranes.

    Science.gov (United States)

    González-Jaramillo, Lina María; Aranda, Francisco José; Teruel, José Antonio; Villegas-Escobar, Valeska; Ortiz, Antonio

    2017-08-01

    Lipopeptide biosurfactants constitute one of the most promising groups of compounds for the treatment and prevention of fungal diseases in plants. Bacillus subtilis strain EA-CB0015 produces iturin A, fengycin C and surfactin and it has been proven useful for the treatment of black Sigatoka disease in banana plants, an important pathology caused by the fungus Mycosphaerella fijiensis (Morelet). We have found that B. subtilis EA-CB0015 cell free supernatants and purified fractions inhibit M. fijiensis cellular growth. The effect of the purified lipopeptides mentioned above on fungal growth has been also evaluated, observing that iturin A and fengycin C inhibit mycelial growth and ascospore germination, whereas surfactin is not effective. On the hypothesis that the antifungal action of the lipopeptides is associated to their incorporation into biological membranes, ultimately leading to membrane permeabilization, a detailed biophysical study on the interaction of a new isoform of fengycin C with model dipalmitoyphosphatidylcholine (DPPC) membranes has been carried out. Differential scanning calorimetry shows that fengycin C alters the thermotropic phase transitions of DPPC, and is laterally segregated in the fluid bilayer forming domains. Fluorescent probe polarization measurements show that fengycin C does not affect the hydrophobic interior of the membrane. This latter perturbation is concomitant with a strong dehydration of the polar region of DPPC, as shown by FTIR. Fengycin-rich domains, where the surrounding DPPC molecules are highly dehydrated, may well constitute sites of membrane permeabilization leading to a leaky target membrane. These results are a solid support to explain the membrane perturbing action of fengycin, which has been related to its antifungal activity. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Family nonuniversal Z' models with protected flavor-changing interactions

    Science.gov (United States)

    Celis, Alejandro; Fuentes-Martín, Javier; Jung, Martin; Serôdio, Hugo

    2015-07-01

    We define a new class of Z' models with neutral flavor-changing interactions at tree level in the down-quark sector. They are related in an exact way to elements of the quark mixing matrix due to an underlying flavored U(1)' gauge symmetry, rendering these models particularly predictive. The same symmetry implies lepton-flavor nonuniversal couplings, fully determined by the gauge structure of the model. Our models allow us to address presently observed deviations from the standard model and specific correlations among the new physics contributions to the Wilson coefficients C9,10' ℓ can be tested in b →s ℓ+ℓ- transitions. We furthermore predict lepton-universality violations in Z' decays, testable at the LHC.

  4. Interaction in Spoken Word Recognition Models: Feedback Helps

    Science.gov (United States)

    Magnuson, James S.; Mirman, Daniel; Luthra, Sahil; Strauss, Ted; Harris, Harlan D.

    2018-01-01

    Human perception, cognition, and action requires fast integration of bottom-up signals with top-down knowledge and context. A key theoretical perspective in cognitive science is the interactive activation hypothesis: forward and backward flow in bidirectionally connected neural networks allows humans and other biological systems to approximate optimal integration of bottom-up and top-down information under real-world constraints. An alternative view is that online feedback is neither necessary nor helpful; purely feed forward alternatives can be constructed for any feedback system, and online feedback could not improve processing and would preclude veridical perception. In the domain of spoken word recognition, the latter view was apparently supported by simulations using the interactive activation model, TRACE, with and without feedback: as many words were recognized more quickly without feedback as were recognized faster with feedback, However, these simulations used only a small set of words and did not address a primary motivation for interaction: making a model robust in noise. We conducted simulations using hundreds of words, and found that the majority were recognized more quickly with feedback than without. More importantly, as we added noise to inputs, accuracy and recognition times were better with feedback than without. We follow these simulations with a critical review of recent arguments that online feedback in interactive activation models like TRACE is distinct from other potentially helpful forms of feedback. We conclude that in addition to providing the benefits demonstrated in our simulations, online feedback provides a plausible means of implementing putatively distinct forms of feedback, supporting the interactive activation hypothesis. PMID:29666593

  5. Interaction in Spoken Word Recognition Models: Feedback Helps.

    Science.gov (United States)

    Magnuson, James S; Mirman, Daniel; Luthra, Sahil; Strauss, Ted; Harris, Harlan D

    2018-01-01

    Human perception, cognition, and action requires fast integration of bottom-up signals with top-down knowledge and context. A key theoretical perspective in cognitive science is the interactive activation hypothesis: forward and backward flow in bidirectionally connected neural networks allows humans and other biological systems to approximate optimal integration of bottom-up and top-down information under real-world constraints. An alternative view is that online feedback is neither necessary nor helpful; purely feed forward alternatives can be constructed for any feedback system, and online feedback could not improve processing and would preclude veridical perception. In the domain of spoken word recognition, the latter view was apparently supported by simulations using the interactive activation model, TRACE, with and without feedback: as many words were recognized more quickly without feedback as were recognized faster with feedback, However, these simulations used only a small set of words and did not address a primary motivation for interaction: making a model robust in noise. We conducted simulations using hundreds of words, and found that the majority were recognized more quickly with feedback than without. More importantly, as we added noise to inputs, accuracy and recognition times were better with feedback than without. We follow these simulations with a critical review of recent arguments that online feedback in interactive activation models like TRACE is distinct from other potentially helpful forms of feedback. We conclude that in addition to providing the benefits demonstrated in our simulations, online feedback provides a plausible means of implementing putatively distinct forms of feedback, supporting the interactive activation hypothesis.

  6. Interaction in Spoken Word Recognition Models: Feedback Helps

    Directory of Open Access Journals (Sweden)

    James S. Magnuson

    2018-04-01

    Full Text Available Human perception, cognition, and action requires fast integration of bottom-up signals with top-down knowledge and context. A key theoretical perspective in cognitive science is the interactive activation hypothesis: forward and backward flow in bidirectionally connected neural networks allows humans and other biological systems to approximate optimal integration of bottom-up and top-down information under real-world constraints. An alternative view is that online feedback is neither necessary nor helpful; purely feed forward alternatives can be constructed for any feedback system, and online feedback could not improve processing and would preclude veridical perception. In the domain of spoken word recognition, the latter view was apparently supported by simulations using the interactive activation model, TRACE, with and without feedback: as many words were recognized more quickly without feedback as were recognized faster with feedback, However, these simulations used only a small set of words and did not address a primary motivation for interaction: making a model robust in noise. We conducted simulations using hundreds of words, and found that the majority were recognized more quickly with feedback than without. More importantly, as we added noise to inputs, accuracy and recognition times were better with feedback than without. We follow these simulations with a critical review of recent arguments that online feedback in interactive activation models like TRACE is distinct from other potentially helpful forms of feedback. We conclude that in addition to providing the benefits demonstrated in our simulations, online feedback provides a plausible means of implementing putatively distinct forms of feedback, supporting the interactive activation hypothesis.

  7. Diversity-interaction modeling: estimating contributions of species identities and interactions to ecosystem function

    DEFF Research Database (Denmark)

    Kirwan, L; Connolly, J; Finn, J A

    2009-01-01

    to the roles of evenness, functional groups, and functional redundancy. These more parsimonious descriptions can be especially useful in identifying general diversity-function relationships in communities with large numbers of species. We provide an example of the application of the modeling framework......We develop a modeling framework that estimates the effects of species identity and diversity on ecosystem function and permits prediction of the diversity-function relationship across different types of community composition. Rather than just measure an overall effect of diversity, we separately....... These models describe community-level performance and thus do not require separate measurement of the performance of individual species. This flexible modeling approach can be tailored to test many hypotheses in biodiversity research and can suggest the interaction mechanisms that may be acting....

  8. Simulation studies of protein-induced bilayer deformations, and lipid-induced protein tilting, on a mesoscopic model for lipid bilayers with embedded proteins

    DEFF Research Database (Denmark)

    Venturoli, M.; Smit, B.; Sperotto, Maria Maddalena

    2005-01-01

    membranes. Here we present a mesoscopic model for lipid bilayers with embedded proteins, which we have studied with the help of the dissipative particle dynamics simulation technique. Because hydrophobic matching is believed to be one of the main physical mechanisms regulating lipid-protein interactions......-induced protein tilt, with the hydrophobic mismatch ( positive and negative) between the protein hydrophobic length and the pure lipid bilayer hydrophobic thickness. The protein-induced bilayer perturbation was quantified in terms of a coherence length, xi(P), of the lipid bilayer hydrophobic thickness pro. le...... for positive values of mismatch; a dependence on the protein size appears as well. In the case of large model proteins experiencing extreme mismatch conditions, in the region next to the so-called lipid annulus, there appears an undershooting ( or overshooting) region where the bilayer hydrophobic thickness...

  9. Exacerbating the Cosmological Constant Problem with Interacting Dark Energy Models.

    Science.gov (United States)

    Marsh, M C David

    2017-01-06

    Future cosmological surveys will probe the expansion history of the Universe and constrain phenomenological models of dark energy. Such models do not address the fine-tuning problem of the vacuum energy, i.e., the cosmological constant problem (CCP), but can make it spectacularly worse. We show that this is the case for "interacting dark energy" models in which the masses of the dark matter states depend on the dark energy sector. If realized in nature, these models have far-reaching implications for proposed solutions to the CCP that require the number of vacua to exceed the fine-tuning of the vacuum energy density. We show that current estimates of the number of flux vacua in string theory, N_{vac}∼O(10^{272 000}), are far too small to realize certain simple models of interacting dark energy and solve the cosmological constant problem anthropically. These models admit distinctive observational signatures that can be targeted by future gamma-ray observatories, hence making it possible to observationally rule out the anthropic solution to the cosmological constant problem in theories with a finite number of vacua.

  10. SeiVis: An interactive visual subsurface modeling application

    KAUST Repository

    Hollt, Thomas

    2012-12-01

    The most important resources to fulfill today’s energy demands are fossil fuels, such as oil and natural gas. When exploiting hydrocarbon reservoirs, a detailed and credible model of the subsurface structures is crucial in order to minimize economic and ecological risks. Creating such a model is an inverse problem: reconstructing structures from measured reflection seismics. The major challenge here is twofold: First, the structures in highly ambiguous seismic data are interpreted in the time domain. Second, a velocity model has to be built from this interpretation to match the model to depth measurements from wells. If it is not possible to obtain a match at all positions, the interpretation has to be updated, going back to the first step. This results in a lengthy back and forth between the different steps, or in an unphysical velocity model in many cases. This paper presents a novel, integrated approach to interactively creating subsurface models from reflection seismics. It integrates the interpretation of the seismic data using an interactive horizon extraction technique based on piecewise global optimization with velocity modeling. Computing and visualizing the effects of changes to the interpretation and velocity model on the depth-converted model on the fly enables an integrated feedback loop that enables a completely new connection of the seismic data in time domain and well data in depth domain. Using a novel joint time/depth visualization, depicting side-by-side views of the original and the resulting depth-converted data, domain experts can directly fit their interpretation in time domain to spatial ground truth data. We have conducted a domain expert evaluation, which illustrates that the presented workflow enables the creation of exact subsurface models much more rapidly than previous approaches. © 2012 IEEE.

  11. SeiVis: An interactive visual subsurface modeling application

    KAUST Repository

    Hollt, Thomas; Freiler, Wolfgang; Gschwantner, Fritz M.; Doleisch, Helmut; Heinemann, Gabor F.; Hadwiger, Markus

    2012-01-01

    The most important resources to fulfill today’s energy demands are fossil fuels, such as oil and natural gas. When exploiting hydrocarbon reservoirs, a detailed and credible model of the subsurface structures is crucial in order to minimize economic and ecological risks. Creating such a model is an inverse problem: reconstructing structures from measured reflection seismics. The major challenge here is twofold: First, the structures in highly ambiguous seismic data are interpreted in the time domain. Second, a velocity model has to be built from this interpretation to match the model to depth measurements from wells. If it is not possible to obtain a match at all positions, the interpretation has to be updated, going back to the first step. This results in a lengthy back and forth between the different steps, or in an unphysical velocity model in many cases. This paper presents a novel, integrated approach to interactively creating subsurface models from reflection seismics. It integrates the interpretation of the seismic data using an interactive horizon extraction technique based on piecewise global optimization with velocity modeling. Computing and visualizing the effects of changes to the interpretation and velocity model on the depth-converted model on the fly enables an integrated feedback loop that enables a completely new connection of the seismic data in time domain and well data in depth domain. Using a novel joint time/depth visualization, depicting side-by-side views of the original and the resulting depth-converted data, domain experts can directly fit their interpretation in time domain to spatial ground truth data. We have conducted a domain expert evaluation, which illustrates that the presented workflow enables the creation of exact subsurface models much more rapidly than previous approaches. © 2012 IEEE.

  12. SeiVis: An Interactive Visual Subsurface Modeling Application.

    Science.gov (United States)

    Hollt, T; Freiler, W; Gschwantner, F; Doleisch, H; Heinemann, G; Hadwiger, M

    2012-12-01

    The most important resources to fulfill today's energy demands are fossil fuels, such as oil and natural gas. When exploiting hydrocarbon reservoirs, a detailed and credible model of the subsurface structures is crucial in order to minimize economic and ecological risks. Creating such a model is an inverse problem: reconstructing structures from measured reflection seismics. The major challenge here is twofold: First, the structures in highly ambiguous seismic data are interpreted in the time domain. Second, a velocity model has to be built from this interpretation to match the model to depth measurements from wells. If it is not possible to obtain a match at all positions, the interpretation has to be updated, going back to the first step. This results in a lengthy back and forth between the different steps, or in an unphysical velocity model in many cases. This paper presents a novel, integrated approach to interactively creating subsurface models from reflection seismics. It integrates the interpretation of the seismic data using an interactive horizon extraction technique based on piecewise global optimization with velocity modeling. Computing and visualizing the effects of changes to the interpretation and velocity model on the depth-converted model on the fly enables an integrated feedback loop that enables a completely new connection of the seismic data in time domain and well data in depth domain. Using a novel joint time/depth visualization, depicting side-by-side views of the original and the resulting depth-converted data, domain experts can directly fit their interpretation in time domain to spatial ground truth data. We have conducted a domain expert evaluation, which illustrates that the presented workflow enables the creation of exact subsurface models much more rapidly than previous approaches.

  13. Modeling the intracellular pathogen-immune interaction with cure rate

    Science.gov (United States)

    Dubey, Balram; Dubey, Preeti; Dubey, Uma S.

    2016-09-01

    Many common and emergent infectious diseases like Influenza, SARS, Hepatitis, Ebola etc. are caused by viral pathogens. These infections can be controlled or prevented by understanding the dynamics of pathogen-immune interaction in vivo. In this paper, interaction of pathogens with uninfected and infected cells in presence or absence of immune response are considered in four different cases. In the first case, the model considers the saturated nonlinear infection rate and linear cure rate without absorption of pathogens into uninfected cells and without immune response. The next model considers the effect of absorption of pathogens into uninfected cells while all other terms are same as in the first case. The third model incorporates innate immune response, humoral immune response and Cytotoxic T lymphocytes (CTL) mediated immune response with cure rate and without absorption of pathogens into uninfected cells. The last model is an extension of the third model in which the effect of absorption of pathogens into uninfected cells has been considered. Positivity and boundedness of solutions are established to ensure the well-posedness of the problem. It has been found that all the four models have two equilibria, namely, pathogen-free equilibrium point and pathogen-present equilibrium point. In each case, stability analysis of each equilibrium point is investigated. Pathogen-free equilibrium is globally asymptotically stable when basic reproduction number is less or equal to unity. This implies that control or prevention of infection is independent of initial concentration of uninfected cells, infected cells, pathogens and immune responses in the body. The proposed models show that introduction of immune response and cure rate strongly affects the stability behavior of the system. Further, on computing basic reproduction number, it has been found to be minimum for the fourth model vis-a-vis other models. The analytical findings of each model have been exemplified by

  14. Unravelling the hydrophobicity of urea in water using thermodiffusion: implications for protein denaturation.

    Science.gov (United States)

    Niether, Doreen; Di Lecce, Silvia; Bresme, Fernando; Wiegand, Simone

    2018-01-03

    Urea is widely used as a protein denaturant in aqueous solutions. Experimental and computer simulation studies have shown that it dissolves in water almost ideally at high concentrations, introducing little disruption in the water hydrogen bonded structure. However, at concentrations of the order of 5 M or higher, urea induces denaturation in a wide range of proteins. The origin of this behaviour is not completely understood, but it is believed to stem from a balance between urea-protein and urea-water interactions, with urea becoming possibly hydrophobic at a specific concentration range. The small changes observed in the water structure make it difficult to connect the denaturation effects to the solvation properties. Here we show that the exquisite sensitivity of thermodiffusion to solute-water interactions allows the identification of the onset of hydrophobicity of urea-water mixtures. The hydrophobic behaviour is reflected in a sign reversal of the temperature dependent slope of the Soret coefficient, which is observed, both in experiments and non-equilibrium computer simulations at ∼5 M concentration of urea in water. This concentration regime corresponds to the one where abrupt changes in the denaturation of proteins are commonly observed. We show that the onset of hydrophobicity is intrinsically connected to the urea-water interactions. Our results allow us to identify correlations between the Soret coefficient and the partition coefficient, log P, hence establishing the thermodiffusion technique as a powerful approach to study hydrophobicity.

  15. Interacting boson model: Microscopic calculations for the mercury isotopes

    Energy Technology Data Exchange (ETDEWEB)

    Druce, C.H.; Pittel, S.; Barrett, B.R.; Duval, P.D.

    1987-05-15

    Microscopic calculations of the parameters of the proton--neutron interacting boson model (IBM-2) appropriate to the even Hg isotopes are reported. The calculations are based on the Otsuka--Arima--Iachello boson mapping procedure, which is briefly reviewed. Renormalization of the parameters due to exclusion of the l = 4 g boson is treated perturbatively. The calculations employ a semi-realistic shell-model Hamiltonian with no adjustable parameters. The calculated parameters of the IBM-2 Hamiltonian are used to generate energy spectra and electromagnetic transition probabilities, which are compared with experimental data and with the result of phenomenological fits. The overall agreement is reasonable with some notable exceptions, which are discussed. Particular attention is focused on the parameters of the Majorana interaction and on the F-spin character of low-lying levels. copyright 1987 Academic Press, Inc.

  16. The interacting boson model: Microscopic calculations for the mercury isotopes

    Science.gov (United States)

    Druce, C. H.; Pittel, S.; Barrett, B. R.; Duval, P. D.

    1987-05-01

    Microscopic calculations of the parameters of the proton-neutron interacting boson model (IBM-2) appropriate to the even Hg isotopes are reported. The calculations are based on the Otsuka-Armia-Iachello boson mapping procedure, which is briefly reviewed. Renormalization of the parameters due to exclusion of the l=4 g boson is treated perturbatively. The calculations employ a semi-realistic shell-model Hamiltonian with no adjustable parameters. The calculated parameters of the IBM-2 Hamiltonian are used to generate energy spectra and electromagnetic transition probabilities, which are compared with experimental data and with the result of phenomenological fits. The overall agreement is reasonable with some notable exceptions, which are discussed. Particular attention is focused on the parameters of the Majorana interaction and on the F-spin character of low-lying levels.

  17. The transverse spin-1 Ising model with random interactions

    Energy Technology Data Exchange (ETDEWEB)

    Bouziane, Touria [Department of Physics, Faculty of Sciences, University of Moulay Ismail, B.P. 11201 Meknes (Morocco)], E-mail: touria582004@yahoo.fr; Saber, Mohammed [Department of Physics, Faculty of Sciences, University of Moulay Ismail, B.P. 11201 Meknes (Morocco); Dpto. Fisica Aplicada I, EUPDS (EUPDS), Plaza Europa, 1, San Sebastian 20018 (Spain)

    2009-01-15

    The phase diagrams of the transverse spin-1 Ising model with random interactions are investigated using a new technique in the effective field theory that employs a probability distribution within the framework of the single-site cluster theory based on the use of exact Ising spin identities. A model is adopted in which the nearest-neighbor exchange couplings are independent random variables distributed according to the law P(J{sub ij})=p{delta}(J{sub ij}-J)+(1-p){delta}(J{sub ij}-{alpha}J). General formulae, applicable to lattices with coordination number N, are given. Numerical results are presented for a simple cubic lattice. The possible reentrant phenomenon displayed by the system due to the competitive effects between exchange interactions occurs for the appropriate range of the parameter {alpha}.

  18. Near-atomic model of microtubule-tau interactions.

    Science.gov (United States)

    Kellogg, Elizabeth H; Hejab, Nisreen M A; Poepsel, Simon; Downing, Kenneth H; DiMaio, Frank; Nogales, Eva

    2018-06-15

    Tau is a developmentally regulated axonal protein that stabilizes and bundles microtubules (MTs). Its hyperphosphorylation is thought to cause detachment from MTs and subsequent aggregation into fibrils implicated in Alzheimer's disease. It is unclear which tau residues are crucial for tau-MT interactions, where tau binds on MTs, and how it stabilizes them. We used cryo-electron microscopy to visualize different tau constructs on MTs and computational approaches to generate atomic models of tau-tubulin interactions. The conserved tubulin-binding repeats within tau adopt similar extended structures along the crest of the protofilament, stabilizing the interface between tubulin dimers. Our structures explain the effect of phosphorylation on MT affinity and lead to a model of tau repeats binding in tandem along protofilaments, tethering together tubulin dimers and stabilizing polymerization interfaces. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  19. Stochastic modeling of mode interactions via linear parabolized stability equations

    Science.gov (United States)

    Ran, Wei; Zare, Armin; Hack, M. J. Philipp; Jovanovic, Mihailo

    2017-11-01

    Low-complexity approximations of the Navier-Stokes equations have been widely used in the analysis of wall-bounded shear flows. In particular, the parabolized stability equations (PSE) and Floquet theory have been employed to capture the evolution of primary and secondary instabilities in spatially-evolving flows. We augment linear PSE with Floquet analysis to formally treat modal interactions and the evolution of secondary instabilities in the transitional boundary layer via a linear progression. To this end, we leverage Floquet theory by incorporating the primary instability into the base flow and accounting for different harmonics in the flow state. A stochastic forcing is introduced into the resulting linear dynamics to model the effect of nonlinear interactions on the evolution of modes. We examine the H-type transition scenario to demonstrate how our approach can be used to model nonlinear effects and capture the growth of the fundamental and subharmonic modes observed in direct numerical simulations and experiments.

  20. A Mesoscopic Model for Protein-Protein Interactions in Solution

    OpenAIRE

    Lund, Mikael; Jönsson, Bo

    2003-01-01

    Protein self-association may be detrimental in biological systems, but can be utilized in a controlled fashion for protein crystallization. It is hence of considerable interest to understand how factors like solution conditions prevent or promote aggregation. Here we present a computational model describing interactions between protein molecules in solution. The calculations are based on a molecular description capturing the detailed structure of the protein molecule using x-ray or nuclear ma...