WorldWideScience

Sample records for crystal packing interactions

  1. Atom interaction propensities of oxygenated chemical functions in crystal packings

    Directory of Open Access Journals (Sweden)

    Christian Jelsch

    2017-03-01

    Full Text Available The crystal contacts of several families of hydrocarbon compounds substituted with one or several types of oxygenated chemical groups were analyzed statistically using the Hirshfeld surface methodology. The propensity of contacts to occur between two chemical types is described with the contact enrichment descriptor. The systematic large enrichment ratios of some interactions like the O—H...O hydrogen bonds suggests that these contacts are a driving force in the crystal packing formation. The same statement holds for the weaker C—H...O hydrogen bonds in ethers, esters and ketones, in the absence of polar H atoms. The over-represented contacts in crystals of oxygenated hydrocarbons are generally of two types: electrostatic attractions (hydrogen bonds and hydrophobic interactions. While Cl...O interactions are generally avoided, in a minority of chloro-oxygenated hydrocarbons, significant halogen bonding does occur. General tendencies can often be derived for many contact types, but outlier compounds are instructive as they display peculiar or rare features. The methodology also allows the detection of outliers which can be structures with errors. For instance, a significant number of hydroxylated molecules displaying over-represented non-favorable oxygen–oxygen contacts turned out to have wrongly oriented hydroxyl groups. Beyond crystal packings with a single molecule in the asymmetric unit, the behavior of water in monohydrate compounds and of crystals with Z′ = 2 (dimers are also investigated. It was found in several cases that, in the presence of several oxygenated chemical groups, cross-interactions between different chemical groups (e.g. water/alcohols; alcohols/phenols are often favored in the crystal packings. While some trends in accordance with common chemical principles are retrieved, some unexpected results can however appear. For example, in crystals of alcohol–phenol compounds, the strong O—H...O hydrogen bonds between

  2. Role of intermolecular interaction in crystal packing: A competition between halogen bond and electrostatic interaction

    Science.gov (United States)

    Chen, Peng-Yuan; Zhang, Lin; Zhu, Shun-Guan; Cheng, Guang-Bin

    2017-03-01

    To investigate the competition between halogen bond and electrostatic interaction and their influence on the crystal packing, four novel solvates of 1,3,5-trichloro-2,4,6-trinitrobenzene (TCTNB) and 1,3,5-tribromo-2,4,6-trinitrobenzene (TBTNB) were synthesized while the intermolecular forces and the contribution of each interaction were analyzed quantitatively. The electrostatic interaction is the main link between TCTNB, TBTNB and 1,4-dioxane respectively, while π-π interaction dominates in these two solvates of TCTNB/1,4-dimethylbenzene (PX) and TCTNB/mesitylene. The solvate interaction changes and varieties were illuminated by Hirshfeld surface analysis, and the group contributions were illustrated respectively. Molecular electrostatic potential surface (MEPs) with density functional theory (DFT) calculation was performed to compare the relative strength of electrostatic interaction and halogen bond. The result shows that MEPs can be used as a descriptor for determining the most possible intermolecular interaction under certain circumstances. The study presented here may provide the guidance for the design and synthesis of the complex with desired properties.

  3. Crystal packing effects on protein loops.

    Science.gov (United States)

    Rapp, Chaya S; Pollack, Rena M

    2005-07-01

    The effects of crystal packing on protein loop structures are examined by (1) a comparison of loops in proteins that have been crystallized in alternate packing arrangements, and (2) theoretical prediction of loops both with and without the inclusion of the crystal environment. Results show that in a minority of cases, loop geometries are dependent on crystal packing effects. Explicit representation of the crystal environment in a loop prediction algorithm can be used to model these effects and to reconstruct the structures, and relative energies, of a loop in alternative packing environments. By comparing prediction results with and without the inclusion of the crystal environment, the loop prediction algorithm can further be used to identify cases in which a crystal structure does not represent the most stable state of a loop in solution. We anticipate that this capability has implications for structural biology.

  4. Br...Br and van der Waals interactions along a homologous series: crystal packing of 1,2-dibromo-4,5-dialkoxybenzenes.

    Science.gov (United States)

    Suarez, Sebastián A; Muller, Federico; Gutiérrez Suburu, Matías E; Fonrouge, Ana; Baggio, Ricardo F; Cukiernik, Fabio D

    2016-10-01

    The crystalline structures of four homologues of the 1,2-dibromo-4,5-dialkoxybenzene series [Br2C6H2(OCnH2n + 1)2 for n = 2, 12, 14 and 18] have been solved by means of single-crystal crystallography. Comparison along the series, including the previously reported n = 10 and n = 16 derivatives, shows a clear metric trend (b and c essentially fixed along the series and a growing linearly with n), in spite of some subtle differences in space groups and/or packing modes. A uniform packing pattern for the aliphatic chains has been found for the n = 12 to 18 homologues, which slightly differs from that of the n = 10 derivative. The crystalline structures of all the higher homologues (n = 10-18) seem to arise from van der Waals interchain interactions and, to a lesser extent, type II Br...Br interactions. The dominant role of interchain interactions provides direct structural support for the usual interpretation of melting point trends like that found along this series. Atoms in Molecules (AIM) analysis allows a comparison of the relative magnitude of the interchain and Br...Br interactions, an analysis validated by the measured melting enthalpies.

  5. An effective packing density of binary cubic crystals

    Science.gov (United States)

    Eremin, I. E.; Eremina, V. V.; Sychev, M. S.; Moiseenko, V. G.

    2015-04-01

    The methodology of effective macroscopic calculation of numerical values of internuclear distances in binary crystals of a cubic crystal system is based on the use of coefficients of the structural packing density of the crystal lattice. The possibility of combining the reference data on the main physicochemical parameters of the substance is implemented by synthesis of the corresponding mathematical models.

  6. Effect of crystal packing on the structures of polymeric metallocenes.

    Science.gov (United States)

    Dinnebier, R E; van Smaalen, Sander; Olbrich, F; Carlson, S

    2005-02-21

    The pressure dependencies of the crystal structures of the polymeric metallocenes lithium cyclopentadienide (LiCp) and potassium cyclopentadienide (KCp) have been determined by synchrotron X-ray powder diffraction. The decrease of the volume of LiCp by 34% up to a pressure of p = 12.2 GPa and of KCp by 23% at p = 5.3 GPa as well as the bulk moduli of K = 7.7 GPa for LiCp and 4.9 GPa for KCp indicate a high compressibility for these compounds. The crystal structures of KCp have been determined up to p = 3.9 GPa. An increase of the bend angle is found from 45 degrees at p = 0 GPa up to 51 degrees at p = 3.9 GPa. This variation is completely explained by a model invoking attractive K+ Cp- interaction and repulsive nonbonded carbon-carbon interactions. It is proposed that the bend angle in the polymeric alkali metal metallocenes is the result of the optimization of the crystal packing.

  7. Tuning of intermolecular interactions results in packing diversity in imidazolin-5-ones

    Indian Academy of Sciences (India)

    Ashish Singh; Basanta Kumar Rajbongshi; Gurunath Ramanathan

    2014-09-01

    Crystal structures of four green fluorescent protein (GFP) chromophore analogues with different packing interactions could be tuned by appropriate substitutions around the imidazolin-5-one ring are reported here. Compound 1 was crystallized from tetrahydrofuran at room temperature while compounds 2-4 have been crystallized from a mixture of methanol and dichloromethane in 3:1 ratio. Molecule 1, 2 and 3 crystallized in monoclinic lattice while molecule 4 preferred to crystallize in a triclinic crystal system. The crystal packing of these molecules was stabilized by C-H$\\ldots$ stacking and C-H $\\ldots$ O type of supramolecular interactions. The results reveal that packing diversity can be easily accomplished in these molecules by tuning the substituents around the imidazolin-5-one ring. Photophysical studies also reveal that all have good quantum yield and fluoresce typically in red region due to presence of electron donating groups around the imidazolin-5-one ring.

  8. Crystal packing in two pH-dependent crystal forms of rhamnogalacturonan acetylesterase

    DEFF Research Database (Denmark)

    Mølgaard, Anne; Larsen, S.

    2004-01-01

    The glycoprotein rhamnogalacturonan acetylesterase from Aspergillus aculeatus has been crystallized in two crystal forms, an orthorhombic and a trigonal crystal form. In the orthorhombic crystal form, the covalently bound carbohydrate at one of the two N-glycosylation sites is involved in crystal...... contacts. The orthorhombic crystal form was obtained at pH 5.0 and the trigonal crystal form at pH 4.5. In one case, the two crystal forms were found in the same drop at pH 4.7. The differences in crystal packing in the two crystal forms can be explained by the pH-dependent variation in the protonation...

  9. Deterioration of organic packing materials commonly used in air biofiltration: effect of VOC-packing interactions.

    Science.gov (United States)

    Lebrero, Raquel; Estrada, José M; Muñoz, Raúl; Quijano, Guillermo

    2014-05-01

    The abiotic deterioration of three conventional organic packing materials used in biofiltration (compost, wood bark and Macadamia nutshells) caused by their interaction with toluene (used as a model volatile organic compound) was here studied. The deterioration of the materials was evaluated in terms of structural damage, release of co-substrates and increase of the packing biodegradability. After 21 days of exposure to toluene, all packing materials released co-substrates able to support microbial growth, which were not released by the control materials not exposed to toluene. Likewise, the exposure to toluene increased the packing material biodegradability by 26% in wood bark, 20% in compost and 17% in Macadamia nutshells. Finally, scanning electron microscopy analysis confirmed the deterioration in the structure of the packing materials evaluated due to the exposure to toluene, Macadamia nutshells being the material with the highest resistance to volatile organic compound attack.

  10. Protein packing interactions and polymorphy of chorismate lyase from E. Coli

    Science.gov (United States)

    Gallagher, Travis

    2001-11-01

    The enzyme chorismate lyase from E. coli crystallizes into three well characterized polymorphs in identical conditions. The Wild-type enzyme tends to aggregate, even in the presence of a reducing agent, and yields monoclinic crystals that grow in intricate clusters. Protein aggregation was largely eliminated by mutating the protein's two cysteines to serines. The double mutant retains full enzymatic activity and grows singly in two new forms: triclinic and orthorhombic. The triclinic crystals diffract to 0.9 Å resolution. A single-cysteine mutant that crystallizes in the orthorhombic form was used to determine the structure, enabling examination of the packing interactions at 2.0 Å resolution or better in all three forms. A novel system for labeling contacts is proposed, and relations between packing patterns and crystal properties are discussed. Diffraction resolution is found to correlate with coordination number and with the root-mean-square deviation from mean extent of the contacts. Implications for contact energies are considered.

  11. Influence of packing interactions on the average conformation of B-DNA in crystalline structures.

    Science.gov (United States)

    Tereshko, V; Subirana, J A

    1999-04-01

    The molecular interactions in crystals of oligonucleotides in the B form have been analysed and in particular the end-to-end interactions. Phosphate-phosphate interactions in dodecamers are also reviewed. A strong influence of packing constraints on the average conformation of the double helix is found. There is a strong relationship between the space group, the end-to-end interactions and the average conformation of DNA. Dodecamers must have a B-form average conformation with 10 +/- 0.1 base pairs per turn in order to crystallize in the P212121 and related space groups usually found. Decamers show a wider range of conformational variation, with 9.7-10. 6 base pairs per turn, depending on the terminal sequence and the space group. The influence of the space group in decamers is quite striking and remains unexplained. Only small variations are allowed in each case. Thus, crystal packing is strongly related to the average DNA conformation in the crystals and deviations from the average are rather limited. The constraints imposed by the crystal lattice explain why the average twist of the DNA in solution (10.6 base pairs per turn) is seldom found in oligonucleotides crystallized in the B form.

  12. Temperature-mediated polymorphism in molecular crystals: The impact on crystal packing and charge transport

    KAUST Repository

    Stevens, Loah A.

    2015-01-13

    We report a novel synthesis to ultra high purity 7,14-bis((trimethylsilyl)ethynyl)dibenzo[b,def]-chrysene (TMS-DBC) and the use of this material in the growth of single crystals by solution and vapor deposition techniques. We observe that the substrate temperature has a dramatic impact on the crystal growth, producing two distinct polymorphs of TMS-DBC; low temperature (LT) fine red needles and high temperature (HT) large yellow platelets. Single crystal X-ray crystallography confirms packing structures where the LT crystals form a 1D slipped-stack structure, while the HT crystals adopt a 2D brickwork motif. These polymorphs also represent a rare example where both are extremely stable and do not interconvert to the other crystal structure upon solvent or thermal annealing. Single crystal organic field-effect transistors of the LT and HT crystals show that the HT 2D brickwork motif produces hole mobilities as high as 2.1 cm2 V-1 s-1, while the mobility of the 1D structure is significantly lower, at 0.028 cm2 V-1 s-1. Electronic-structure calculations indicate that the superior charge transport in the brickwork polymorph in comparison to the slipped-stack polymorph is due to the presence of an increased dimensionality of the charge migration pathways.

  13. On plastic flow in notched hexagonal close packed single crystals

    Science.gov (United States)

    Selvarajou, Balaji; Kondori, Babak; Benzerga, A. Amine; Joshi, Shailendra P.

    2016-09-01

    The micromechanics of anisotropic plastic flow by combined slip and twinning is investigated computationally in single crystal notched specimens. Constitutive relations for hexagonal close packed materials are used which take into account elastic anisotropy, thirty potential deformation systems, various hardening mechanisms and rate-sensitivity. The specimens are loaded perpendicular to the c-axis but the presence of a notch generates three-dimensional triaxial stress states. The study is motivated by recent experiments on a polycrystalline magnesium alloy. To enable comparisons with these where appropriate, three sets of activation thresholds for the various deformation systems are used. For the conditions that most closely mimic the alloy material, attention is focused on the relative roles of pyramidal and prismatic slip, as well as on the emergence of {1012bar}[101bar1] extension twinning at sufficiently high triaxiality. In all cases, the spatial variations of stress triaxiality and plastic strain, inclusive of various system activities, are quantified along with their evolution upon straining. The implications of these findings in fundamental understanding of ductile failure of HCP alloys in general and Mg alloys in particular are discussed.

  14. Non-covalent interactions in 2-methylimidazolium copper(II) complex (MeImH)2[Cu(pfbz)4]: Synthesis, characterization, single crystal X-ray structure and packing analysis

    Science.gov (United States)

    Sharma, Raj Pal; Saini, Anju; Kumar, Santosh; Kumar, Jitendra; Sathishkumar, Ranganathan; Venugopalan, Paloth

    2017-01-01

    A new anionic copper(II) complex, (MeImH)2 [Cu(pfbz)4] (1) where, MeImH = 2-methylimidazolium and pfbz = pentafluorobenzoate has been isolated by reacting copper(II) sulfate pentahydrate, pentafluorobenzoic acid and 2-methylimidazole in ethanol: water mixture in 1:2:2 molar ratio. This complex 1 has been characterized by elemental analysis, thermogravimetric analysis, spectroscopic techniques (UV-Vis, FT-IR) and conductance measurements. The complex salt crystallizes in monoclinic crystal system with space group C2/c. Single crystal X-ray structure determination revealed the presence of discrete ions: [Cu(pfbz)4]2- anion and two 2-methylimidazolium cation (C4H7N2)+. The crystal lattice is stabilized by strong hydrogen bonding and F⋯F interactions between cationic-anionic and the anionic-anionic moieties respectively, besides π-π interactions.

  15. Polymorphism in two biologically active dihydropyrimidinium hydrochloride derivatives: quantitative inputs towards the energetics associated with crystal packing.

    Science.gov (United States)

    Panini, Piyush; Venugopala, K N; Odhav, Bharti; Chopra, Deepak

    2014-08-01

    A new polymorph belonging to the tetrahydropyrimidinium class of compounds, namely 6-(4-chlorophenyl)-5-(methoxycarbonyl)-4-methyl-2-(3-(trifluoromethylthio)phenylamino)-3,6-dihydropyrimidin-1-ium chloride, and a hydrate of 2-(3-bromophenylamino)-6-(4-chlorophenyl)-5-(methoxycarbonyl)-4-methyl-3,6-dihydropyrimidin-1-ium chloride, have been isolated and characterized using single-crystal X-ray diffraction (XRD). A detailed comprehensive analysis of the crystal packing in terms of the associated intermolecular interactions and a quantification of their interaction energies have been performed for both forms of the two different organic salts (A and B) using X-ray crystallography and computational methods such as density functional theory (DFT) quantum mechanical calculations, PIXEL lattice-energy calculations (with decomposition of total lattice energy into the Coulombic, polarization, dispersion and repulsion contribution), the calculation of the Madelung constant (the EUGEN method), Hirshfeld and two-dimensional fingerprint plots. The presence of ionic [N-H](+)···Cl(-) and [C-H](+)···Cl(-) hydrogen bonds mainly stabilizes the crystal packing in both forms A and B, while in the case of B·H2O [N-H](+)···O(water) and O(water)-H···Cl(-) hydrogen bonds along with [N-H](+)···Cl(-) and [C-H](+)···Cl(-) provide stability to the crystal packing. The lattice-energy calculations from both PIXEL and EUGEN methods revealed that in the case of A, form (I) (monoclinic) is more stable whereas for B it is the anhydrous form that is more stable. The analysis of the `Madelung mode' of crystal packing of two forms of A and B and its hydrates suggest that differences exist in the position of the charged ions/atoms in the organic solid state. The R/E (distance-energy) plots for all the crystal structures show that the molecular pairs in their crystal packing are connected with either highly stabilizing (due to the presence of organic R(+) and Cl(-)) or highly

  16. Probing crystal packing of uniformly (13)C-enriched powder samples using homonuclear dipolar coupling measurements.

    Science.gov (United States)

    Mollica, Giulia; Dekhil, Myriam; Ziarelli, Fabio; Thureau, Pierre; Viel, Stéphane

    2015-02-01

    The relationship between the crystal packing of powder samples and long-range (13)C-(13)C homonuclear dipolar couplings is presented and illustrated for the case of uniformly (13)C-enriched L-alanine and L-histidine·HCl·H2O. Dipolar coupling measurement is based on the partial reintroduction of dipolar interactions by spinning the sample slightly off-magic-angle, while the coupling of interest for a given spin pair is isolated with a frequency-selective pulse. A cost function is used to correlate the so-derived dipolar couplings to trial crystal structures of the samples under study. This procedure allowed for the investigation of the l-alanine space group and L-histidine·HCl·H2O space group and unit-cell parameters.

  17. Packing interface energetics in different crystal forms of the λ Cro dimer.

    Science.gov (United States)

    Ahlstrom, Logan S; Miyashita, Osamu

    2014-07-01

    Variation among crystal structures of the λ Cro dimer highlights conformational flexibility. The structures range from a wild type closed to a mutant fully open conformation, but it is unclear if each represents a stable solution state or if one may be the result of crystal packing. Here we use molecular dynamics (MD) simulation to investigate the energetics of crystal packing interfaces and the influence of site-directed mutagenesis on them in order to examine the effect of crystal packing on wild type and mutant Cro dimer conformation. Replica exchange MD of mutant Cro in solution shows that the observed conformational differences between the wild type and mutant protein are not the direct consequence of mutation. Instead, simulation of Cro in different crystal environments reveals that mutation affects the stability of crystal forms. Molecular Mechanics Poisson-Boltzmann Surface Area binding energy calculations reveal the detailed energetics of packing interfaces. Packing interfaces can have diverse properties in strength, energetic components, and some are stronger than the biological dimer interface. Further analysis shows that mutation can strengthen packing interfaces by as much as ∼5 kcal/mol in either crystal environment. Thus, in the case of Cro, mutation provides an additional energetic contribution during crystal formation that may stabilize a fully open higher energy state. Moreover, the effect of mutation in the lattice can extend to packing interfaces not involving mutation sites. Our results provide insight into possible models for the effect of crystallization on Cro conformational dynamics and emphasize careful consideration of protein crystal structures.

  18. Can Crystal Symmetry and Packing Influence the Active Site Conformation of Homohexameric Purine Nucleoside Phosphorylases?

    Directory of Open Access Journals (Sweden)

    Marija Luić

    2016-06-01

    Full Text Available It is generaly believed that enzymes retain most of their functionality in the crystal form due to the large solvent content of protein crystals. This is facilitated by the fact that their natural environment in solution is not too far from the one found in the crystal form. Nevertheless, if the nature of the enzyme is such to require conformational changes, overcoming of the crystal packing constraints may prove to be too difficult. Such conformational change is present in one class of enzymes (purine nucleoside phosphorylases, that is the subject of our scientific interest for many years. The influence of crystal symmetry and crystal packing on the conformation of the active sites in the case of homohexameric purine nucleoside phosphorylases is presented and analysed. This work is licensed under a Creative Commons Attribution 4.0 International License.

  19. Substituent effect on the thermodynamic solubility of structural analogs: relative contribution of crystal packing and hydration.

    Science.gov (United States)

    Ozaki, Shunsuke; Nakagawa, Yoshiaki; Shirai, Osamu; Kano, Kenji

    2014-11-01

    Thermodynamic analysis of the solubility of benzoylphenylurea (BPU) derivatives was conducted to investigate the relative importance of crystal packing and hydration for improving solubility with minor structural modification. The contribution of crystal packing to solubility was evaluated from the change in Gibbs energy on the transition from the crystalline to liquid state. Hydration Gibbs energy was estimated using a linear free-energy relationship between octanol-water partition coefficients and gas-water partition coefficients. The established solubility model satisfactorily explained the relative thermodynamic solubility of the model compounds and revealed that crystal packing and hydration equally controlled solubility of the structural analogs. All hydrophobic substituents were undesirable for solubility in terms of hydration, as expected. On the other hand, some of these hydrophobic substituents destabilized crystal packing and improved the solubility of the BPU derivatives when their impact on crystal packing exceeded their negative influence on hydration. The replacement of a single substituent could cause more than a 10-fold enhancement in thermodynamic solubility; this degree of improvement was comparable to that generally achieved by amorphous formulations. Detailed analysis of thermodynamic solubility will allow us to better understand the true substituent effect and design drug-like candidates efficiently.

  20. Solution Coating of Superior Large-Area Flexible Perovskite Thin Films with Controlled Crystal Packing

    KAUST Repository

    Li, Jianbo

    2017-05-08

    Solution coating of organohalide lead perovskites offers great potential for achieving low-cost manufacturing of large-area flexible optoelectronics. However, the rapid coating speed needed for industrial-scale production poses challenges to the control of crystal packing. Herein, this study reports using solution shearing to confine crystal nucleation and growth in large-area printed MAPbI3 thin films. Near single-crystalline perovskite microarrays are demonstrated with a high degree of controlled macroscopic alignment and crystal orientation, which exhibit significant improvements in optical and optoelectronic properties comparing with their random counterparts, spherulitic, and nanograined films. In particular, photodetectors based on the confined films showing intense anisotropy in charge transport are fabricated, and the device exhibits significantly improved performance in all aspects by one more orders of magnitude relative to their random counterparts. It is anticipated that perovskite films with controlled crystal packing may find applications in high-performance, large-area printed optoelectronics, and solar cells.

  1. Low-density crystal packing of human protein kinase CK2 catalytic subunit in complex with resorufin or other ligands

    DEFF Research Database (Denmark)

    Klopffleisch, Karsten; Issinger, Olaf Georg; Niefind, Karsten

    2012-01-01

    adopts a closed conformation correlating to a canonically established catalytic spine as is typical for eukaryotic protein kinases. In the corresponding crystal packing the hinge/helix αD region is nearly unaffected by crystal contacts, so that largely unbiased conformational adaptions are possible....... This is documented by published human CK2α structures with the same crystal packing but with an open hinge/helix αD region, one of which has been redetermined here with a higher symmetry. An overview of all published human CK2α crystal packings serves as the basis for a discussion of the factors that determine...

  2. Understanding Packing Patterns in Crystals by Analysis of Small Aggregates: A Case Study of CS2.

    Science.gov (United States)

    Singh, Gurmeet; Verma, Rahul; Gadre, Shridhar R

    2015-12-31

    The molecular electrostatic potential (MESP) of the CS2 molecule, in conjunction with the cluster building algorithm, is utilized for generating trial geometries of medium-sized (CS2)n (n = 5-8) aggregates. MESP features suggest crossed, parallel stacked, T-shaped and L-shaped geometries for CS2 clusters. These initial geometries are subjected to geometry optimization employing second-order Møller-Plesset (MP2) theory, with correlation consistent aug-cc-pvDZ (aDZ) basis set. Single-point energies at MP2/aTZ levels are calculated for the estimation of binding energies at complete basis set (CBS) limit. The minimal nature of the reported structures is confirmed by doing vibrational frequency run at MP2/aDZ level of theory using the molecular tailoring approach (MTA). The two- and three-body interaction energies are computed for clusters with n = 5, 6, and 7 and these are suggestive of change in contact patterns with increasing n. Such an analysis is found to offer a qualitative explanation of the packing pattern found in the crystal structure.

  3. Hydrogen Bonding: Between Strengthening the Crystal Packing and Improving Solubility of Three Haloperidol Derivatives

    Directory of Open Access Journals (Sweden)

    Hardeep Saluja

    2016-06-01

    Full Text Available The purpose of this study is to confirm the impact of polar functional groups on inter and intra-molecular hydrogen bonding in haloperidol (HP and droperidol (DP and, hence, their effects on dissolution using a new approach. To confirm our theory, a new molecule: deshydroxy-haloperidol (DHP was designed and its synthesis was requested from a contract laboratory. The molecule was then studied and compared to DP and HP. Unlike DHP, both the HP and DP molecules have hydrogen donor groups, therefore, DHP was used to confirm the relative effects of the hydrogen donor group on solubility and crystal packing. The solid dispersions of the three structurally related molecules: HP, DP, and DHP were prepared using PVPK30, and characterized using XRPD and IR. A comparative dissolution study was carried out in aqueous medium. The absence of a hydrogen bonding donor group in DHP resulted in an unexpected increase in its aqueous solubility and dissolution rate from solid dispersion, which is attributed to weaker crystal pack. The increased dissolution rate of HP and DP from solid dispersions is attributed to drug-polymer hydrogen bonding that interferes with the drug-drug intermolecular hydrogen bonding and provides thermodynamic stability of the dispersed drug molecules. The drug-drug intermolecular hydrogen bond is the driving force for precipitation and crystal packing.

  4. Crystals of Janus colloids at various interaction ranges

    Science.gov (United States)

    Preisler, Z.; Vissers, T.; Smallenburg, F.; Sciortino, F.

    2016-08-01

    We investigate the effect of interaction range on the phase behaviour of Janus particles with a Kern-Frenkel potential. Specifically, we study interaction ranges Δ = 0.1σ, 0.3σ, 0.4σ, 0.5σ with σ the particle diameter, and use variable box shape simulations to predict crystal structures. We found that changing the interaction range beyond 0.2σ drastically increases the variety of possible crystal structures. In addition to close-packed structures, we find body-centered tetragonal and AA-stacked hexagonal crystals, as well as several lamellar crystals. For long interaction ranges and low temperatures, we also observe an extremely large number of metastable structures which compete with the thermodynamically stable ones. These competing structures hinder the detection of the lowest-energy crystal structures, and are also likely to interfere with the spontaneous formation of the ground-state structure. Finally, we determine the gas-liquid coexistence curves for several interaction ranges, and observe that these are metastable with respect to crystallization.

  5. Packing schemes of cavities in selected clathrasils and zeolites and the analogous packings of atoms in crystal structures

    DEFF Research Database (Denmark)

    Hem, Caroline Piper; Makovicky, Emil; Balic Zunic, Tonci

    2010-01-01

    Sizes of cavities and their packing schemes in selected zeolites and clathrasils were studied by means of least squares fitting of circumscribed spheres to them. Resulting packing of spheres of different diameters was analyzed by the coordinates of their centers, their volumes and sphericity...

  6. Packing schemes of cavities in selected clathrasils and zeolites and the analogous packings of atoms in crystal structures

    DEFF Research Database (Denmark)

    Hem, Caroline Piper; Makovicky, Emil; Balic Zunic, Tonci

    2010-01-01

    Sizes of cavities and their packing schemes in selected zeolites and clathrasils were studied by means of least squares fitting of circumscribed spheres to them. Resulting packing of spheres of different diameters was analyzed by the coordinates of their centers, their volumes and sphericity, and...

  7. Close-packed polymer crystals from two-monomer-connected precursors

    Science.gov (United States)

    Lee, Hong-Joon; Jo, Yong-Ryun; Kumar, Santosh; Yoo, Seung Jo; Kim, Jin-Gyu; Kim, Youn-Joong; Kim, Bong-Joong; Lee, Jae-Suk

    2016-09-01

    The design of crystalline polymers is intellectually stimulating and synthetically challenging, especially when the polymerization of any monomer occurs in a linear dimension. Such linear growth often leads to entropically driven chain entanglements and thus is detrimental to attempts to realize the full potential of conjugated molecular structures. Here we report the polymerization of two-monomer-connected precursors (TMCPs) in which two pyrrole units are linked through a connector, yielding highly crystalline polymers. The simultaneous growth of the TMCP results in a close-packed crystal in polypyrrole (PPy) at the molecular scale with either a hexagonal close-packed or face-centred cubic structure, as confirmed by high-voltage electron microscopy, and the structure that formed could be controlled by simply changing the connector. The electrical conductivity of the TMCP-based PPy is almost 35 times that of single-monomer-based PPy, demonstrating its promise for application in diverse fields.

  8. Effect of packing motifs on the energy ranking and electronic properties of putative crystal structures of tricyano-1,4-dithiino[c]-isothiazole.

    Science.gov (United States)

    Curtis, Farren; Wang, Xiaopeng; Marom, Noa

    2016-08-01

    We present an analysis of putative structures of tricyano-1,4-dithiino[c]-isothiazole (TCS3), generated within the sixth crystal structure prediction blind test. Typical packing motifs are identified and characterized in terms of distinct patterns of close contacts and regions of electrostatic and dispersion interactions. We find that different dispersion-inclusive density functional theory (DFT) methods systematically favor specific packing motifs, which may affect the outcome of crystal structure prediction efforts. The effect of crystal packing on the electronic and optical properties of TCS3 is investigated using many-body perturbation theory within the GW approximation and the Bethe-Salpeter equation (BSE). We find that a structure with Pna21 symmetry and a bilayer packing motif exhibits intermolecular bonding patterns reminiscent of π-π stacking and has markedly different electronic and optical properties than the experimentally observed P21/n structure with a cyclic dimer motif, including a narrower band gap, enhanced band dispersion and broader optical absorption. The Pna21 bilayer structure is close in energy to the observed structure and may be feasible to grow.

  9. Interrelation between crystal packing and small-molecule organic solar cell performance

    Energy Technology Data Exchange (ETDEWEB)

    Fitzner, Roland; Reinold, Egon; Mena-Osteritz, Elena; Baeuerle, Peter [Institut fuer Organische Chemie II und Neue Materialien, Universitaet Ulm (Germany); Elschner, Chris; Koerner, Christian; Riede, Moritz; Leo, Karl [Institut fuer Angewandte Photophysik, TU Dresden (Germany); Weil, Matthias [Institut fuer Chemische Technologien und Analytik, Abteilung Strukturchemie, TU Wien, Vienna (Austria); Uhrich, Christian; Pfeiffer, Martin [Heliatek GmbH, Dresden (Germany)

    2012-02-02

    X-ray investigations on single crystals of a series of terminally dicyanovinyl-substituted quaterthiophenes and co-evaporated blend layers with C{sub 60} give insight into molecular packing behavior and morphology, which are crucial parameters in the field of organic electronics. Structural characteristics on various levels and length scales are correlated with the photovoltaic performance of bulk heterojunction small-molecule organic solar cells. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  10. Effect of long-range repulsive Coulomb interactions on packing structure of adhesive particles.

    Science.gov (United States)

    Chen, Sheng; Li, Shuiqing; Liu, Wenwei; Makse, Hernán A

    2016-02-14

    The packing of charged micron-sized particles is investigated using discrete element simulations based on adhesive contact dynamic model. The formation process and the final obtained structures of ballistic packings are studied to show the effect of interparticle Coulomb force. It is found that increasing the charge on particles causes a remarkable decrease of the packing volume fraction ϕ and the average coordination number 〈Z〉, indicating a looser and chainlike structure. Force-scaling analysis shows that the long-range Coulomb interaction changes packing structures through its influence on particle inertia before they are bonded into the force networks. Once contact networks are formed, the expansion effect caused by repulsive Coulomb forces are dominated by short-range adhesion. Based on abundant results from simulations, a dimensionless adhesion parameter Ad*, which combines the effects of the particle inertia, the short-range adhesion and the long-range Coulomb interaction, is proposed and successfully scales the packing results for micron-sized particles within the latest derived adhesive loose packing (ALP) regime. The structural properties of our packings follow well the recent theoretical prediction which is described by an ensemble approach based on a coarse-grained volume function, indicating some kind of universality in the low packing density regime of the phase diagram regardless of adhesion or particle charge. Based on the comprehensive consideration of the complicated inter-particle interactions, our findings provide insight into the roles of short-range adhesion and repulsive Coulomb force during packing formation and should be useful for further design of packings.

  11. Absolute configuration and crystal packing for three chiral drugs prone to spontaneous resolution: Guaifenesin, methocarbamol and mephenesin

    Science.gov (United States)

    Bredikhin, Alexander A.; Gubaidullin, Aidar T.; Bredikhina, Zemfira A.; Krivolapov, Dmitry B.; Pashagin, Alexander V.; Litvinov, Igor A.

    2009-02-01

    Popular chiral drugs, guaifenesin, methocarbamol, and mephenesin were investigated by single-crystal X-ray analysis both for enantiopure and racemic samples. The absolute configurations for all substances were established through Flack parameter method. The conglomerate-forming nature for the compounds was confirmed by equivalence of crystal characteristics of enantiopure and racemic samples. The molecular structures and crystal packing details were evaluated and compared with one another for all three investigated substances.

  12. Structure and stability of designed TPR protein superhelices: unusual crystal packing and implications for natural TPR proteins.

    Science.gov (United States)

    Kajander, Tommi; Cortajarena, Aitziber L; Mochrie, Simon; Regan, Lynne

    2007-07-01

    The structure and stability of repeat proteins has been little studied in comparison to the properties of the more familiar globular proteins. Here, the structure and stability of designed tetratricopeptide-repeat (TPR) proteins is described. The TPR is a 34-amino-acid motif which adopts a helix-turn-helix structure and occurs as tandem repeats. The design of a consensus TPR motif (CTPR) has previously been described. Here, the crystal structures and stabilities of proteins that contain eight or 20 identical tandem repeats of the CTPR motif (CTPR8 and CTPR20) are presented. Both CTPR8 and CTPR20 adopt a superhelical overall structure. The structures of the different-length CTPR proteins are compared with each other and with the structures of natural TPR domains. Also, the unusual and perhaps unique crystal-packing interactions resulting in pseudo-infinite crystalline superhelices observed in the different crystal forms of CTPR8 and CTPR20 are discussed. Finally, it is shown that the thermodynamic behavior of CTPR8 and CTPR20 can be predicted from the behavior of other TPRs in this series using an Ising model-based analysis. The designed protein series CTPR2-CTPR20 covers the natural size repertoire of TPR domains and as such is an excellent model system for natural TPR proteins.

  13. Effect of the packing structure of silicon chunks on the melting process and carbon reduction in Czochralski silicon crystal growth

    Science.gov (United States)

    Liu, Xin; Nakano, Satoshi; Kakimoto, Koichi

    2017-06-01

    Carbon (C) contamination in Czochralski silicon (CZ-Si) crystal growth mainly originates from carbon monoxide (CO) generation on the graphite components, which reaches a maximum during the melting stage. Loading a crucible with poly-Si feedstock includes many technical details for optimization of the melting and growth processes. To investigate the effect of the packing structure of Si chunks on C accumulation in CZ-Si crystal growth, transient global simulations of heat and mass transport were performed for the melting process with different packing structures of poly-Si. The heat transport modeling took into account the effective thermal conductivity (ETC) of the Si feedstock, which is affected by the packing structure. The effect of the chunk size on the melting process and C accumulation were investigated by parametric studies of different packing structures. The heat transport and melting process in the crucible were affected by the ETC and the emissivity of the Si feedstock. It was found that smaller Si chunks packed in the upper part could speed up the melting process and smooth the power profile. Decreasing the duration of the melting process is favorable for reduction of C contamination in the Si feedstock. Parametric studies indicated that optimization of the melting process by the packing structure is possible and essential for C reduction in CZ-Si crystal growth.

  14. Two-phase modelling of equiaxed crystal sedimentation and thermomechanic stress development in the sedimented packed bed

    Science.gov (United States)

    Ludwig, A.; Vakhrushev, A.; Holzmann, T.; Wu, M.; Kharicha, A.

    2015-06-01

    During many industrial solidification processes equiaxed crystals form, grow and move. When those crystals are small they are carried by the melt, whereas when getting larger they sediment. As long as the volume fraction of crystals is below the packing limit, they are able to move relatively free. Crystals being backed in a so called packed bed form a semi-solid slurry, which may behave like a visco-plastic material. In addition, cooling-induced density increase of both, liquid and solid phases might lead to shrinkage of the whole casting domain. So deformation happens and gaps between casting and mold occur. In the present work, a two-phase Eulerian-Eulerian volume averaging model for describing the motion of equiaxed crystals in the melt is combined with a similar two-phase model for describing the dynamic of the packed bed. As constitutive equation for the solid skeleton in the packed bed Norton-Hoff law is applied. Shrinkage induced by density changes in the liquid or the solid phase is explicitly taken into account and handled by remeshing the calculation domain accordantly.

  15. Ab initio studies on the structure of and atomic interactions in cellulose III(I) crystals.

    Science.gov (United States)

    Ishikawa, Tetsuya; Hayakawa, Daichi; Miyamoto, Hitomi; Ozawa, Motoyasu; Ozawa, Tomonaga; Ueda, Kazuyoshi

    2015-11-19

    The crystal structure of cellulose III(I)was analyzed using first-principles density functional theory (DFT). The geometry was optimized using variable-cell relaxation, as implemented in Quantum ESPRESSO. The Perdew-Burke-Ernzerhof (PBE) functional with a correction term for long-range van der Waals interactions (PBE-D) reproduced the experimental structure well. By using the optimized crystal structure, the interactions existed among the cellulose chains in the crystal were precisely investigated using the NBO analysis. The results showed that the weak bonding nature of CH/O and the hydrogen bonding occur among glucose molecules in the optimized crystal structure. To investigate the strength of interaction, dimeric and trimeric glucose units were extracted from the crystal, and analyzed using MP2 ab initio counterpoise methods with BSSE correction. The results estimated the strength of the interactions. That is, the packed chains along with a-axis interacts with weak bonding nature of CH/O and dispersion interactions by -7.50 kcal/mol, and two hydrogen bonds of O2HO2…O6 and O6HO6…O2 connect the neighboring packed chains with -11.9 kcal/mol. Moreover, FMO4 calculation was also applied to the optimized crystal structure to estimate the strength of the interactions. These methods can well estimate the interactions existed in the crystal structure of cellulose III(I).

  16. Organic Semiconductor-Containing Supramolecules: Effect of Small Molecule Crystallization and Molecular Packing

    KAUST Repository

    Rancatore, Benjamin J.

    2016-01-21

    © 2016 American Chemical Society. Small molecules (SMs) with unique optical or electronic properties provide an opportunity to incorporate functionality into block copolymer (BCP)-based supramolecules. However, the assembly of supramolecules based on these highly crystalline molecules differs from their less crystalline counterparts. Here, two families of organic semiconductor SMs are investigated, where the composition of the crystalline core, the location (side- vs end-functionalization) of the alkyl solubilizing groups, and the constitution (branched vs linear) of the alkyl groups are varied. With these SMs, we present a systematic study of how the phase behavior of the SMs affects the overall assembly of these organic semiconductor-based supramolecules. The incorporation of SMs has a large effect on the interfacial curvature, the supramolecular periodicity, and the overall supramolecular morphology. The crystal packing of the SM within the supramolecule does not necessarily lead to the assembly of the comb block within the BCP microdomains, as is normally observed for alkyl-containing supramolecules. An unusual lamellar morphology with a wavy interface between the microdomains is observed due to changes in the packing structure of the small molecule within BCP microdomains. Since the supramolecular approach is modular and small molecules can be readily switched out, present studies provide useful guidance toward access supramolecular assemblies over several length scales using optically active and semiconducting small molecules.

  17. Decisive Interactions between the Heterocyclic Moiety and the Cluster Observed in Polyoxometalate-Surfactant Hybrid Crystals

    Directory of Open Access Journals (Sweden)

    Saki Otobe

    2015-04-01

    Full Text Available Inorganic-organic hybrid crystals were successfully obtained as single crystals by using polyoxotungstate anion and cationic dodecylpyridazinium (C12pda and dodecylpyridinium (C12py surfactants. The decatungstate (W10 anion was used as the inorganic component, and the crystal structures were compared. In the crystal comprising C12pda (C12pda-W10, the heterocyclic moiety directly interacted with W10, which contributed to a build-up of the crystal structure. On the other hand, the crystal consisting of C12py (C12py-W10 had similar crystal packing and molecular arrangement to those in the W10 crystal hybridized with other pyridinium surfactants. These results indicate the significance of the heterocyclic moiety of the surfactant to construct hybrid crystals with polyoxometalate anions.

  18. Decisive interactions between the heterocyclic moiety and the cluster observed in polyoxometalate-surfactant hybrid crystals.

    Science.gov (United States)

    Otobe, Saki; Fujioka, Natsumi; Hirano, Takuro; Ishikawa, Eri; Naruke, Haruo; Fujio, Katsuhiko; Ito, Takeru

    2015-04-16

    Inorganic-organic hybrid crystals were successfully obtained as single crystals by using polyoxotungstate anion and cationic dodecylpyridazinium (C12pda) and dodecylpyridinium (C12py) surfactants. The decatungstate (W10) anion was used as the inorganic component, and the crystal structures were compared. In the crystal comprising C12pda (C12pda-W10), the heterocyclic moiety directly interacted with W10, which contributed to a build-up of the crystal structure. On the other hand, the crystal consisting of C12py (C12py-W10) had similar crystal packing and molecular arrangement to those in the W10 crystal hybridized with other pyridinium surfactants. These results indicate the significance of the heterocyclic moiety of the surfactant to construct hybrid crystals with polyoxometalate anions.

  19. Modulating two-dimensional non-close-packed colloidal crystal arrays by deformable soft lithography.

    Science.gov (United States)

    Li, Xiao; Wang, Tieqiang; Zhang, Junhu; Yan, Xin; Zhang, Xuemin; Zhu, Difu; Li, Wei; Zhang, Xun; Yang, Bai

    2010-02-16

    We report a simple method to fabricate two-dimensional (2D) periodic non-close-packed (ncp) arrays of colloidal microspheres with controllable lattice spacing, lattice structure, and pattern arrangement. This method combines soft lithography technique with controlled deformation of polydimethylsiloxane (PDMS) elastomer to convert 2D hexagonal close-packed (hcp) silica microsphere arrays into ncp ones. Self-assembled 2D hcp microsphere arrays were transferred onto the surface of PDMS stamps using the lift-up technique, and then their lattice spacing and lattice structure could be adjusted by solvent swelling or mechanical stretching of the PDMS stamps. Followed by a modified microcontact printing (microcp) technique, the as-prepared 2D ncp microsphere arrays were transferred onto a flat substrate coated with a thin film of poly(vinyl alcohol) (PVA). After removing the PVA film by calcination, the ncp arrays that fell on the substrate without being disturbed could be lifted up, deformed, and transferred again by another PDMS stamp; therefore, the lattice feature could be changed step by step. Combining isotropic solvent swelling and anisotropic mechanical stretching, it is possible to change hcp colloidal arrays into full dimensional ncp ones in all five 2D Bravais lattices. This deformable soft lithography-based lift-up process can also generate patterned ncp arrays of colloidal crystals, including one-dimensional (1D) microsphere arrays with designed structures. This method affords opportunities and spaces for fabrication of novel and complex structures of 1D and 2D ncp colloidal crystal arrays, and these as-prepared structures can be used as molds for colloidal lithography or prototype models for optical materials.

  20. Double hexagonal close-packed structure revealed in a single colloidal crystal grain by Bragg rod analysis

    NARCIS (Netherlands)

    Meijer, J. M.; Shabalin, A.; Dronyak, R.; Yefanov, O. M.; Singer, A.; Kurta, R. P.; Lorenz, U.; Gorobstov, O.; Dzhigaev, D.; Gulden, J.; Byelov, D. V.; Zozulya, A. V.; Sprung, M.; Vartanyants, I. A.; Petukhov, Andrei V.

    2014-01-01

    A coherent X-ray diffraction study of a single colloidal crystal grain composed of silica spheres is reported. The diffraction data contain Bragg peaks and additional features in the form of Bragg rods, which are related to the stacking of the hexagonally close-packed layers. The profile of the Brag

  1. The fourth crystallographic closest packing unveiled in the gold nanocluster crystal

    Science.gov (United States)

    Gan, Zibao; Chen, Jishi; Wang, Juan; Wang, Chengming; Li, Man-Bo; Yao, Chuanhao; Zhuang, Shengli; Xu, An; Li, Lingling; Wu, Zhikun

    2017-03-01

    Metal nanoclusters have recently attracted extensive interest not only for fundamental scientific research, but also for practical applications. For fundamental scientific research, it is of major importance to explore the internal structure and crystallographic arrangement. Herein, we synthesize a gold nanocluster whose composition is determined to be Au60S6(SCH2Ph)36 by using electrospray ionization mass spectrometry and single crystal X-ray crystallography (SCXC). SCXC also reveals that Au60S6(SCH2Ph)36 consists of a fcc-like Au20 kernel protected by a pair of giant Au20S3(SCH2Ph)18 staple motifs, which contain 6 tetrahedral-coordinate μ4-S atoms not previously reported in the Au-S interface. Importantly, the fourth crystallographic closest-packed pattern, termed 6H left-handed helical (6HLH) arrangement, which results in the distinct loss of solid photoluminescence of amorphous Au60S6(SCH2Ph)36, is found in the crystals of Au60S6(SCH2Ph)36. The solvent-polarity-dependent solution photoluminescence is also demonstrated. Overall, this work provides important insights about the structure, Au-S bonding and solid photoluminescence of gold nanoclusters.

  2. Crystal structures of two bis-(iodo-meth-yl)benzene derivatives: similarities and differences in the crystal packing.

    Science.gov (United States)

    McAdam, C John; Hanton, Lyall R; Moratti, Stephen C; Simpson, Jim

    2015-12-01

    The isomeric derivatives 1,2-bis-(iodo-meth-yl)benzene, (I), and 1,3-bis-(iodo-meth-yl)benzene (II), both C8H8I2, were prepared by metathesis from their di-bromo analogues. The ortho-derivative, (I), lies about a crystallographic twofold axis that bis-ects the C-C bond between the two iodo-methyl substituents. The packing in (I) relies solely on C-H⋯I hydrogen bonds supported by weak parallel slipped π-π stacking inter-actions [inter-centroid distance = 4.0569 (11) Å, inter-planar distance = 3.3789 (8) Å and slippage = 2.245 Å]. While C-H⋯I hydrogen bonds are also found in the packing of (II), type II, I⋯I halogen bonds [I⋯I = 3.8662 (2) Å] and C-H⋯π contacts feature prominently in stabilizing the three-dimensional structure.

  3. Interaction between Proppant Packing, Reservoir Depletion, and Fluid Flow in Pore Space

    Science.gov (United States)

    Fan, M.; McClure, J. E.; Han, Y.; Chen, C.

    2016-12-01

    In the oil and gas industry, the performance of proppant pack in hydraulically created fractures has a significant influence on fracture conductivity. A better understanding of proppant transport and deposition pattern in a hydraulic fracture is vital for effective and economical production within oil and gas reservoirs. In this research, a numerical modeling approach, combining Particle Flow Code (PFC) and GPU-enhanced lattice Boltzmann simulator (GELBS), is adopted to advance the understanding of the interaction between proppant particle packing, depletion of reservoir formation, and transport of reservoir flow through the pore space. In this numerical work flow, PFC is used to simulate effective stress increase and proppant particle movement and rearrangement under increasing mechanical loading. The pore structure of the proppant pack evolves subsequently and the geometrical data are output for lattice Boltzmann (LB) simulation of proppant pack permeability. Three different proppant packs with fixed particle concentration and 12/18, 16/30, and 20/40 mesh sizes are generated. These proppant packs are compressed with specified loading stress and their subsequent geometries are used for fluid flow simulations. The simulation results are in good agreement with experimental observations, e.g., the conductivity of proppant packs decreases with increasing effective stress. Three proppant packs with the same average diameter were generated using different coefficients of variation (COVs) for the proppant diameter (namely cov5%, cov20%, and cov30%). By using the coupled PFC-LBM work flow, the proppant pack permeability as functions of effective stress and porosity is investigated. The results show that the proppant pack with a higher proppant diameter COV has lower permeability and porosity under the same effective stress, because smaller particles fill in the pore space between bigger particles. The relationship between porosity and permeability is also consistent with

  4. Sent packing: protein engineering generates a new crystal form of Pseudomonas aeruginosa DsbA1 with increased catalytic surface accessibility

    Energy Technology Data Exchange (ETDEWEB)

    McMahon, Roisin M., E-mail: r.mcmahon1@uq.edu.au; Coinçon, Mathieu; Tay, Stephanie; Heras, Begoña [University of Queensland, 306 Carmody Road, Brisbane, Queensland 4072 (Australia); Morton, Craig J. [Biota Holdings Limited, Unit 10, 585 Blackburn Road, Notting Hill, Victoria 3168 (Australia); Scanlon, Martin J. [Monash University, 381 Royal Parade, Parkville, Victoria 3052 (Australia); Martin, Jennifer L. [University of Queensland, 306 Carmody Road, Brisbane, Queensland 4072 (Australia)

    2015-11-26

    The crystal structure of a P. aeruginosa DsbA1 variant is more suitable for fragment-based lead discovery efforts to identify inhibitors of this antimicrobial drug target. In the reported structures the active site of the protein can simultaneously bind multiple ligands introduced in the crystallization solution or via soaking. Pseudomonas aeruginosa is an opportunistic human pathogen for which new antimicrobial drug options are urgently sought. P. aeruginosa disulfide-bond protein A1 (PaDsbA1) plays a pivotal role in catalyzing the oxidative folding of multiple virulence proteins and as such holds great promise as a drug target. As part of a fragment-based lead discovery approach to PaDsbA1 inhibitor development, the identification of a crystal form of PaDsbA1 that was more suitable for fragment-soaking experiments was sought. A previously identified crystallization condition for this protein was unsuitable, as in this crystal form of PaDsbA1 the active-site surface loops are engaged in the crystal packing, occluding access to the target site. A single residue involved in crystal-packing interactions was substituted with an amino acid commonly found at this position in closely related enzymes, and this variant was successfully used to generate a new crystal form of PaDsbA1 in which the active-site surface is more accessible for soaking experiments. The PaDsbA1 variant displays identical redox character and in vitro activity to wild-type PaDsbA1 and is structurally highly similar. Two crystal structures of the PaDsbA1 variant were determined in complex with small molecules bound to the protein active site. These small molecules (MES, glycerol and ethylene glycol) were derived from the crystallization or cryoprotectant solutions and provide a proof of principle that the reported crystal form will be amenable to co-crystallization and soaking with small molecules designed to target the protein active-site surface.

  5. The dominant role of chalcogen bonding in the crystal packing of 2D/3D aromatics.

    Science.gov (United States)

    Fanfrlík, Jindřich; Přáda, Adam; Padělková, Zdeňka; Pecina, Adam; Macháček, Jan; Lepšík, Martin; Holub, Josef; Růžička, Aleš; Hnyk, Drahomír; Hobza, Pavel

    2014-09-15

    The chalcogen bond is a nonclassical σ-hole-based noncovalent interaction with emerging applications in medicinal chemistry and material science. It is found in organic compounds, including 2D aromatics, but has so far never been observed in 3D aromatic inorganic boron hydrides. Thiaboranes, harboring a sulfur heteroatom in the icosahedral cage, are candidates for the formation of chalcogen bonds. The phenyl-substituted thiaborane, synthesized and crystalized in this study, forms sulfur⋅⋅⋅π type chalcogen bonds. Quantum chemical analysis revealed that these interactions are considerably stronger than both in their organic counterparts and in the known halogen bond. The reason is the existence of a highly positive σ-hole on the positively charged sulfur atom. This discovery expands the possibilities of applying substituted boron clusters in crystal engineering and drug design.

  6. Fabrication of size-controllable hexagonal non-close-packed colloidal crystals and binary colloidal crystals by pyrolysis combined with plasma-electron coirradiation of polystyrene colloidal monolayer.

    Science.gov (United States)

    Kim, Jae Joon; Li, Yue; Lee, Eun Je; Cho, Sung Oh

    2011-03-15

    We present an unprecedented and systematic route to controllably fabricate hexagonal non-close-packed (hncp) monolayer colloidal crystals and binary colloidal crystals (BCCs) based on plasma-electron coirradiation of polystyrene colloidal monolayers followed by thermal decomposition. Hncp colloidal crystals with tunable particle sizes and periods could be fabricated by changing the pristine colloidal particle size and the thermal decomposition time. In addition, BCCs and trimodal colloidal crystals that are composed of different-sized colloidal particles can also be fabricated by adding small particles on the prepared hncp colloidal crystals. Both the particle size ratio and the volume fraction of the BCCs can be widely tuned. These hncp colloidal crystals and BCCs have various potential applications as optical and photonic materials as well as in catalysis and sensors.

  7. A novel opal closest-packing photonic crystal for naked-eye glucose detection.

    Science.gov (United States)

    Hong, Xiaodi; Peng, Yuan; Bai, Jialei; Ning, Baoan; Liu, Yuanyuan; Zhou, Zhijiang; Gao, Zhixian

    2014-04-09

    A novel opal closest-packing (OCP) photonic crystal (PC) is successfully prepared for naked-eye glucose detection. This PC is fabricated via a vertical convective self-assembly method with a new type of monodisperse microsphere polymerized by co-monomers, namely, methyl methacrylate (MMA), N-isopropylacrylamide (NIPA), and 3-acrylamidophenylboronic acid (AAPBA). The OCP PC has high stability and periodically-ordered structure, showing the desired structural color. The proposed PC material displays a red shift and reduced reflection intensity when detecting glucose molecules. The red-shift wavelength reaches 75 nm, which clearly changes the structural color from brilliant blue to emerald green. This visually distinguishable color change facilitates the detection of the glucose concentrations from 3 to 20 mm, which demonstrates the potential of the opal PC material for naked-eye detection. Thus, the novel PMMA–NIPA–AAPBA OCP PC is a simply prepared and sensitive material, which shows promising use in the diagnosis of diabetes mellitus and in real-time monitoring of diabetes. Different types of appropriated recognition groups are expected to be introduced into the 3D OCP PC to form new functional materials or chemical sensors, which will extensively broaden the PC material application.

  8. Z-score biological significance of binding hot spots of protein interfaces by using crystal packing as the reference state.

    Science.gov (United States)

    Liu, Qian; Wong, Limsoon; Li, Jinyan

    2012-12-01

    Characterization of binding hot spots of protein interfaces is a fundamental study in molecular biology. Many computational methods have been proposed to identify binding hot spots. However, there are few studies to assess the biological significance of binding hot spots. We introduce the notion of biological significance of a contact residue for capturing the probability of the residue occurring in or contributing to protein binding interfaces. We take a statistical Z-score approach to the assessment of the biological significance. The method has three main steps. First, the potential score of a residue is defined by using a knowledge-based potential function with relative accessible surface area calculations. A null distribution of this potential score is then generated from artifact crystal packing contacts. Finally, the Z-score significance of a contact residue with a specific potential score is determined according to this null distribution. We hypothesize that residues at binding hot spots have big absolute values of Z-score as they contribute greatly to binding free energy. Thus, we propose to use Z-score to predict whether a contact residue is a hot spot residue. Comparison with previously reported methods on two benchmark datasets shows that this Z-score method is mostly superior to earlier methods. This article is part of a Special Issue entitled: Computational Methods for Protein Interaction and Structural Prediction.

  9. How the Molecular Packing Affects the Room Temperature Phosphorescence in Pure Organic Compounds: Ingenious Molecular Design, Detailed Crystal Analysis, and Rational Theoretical Calculations.

    Science.gov (United States)

    Xie, Yujun; Ge, Yuwei; Peng, Qian; Li, Conggang; Li, Qianqian; Li, Zhen

    2017-02-21

    Long-lived phosphorescence at room temperature (RTP) from pure organic molecules is rare. Recent research reveals various crystalline organic molecules can realize RTP with lifetimes extending to the magnitude of second. There is little research on how molecular packing affecting RTP. Three compounds are designed with similar optical properties in solution, but tremendously different solid emission characteristics. By investigating the molecular packing arrangement in single crystals, it is found that the packing style of the compact face to face favors of long phosphorescence lifetime and high photoluminescence efficiency, with the lifetime up to 748 ms observed in the crystal of CPM ((9H-carbazol-9-yl)(phenyl)methanone). Theoretical calculation analysis also reveals this kind of packing style can remarkably reduce the singlet excited energy level and prompt electron communication between dimers. Surprisingly, CPM has two very similar single crystals, labeled as CPM and CPM-A, with almost identical crystal data, and the only difference is that molecules in CPM-A crystal take a little looser packing arrangement. X-ray diffraction and cross-polarization under magic spinning (13) C NMR spectra double confirm that they are different crystals. Interestingly, CPM-A crystal shows negligible RTP compared to the CPM crystal, once again proving that the packing style is critical to the RTP property.

  10. One more chiral drug prone to spontaneous resolution: Binary phase diagram, absolute configuration, and crystal packing of bevantolol hydrochloride

    Science.gov (United States)

    Bredikhina, Zemfira A.; Zakharychev, Dmitry V.; Gubaidullin, Aidar T.; Bredikhin, Alexander A.

    2009-11-01

    Spontaneous resolution of cardioselective β1-adrenergic blocker bevantolol hydrochloride1·HCl was established by IR spectroscopy, differential scanning calorimetry, and by single crystal X-ray analysis both for enantiopure and racemic samples. The absolute configuration of 1·HCl was evaluated through Flack parameter method. The molecular structure and crystal packing details were evaluated; the symmetry independent fragment of the P1 unit cell consists of two molecules which have almost identical spatial arrangement, but differ sufficiently in the nature of nitrogen atoms: quaternary form in one case and free amine form in the other.

  11. TVB-EduPack-An Interactive Learning and Scripting Platform for The Virtual Brain.

    Science.gov (United States)

    Matzke, Henrik; Schirner, Michael; Vollbrecht, Daniel; Rothmeier, Simon; Llarena, Adalberto; Rojas, Raúl; Triebkorn, Paul; Domide, Lia; Mersmann, Jochen; Solodkin, Ana; Jirsa, Viktor K; McIntosh, Anthony Randal; Ritter, Petra

    2015-01-01

    The Virtual Brain (TVB; thevirtualbrain.org) is a neuroinformatics platform for full brain network simulation based on individual anatomical connectivity data. The framework addresses clinical and neuroscientific questions by simulating multi-scale neural dynamics that range from local population activity to large-scale brain function and related macroscopic signals like electroencephalography and functional magnetic resonance imaging. TVB is equipped with a graphical and a command-line interface to create models that capture the characteristic biological variability to predict the brain activity of individual subjects. To enable researchers from various backgrounds a quick start into TVB and brain network modeling in general, we developed an educational module: TVB-EduPack. EduPack offers two educational functionalities that seamlessly integrate into TVB's graphical user interface (GUI): (i) interactive tutorials introduce GUI elements, guide through the basic mechanics of software usage and develop complex use-case scenarios; animations, videos and textual descriptions transport essential principles of computational neuroscience and brain modeling; (ii) an automatic script generator records model parameters and produces input files for TVB's Python programming interface; thereby, simulation configurations can be exported as scripts that allow flexible customization of the modeling process and self-defined batch- and post-processing applications while benefitting from the full power of the Python language and its toolboxes. This article covers the implementation of TVB-EduPack and its integration into TVB architecture. Like TVB, EduPack is an open source community project that lives from the participation and contribution of its users. TVB-EduPack can be obtained as part of TVB from thevirtualbrain.org.

  12. TVB-EduPack - An interactive learning and scripting platform for The Virtual Brain

    Directory of Open Access Journals (Sweden)

    Henrik eMatzke

    2015-11-01

    Full Text Available The Virtual Brain (TVB; www.thevirtualbrain.org is a neuroinformatics platform for full brain network simulation based on individual anatomical connectivity data. The framework addresses clinical and neuroscientific questions by simulating multi-scale neural dynamics that range from local population activity to large-scale brain function and related macroscopic signals like electroencephalography and functional magnetic resonance imaging. TVB is equipped with a graphical and a command-line interface to create models that capture the characteristic biological variability to predict the brain activity of individual subjects. To enable researchers from various backgrounds a quick start into TVB and brain network modelling in general, we developed an educational module: TVB-EduPack. EduPack offers two educational functionalities that seamlessly integrate into TVB’s graphical user interface (GUI: (i interactive tutorials introduce GUI elements, guide through the basic mechanics of software usage and develop complex use-case scenarios; animations, videos and textual descriptions transport essential principles of computational neuroscience and brain modelling; (ii an automatic script generator records model parameters and produces input files for TVB’s Python programming interface; thereby, simulation configurations can be exported as scripts that allow flexible customization of the modelling process and self-defined batch- and post-processing applications while benefitting from the full power of the Python language and its toolboxes. This article covers the implementation of TVB-EduPack and its integration into TVB architecture. Like TVB, EduPack is an open source community project that lives from the participation and contribution of its users. TVB-EduPack can be obtained as part of TVB from thevirtualbrain.org.

  13. Three interactive scenes of The Crystal Cabinet

    OpenAIRE

    Unander-Scharin, Åsa

    2010-01-01

    The interactive scenes of The Crystal Cabinet (2008) constitute the first part in my choreographic research project exploring volatile bodies and multistable corporealities. This performance took the form of a dream play opera in twelve scenes including texts and images from William Blake’s (1757-1827) illuminated books. To create his books Blake invented a printing-machine with which he could print his handwritten poems and images. We transformed this idea into an interactive stage area wher...

  14. Attractive particle interaction forces and packing density of fine glass powders.

    Science.gov (United States)

    Parteli, Eric J R; Schmidt, Jochen; Blümel, Christina; Wirth, Karl-Ernst; Peukert, Wolfgang; Pöschel, Thorsten

    2014-09-02

    We study the packing of fine glass powders of mean particle diameter in the range (4-52) μm both experimentally and by numerical DEM simulations. We obtain quantitative agreement between the experimental and numerical results, if both types of attractive forces of particle interaction, adhesion and non-bonded van der Waals forces are taken into account. Our results suggest that considering only viscoelastic and adhesive forces in DEM simulations may lead to incorrect numerical predictions of the behavior of fine powders. Based on the results from simulations and experiments, we propose a mathematical expression to estimate the packing fraction of fine polydisperse powders as a function of the average particle size.

  15. Interaction of antimicrobial preservatives with blow-fill-seal packs: correlating sorption with solubility parameters.

    Science.gov (United States)

    Amin, Aeshna; Dare, Manish; Sangamwar, Abhay; Bansal, Arvind Kumar

    2012-01-01

    The aim of this work was to study the interaction of four commonly used ophthalmic antimicrobial preservatives [benzyl alcohol (BA), chlorbutol (CBL), benzalkonium chloride (BKC), and chlorhexidine gluconate (CG)] with Blow-Fill-Seal (BFS) packs. Effect of packaging material [low-density polyethylene (LDPE), polypropylene (PP)], humidity (25% RH, 75% RH) and concentration (0.5, 1.0, 2.0 mM BA/CBL in LDPE) was studied. BKC and CG gave negligible loss (preservative. Loss of BA switched from Case II to anomalous behavior with increasing initial concentration. A two-stage sorption behavior was inherent at all concentrations. Loss of CBL followed anomalous behavior with biphasic kinetics of loss. It was concluded that all the four preservatives were appropriate for use in PP BFS packs. However, only BKC and CG were amenable to be used in LDPE BFS packs. Lastly, an empirical expression consisting of the "solubility parameter distance" and "molar volume" of preservatives was developed to correlate the preservative loss in LDPE with the physicochemical properties of the preservatives.

  16. Modelling packing interactions in parallel helix bundles: pentameric bundles of nicotinic receptor M2 helices.

    Science.gov (United States)

    Sankararamakrishnan, R; Sansom, M S

    1995-11-01

    The transbilayer pore of the nicotinic acetylcholine receptor (nAChR) is formed by a pentameric bundle of M2 helices. Models of pentameric bundles of M2 helices have been generated using simulated annealing via restrained molecular dynamics. The influence of: (a) the initial C alpha template; and (b) screening of sidechain electrostatic interactions on the geometry of the resultant M2 helix bundles is explored. Parallel M2 helices, in the absence of sidechain electrostatic interactions, pack in accordance with simple ridges-in-grooves considerations. This results in a helix crossing angle of ca. +12 degrees, corresponding to a left-handed coiled coil structure for the bundle as a whole. Tilting of M2 helices away from the central pore axis at their C-termini and/or inclusion of sidechain electrostatic interactions may perturb such ridges-in-grooves packing. In the most extreme cases right-handed coiled coils are formed. An interplay between inter-helix H-bonding and helix bundle geometry is revealed. The effects of changes in electrostatic screening on the dimensions of the pore mouth are described and the significance of these changes in the context of models for the nAChR pore domain is discussed.

  17. Closely packed Ge quantum dots in ITO matrix: influence of Ge crystallization on optical and electrical properties

    Science.gov (United States)

    Car, Tihomir; Nekić, Nikolina; Jerčinović, Marko; Salamon, Krešimir; Bogdanović-Radović, Iva; Delač Marion, Ida; Dasović, Jasna; Dražić, Goran; Ivanda, Mile; Bernstorff, Sigrid; Pivac, Branko; Kralj, Marko; Radić, Nikola; Buljan, Maja

    2016-06-01

    In the present work, a method for the low-temperature production of the material consisting of closely packed Ge QDs embedded in ITO matrix is described. The films are produced by magnetron sputtering deposition followed by thermal annealing. It is shown that the conductivity and optical properties of the films depend on the structure, Ge content in the ITO matrix as well as on the annealing conditions. The conductivity of the films changes up to seven orders of magnitude in dependence on the annealing conditions, and it shows transformation from semiconductor to metallic behavior. The optical properties are also strongly affected by the preparation and annealing conditions, so both conductivity and optical properties can be controllably manipulated. In addition, the crystallization of Ge is found to occur already at 300 °C, which is significantly lower than the crystallization temperature of Ge produced by the same method in silica and alumina matrices.

  18. Crystal-Structure Analysis with Moments of the Density-of-States: Application to Intermetallic Topologically Close-Packed Phases

    Directory of Open Access Journals (Sweden)

    Thomas Hammerschmidt

    2016-02-01

    Full Text Available The moments of the electronic density-of-states provide a robust and transparent means for the characterization of crystal structures. Using d-valent canonical tight-binding, we compute the moments of the crystal structures of topologically close-packed (TCP phases as obtained from density-functional theory (DFT calculations. We apply the moments to establish a measure for the difference between two crystal structures and to characterize volume changes and internal relaxations. The second moment provides access to volume variations of the unit cell and of the atomic coordination polyhedra. Higher moments reveal changes in the longer-ranged coordination shells due to internal relaxations. Normalization of the higher moments leads to constant (A15,C15 or very similar (χ, C14, C36, μ, and σ higher moments of the DFT-relaxed TCP phases across the 4d and 5d transition-metal series. The identification and analysis of internal relaxations is demonstrated for atomic-size differences in the V-Ta system and for different magnetic orderings in the C14-Fe 2 Nb Laves phase.

  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. Atom-Light Interactions in Photonic Crystals

    CERN Document Server

    Goban, A; Yu, S -P; Hood, J D; Muniz, J A; Lee, J H; Martin, M J; McClung, A C; Choi, K S; Chang, D E; Painter, O; Kimble, H J

    2013-01-01

    The integration of nanophotonics and atomic physics has been a long-sought goal that would open new frontiers for optical physics. Here, we report the development of the first integrated optical circuit with a photonic crystal capable of both localizing and interfacing atoms with guided photons in the device. By aligning the optical bands of a photonic crystal waveguide (PCW) with selected atomic transitions, our platform provides new opportunities for novel quantum transport and many-body phenomena by way of photon-mediated atomic interactions along the PCW. From reflection spectra measured with average atom number N = 1.1$\\pm$0.4, we infer that atoms are localized within the PCW by Casimir-Polder and optical dipole forces. The fraction of single-atom radiative decay into the PCW is $\\Gamma_{\\rm 1D}/\\Gamma'$ = 0.32$\\pm$0.08, where $\\Gamma_{1D}$ is the rate of emission into the guided mode and $\\Gamma'$ is the decay rate into all other channels. $\\Gamma_{\\rm 1D}/\\Gamma'$ is quoted without enhancement due to a...

  1. Effects of hydrodynamic interaction on random adhesive loose packings of micron-sized particles

    Directory of Open Access Journals (Sweden)

    Liu Wenwei

    2017-01-01

    Full Text Available Random loose packings of monodisperse spherical micron-sized particles under a uniform flow field are investigated via an adhesive discrete-element method with the two-way coupling between the particles and the fluid. Characterized by a dimensionless adhesion parameter, the packing fraction follows the similar law to that without fluid, but results in larger values due to the hydrodynamic compression. The total pressure drop through the packed bed shows a critical behaviour at the packing fraction of ϕ ≈ 0.22 in the present study. The normalized permeability of the packed bed for different parameters increases with the increase of porosities and is also in consistent with the Kozeny-Carman equation.

  2. Effects of hydrodynamic interaction on random adhesive loose packings of micron-sized particles

    Science.gov (United States)

    Liu, Wenwei; Tao, Ran; Chen, Sheng; Zhang, Huang; Li, Shuiqing

    2017-06-01

    Random loose packings of monodisperse spherical micron-sized particles under a uniform flow field are investigated via an adhesive discrete-element method with the two-way coupling between the particles and the fluid. Characterized by a dimensionless adhesion parameter, the packing fraction follows the similar law to that without fluid, but results in larger values due to the hydrodynamic compression. The total pressure drop through the packed bed shows a critical behaviour at the packing fraction of ϕ ≈ 0.22 in the present study. The normalized permeability of the packed bed for different parameters increases with the increase of porosities and is also in consistent with the Kozeny-Carman equation.

  3. Vitamin K 3 family members - Part II: Single crystal X-ray structures, temperature-induced packing polymorphism, magneto-structural correlations and probable anti-oncogenic candidature

    Science.gov (United States)

    Rane, Sandhya; Ahmed, Khursheed; Salunke-Gawali, Sunita; Zaware, Santosh B.; Srinivas, D.; Gonnade, Rajesh; Bhadbhade, Mohan

    2008-12-01

    Temperature-induced packing polymorphism is observed for vitamin K 3 (menadione, 3-methyl-1,4-naphthoquinone, 1). Form 1a crystallizes at 300 K and 1b at 277 K both in the same space group P2 1/ c. Form 1b contains one molecule per asymmetric unit, performing anisotropy in g-factor viz. g z = 2.0082, g y = 2.0055 and g x = 2.0025, whereas form 1a contains two molecules in its asymmetric unit. Vitamin K 3 family members 2, [2-hydroxy vitamin K 3] and 3, [2-hydroxy-1-oximino vitamin K 3] also perform intrinsic neutral active naphthosemiquinone valence tautomers even in dark having spin concentrations due to hydrogen bonding and aromatic stacking interactions which are compared to vitamin K 3. The significant lateral C-H⋯O and O-H⋯π bifurcated or π-π ∗ interactions are discussed for molecular associations and radical formations. X-ray structure of 3 revealed π-π ∗ stack dimers as radicals signatured in EPR as triplet with five hyperfine splits [ Ā( 14N) = 11.9 G]. The centrosymmetric biradicals in 3 show diamagnetism at high temperature but below 10 K it shows paramagnetism with μeff as 0.19 B.M. Vitamin K 3 and its family members inhibit biological activities of acid phosphatase ( APase), which are proportional to their spin concentrations. This may relate to their probable anti-oncogenic candidature in future.

  4. The quaternary structure of the amidase from Geobacillus pallidus RAPc8 is revealed by its crystal packing

    Energy Technology Data Exchange (ETDEWEB)

    Agarkar, Vinod B. [Advanced Research Centre for Applied Microbiology, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535 (South Africa); Kimani, Serah W. [Department of Molecular and Cell Biology, University of Cape Town, Rondebosch (South Africa); Cowan, Donald A.; Sayed, Muhammed F.-R. [Advanced Research Centre for Applied Microbiology, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535 (South Africa); Sewell, B. Trevor, E-mail: sewell@uctvms.uct.ac.za [Electron Microscope Unit, University of Cape Town, Rondebosch (South Africa); Advanced Research Centre for Applied Microbiology, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535 (South Africa)

    2006-12-01

    The amidase from G. pallidus RAPc8, a moderate thermophile, converts amides to the corresponding acids and ammonia and has application as an industrial catalyst. RAPc8 amidase has been cloned, expressed and purified, and then crystallized using the hanging-drop vapour-diffusion method. The amidase from Geobacillus pallidus RAPc8, a moderate thermophile, is a member of the nitrilase enzyme superfamily. It converts amides to the corresponding acids and ammonia and has application as an industrial catalyst. RAPc8 amidase has been cloned and functionally expressed in Escherichia coli and has been purified by heat treatment and a number of chromatographic steps. The enzyme was crystallized using the hanging-drop vapour-diffusion method. Crystals produced in the presence of 1.2 M sodium citrate, 400 mM NaCl, 100 mM sodium acetate pH 5.6 were selected for X-ray diffraction studies. A data set having acceptable statistics to 1.96 Å resolution was collected under cryoconditions using an in-house X-ray source. The space group was determined to be primitive cubic P4{sub 2}32, with unit-cell parameter a = 130.49 (±0.05) Å. The structure was solved by molecular replacement using the backbone of the hypothetical protein PH0642 from Pyrococcus horikoshii (PDB code 1j31) with all non-identical side chains substituted with alanine as a probe. There is one subunit per asymmetric unit. The subunits are packed as trimers of dimers with D3 point-group symmetry around the threefold axis in such a way that the dimer interface seen in the homologues is preserved.

  5. Overview of the Structure of All-AT Oligonucleotides: Organization in Helices and Packing Interactions

    Science.gov (United States)

    Campos, Lourdes; Valls, Núria; Urpí, Lourdes; Gouyette, Catherine; Sanmartín, Trinidad; Richter, Michael; Alechaga, Elida; Santaolalla, Alicia; Baldini, Roberto; Creixell, Marc; Ciurans, Ruth; Skokan, Petr; Pous, Joan; Subirana, Juan A.

    2006-01-01

    We present the crystalline organization of 33 all-AT deoxyoligonucleotide duplexes, studied by x-ray diffraction. Most of them have very similar structures, with Watson-Crick basepairs and a standard average twist close to 36°. The molecules are organized as parallel columns of stacked duplexes in a helical arrangement. Such organization of duplexes is very regular and repetitive: all sequences show the same pattern. It is mainly determined by the stacking of the terminal basepairs, so that the twist in the virtual TA base step between neighbor duplexes is always negative, ∼−22°. The distance between the axes of parallel columns is practically identical in all cases, ∼26 Å. Interestingly, it coincides with that found in DNA viruses and fibers in their hexagonal phase. It appears to be a characteristic distance for ordered parallel DNA molecules. This feature is due to the absence of short range intermolecular forces, which are usually due to the presence of CG basepairs at the end of the oligonucleotide sequence. The duplexes apparently interact only through their diffuse ionic atmospheres. The results obtained can thus be considered as intermediate between liquid crystals, fibers, and standard crystal structures. They provide new information on medium range DNA-DNA interactions. PMID:16698788

  6. Elastic interaction of point defects in crystals with cubic symmetry

    Science.gov (United States)

    Kuz'michev, S. V.; Kukushkin, S. A.; Osipov, A. V.

    2013-07-01

    The energy of elastic mechanical interaction between point defects in cubic crystals is analyzed numerically. The finite-element complex ANSYS is used to investigate the character of interaction between point defects depending on their location along the crystallographic directions , , and on the distance from the free boundary of the crystal. The numerical results are compared with the results of analytic computations of the energy of interaction between two point defects in an infinite anisotropic medium with cubic symmetry. The interaction between compressible and incompressible defects of general type is studied. Conditions for onset of elastic attraction between the defects, which leads to general relaxation of the crystal elastic energy, are obtained.

  7. Molecular imprinted opal closest-packing photonic crystals for the detection of trace 17β-estradiol in aqueous solution.

    Science.gov (United States)

    Sai, Na; Wu, Yuntang; Sun, Zhong; Huang, Guowei; Gao, Zhixian

    2015-11-01

    A novel opal closest-packing (OCP) photonic crystal (PC) was prepared by the introduction of molecular imprinting technique into the OCP PC. This molecular imprinted (MI)-OCP PC was fabricated via a vertical convective self-assembly method using 17β-estradiol (E2) as template molecules for monitoring E2 in aqueous solution. Morphology characterization showed that the MI-OCP PC possessed a highly ordered three-dimensional (3D) periodically-ordered structure, showing the desired structural color. The proposed PC material displayed a reduced reflection intensity when detecting E2 in water environment, because the molecular imprinting recognition events make the optical characteristics of PC change. The Bragg diffraction intensity decreased by 19.864 a.u. with the increase of E2 concentration from 1.5 ng mL(-1) to 364.5 ng mL(-1) within 6 min, whereas there were no obvious peak intensity changes for estriol, estrone, cholesterol, testosterone and diethylstilbestrol, indicating that the MI-OCP PC had selective and rapid response for E2 molecules. The adsorption results showed that the OCP structure and homogeneous layers were created in the MI-OCP PC with higher adsorption capacity. Thus, it was learned the MI-OCP PC is a simple prepared, sensitive, selective, and easy operative material, which shows promising use in routine supervision for residue detection in food and environment.

  8. Fabrication of size-controllable hexagonal non-close-packed colloidal crystals and binary colloidal crystals by pyrolysis combined with plasma-electron co-irradiation of polystyrene colloidal monolaye

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jae Joon

    2011-02-15

    We present an unprecedented and systematic route to controllably fabricate hexagonal non-close-packed (HNCP) monolayer colloidal crystals and binary colloidal crystals (BCCs) based on plasma-electron co-irradiation of polystyrene colloidal monolayers followed by thermal decomposition. HNCP colloidal crystals with tunable particle sizes and periods could be fabricated by changing the pristine colloidal particle size and the thermal decomposition time. In addition, BCCs and trimodal colloidal crystals that are composed of different-sized colloidal particles can also be fabricated by adding small particles on the prepared HNCP colloidal crystals. Both the particle size ratio and the volume fraction of the BCCs can be widely tuned. These HNCP colloidal crystals and BCCs have various potential applications as optical and photonic materials as well as in catalysis and sensors.

  9. Noncovalent Intermolecular Interactions in Organic Electronic Materials: Implications for the Molecular Packing vs Electronic Properties of Acenes

    KAUST Repository

    Sutton, Christopher

    2015-10-30

    Noncovalent intermolecular interactions, which can be tuned through the toolbox of synthetic chemistry, determine not only the molecular packing but also the resulting electronic, optical, and mechanical properties of materials derived from π-conjugated molecules, oligomers, and polymers. Here, we provide an overview of the theoretical underpinnings of noncovalent intermolecular interactions and briefly discuss the computational chemistry approaches used to understand the magnitude of these interactions. These methodologies are then exploited to illustrate how noncovalent intermolecular interactions impact important electronic properties-such as the electronic coupling between adjacent molecules, a key parameter for charge-carrier transport-through a comparison between the prototype organic semiconductor pentacene with a series of N-substituted heteropentacenes. Incorporating an understanding of these interactions into the design of organic semiconductors can assist in developing novel materials systems from this fascinating molecular class. © 2015 American Chemical Society.

  10. Patchy particle packing under electric fields.

    Science.gov (United States)

    Song, Pengcheng; Wang, Yufeng; Wang, Yu; Hollingsworth, Andrew D; Weck, Marcus; Pine, David J; Ward, Michael D

    2015-03-01

    Colloidal particles equipped with two, three, or four negatively charged patches, which endow the particles with 2-fold, 3-fold, or tetrahedral symmetries, form 1D chains, 2D layers, and 3D packings when polarized by an AC electric field. Two-patch particles, with two patches on opposite sides of the particle (2-fold symmetry) pack into the cmm plane group and 3D packings with I4mm space group symmetry, in contrast to uncharged spherical or ellipsoidal colloids that typically crystallize into a face-centered ABC layer packing. Three-patch particles (3-fold symmetry) form chains having a 21 screw axis symmetry, but these chains pair in a manner such that each individual chain has one-fold symmetry but the pair has 21 screw axis symmetry, in an arrangement that aligns the patches that would favor Coulombic interactions along the chain. Surprisingly, some chain pairs form unanticipated double-helix regions that result from mutual twisting of the chains about each other, illustrating a kind of polymorphism that may be associated with nucleation from short chain pairs. Larger 2D domains of the three-patch particles crystallize in the p6m plane group with alignment (with respect to the field) and packing densities that suggest random disorder in the domains, whereas four-patch particles form 2D domains in which close-packed rows are aligned with the field.

  11. Real-Time Packing Behavior of Core-Shell Silica@Poly(N-isopropylacrylamide Microspheres as Photonic Crystals for Visualizing in Thermal Sensing

    Directory of Open Access Journals (Sweden)

    Karthikeyan Manivannan

    2016-12-01

    Full Text Available We grafted thermo-responsive poly(N-isopropylacrylamide (PNIPAM brushes from monodisperse SiO2 microspheres through surface-initiated atom transfer radical polymerization (SI ATRP to generate core-shell structured SiO2@PNIPAM microspheres (SPMs. Regular-sized SPMs dispersed in aqueous solution and packed as photonic crystals (PCs in dry state. Because of the microscale of the SPMs, the packing behavior of the PCs in water can be observed by optical microscopy. By increasing the temperature above the lower critical solution temperature (LCST of PNIPAM, the reversible swelling and shrinking of the PNIPAM shell resulted in dispersion and precipitation (three-dimensional aggregation of the SPM in aqueous solution. The SPMs were microdispersed in a water layer to accommodate the aggregation along two dimensions. In the microdispersion, the SPMs are packed as PCs with microscale spacing between SPMs below the LCST. When the temperature is increased above the LCST, the microdispersed PCs exhibited a close-packed arrangement along two dimensions with decreased spacing between SPMs. The change in spacing with increasing temperature above the LCST resulted in a color change from red to blue, which could be observed by the naked eye at an incident angle. Thus, the SPM array could be applied as a visual temperature sensor.

  12. Interactions of salicylic acid derivatives with calcite crystals.

    Science.gov (United States)

    Ukrainczyk, Marko; Gredičak, Matija; Jerić, Ivanka; Kralj, Damir

    2012-01-01

    Investigation of basic interactions between the active pharmaceutical compounds and calcium carbonates is of great importance because of the possibility to use the carbonates as a mineral carrier in drug delivery systems. In this study the mode and extent of interactions of salicylic acid and its amino acid derivates, chosen as pharmaceutically relevant model compounds, with calcite crystals are described. Therefore, the crystal growth kinetics of well defined rhombohedral calcite seed crystals in the systems containing salicylic acid (SA), 5-amino salicylic acid (5-ASA), N-salicyloil-l-aspartic acid (N-Sal-Asp) or N-salicyloil-l-glutamic acid (N-Sal-Glu), were investigated. The precipitation systems were of relatively low initial supersaturation and of apparently neutral pH. The data on the crystal growth rate reductions in the presence of the applied salicylate molecules were analyzed by means of Cabrera & Vermileya's, and Kubota & Mullin's models of interactions of the dissolved additives and crystal surfaces. The crystal growth kinetic experiments were additionally supported with the appropriate electrokinetic, spectroscopic and adsorption measurements. The Langmuir adsorption constants were determined and they were found to be in a good correlation with values obtained from crystal growth kinetic analyses. The results indicated that salicylate molecules preferentially adsorb along the steps on the growing calcite surfaces. The values of average spacing between the adjacent salicylate adsorption active sites and the average distance between the neighboring adsorbed salicylate molecules were also estimated.

  13. Non-Covalent Interactions and Impact of Charge Penetration Effects in Linear Oligoacene Dimers and Single Crystals

    KAUST Repository

    Ryno, Sean M

    2016-05-18

    Non-covalent interactions determine in large part the thermodynamic aspects of molecular packing in organic crystals. Using a combination of symmetry-adapted perturbation theory (SAPT) and classical multipole electrostatics, we describe the interaction potential energy surfaces for dimers of the oligoacene family, from benzene to hexacene. An analysis of these surfaces and a thorough assessment of dimers extracted from the reported crystal structures underline that high-order interactions (i.e., three-body non-additive interactions) must be considered in order to rationalize the details of the crystal structures. A comparison of the SAPT electrostatic energy with the multipole interaction energy demonstrates the importance of the contribution of charge penetration, which is shown to account for up to 50% of the total interaction energy in dimers extracted from the experimental single crystals; in the case of the most stable co-facial model dimers, this contribution is even larger than the total interaction energy. Our results highlight the importance of taking account of charge penetration in studies of the larger oligoacenes.

  14. Packing interactions between transmembrane helices alter ion selectivity of the yeast Golgi Ca2+/Mn2+-ATPase PMR1.

    Science.gov (United States)

    Mandal, Debjani; Rulli, Samuel J; Rao, Rajini

    2003-09-12

    PMR1 is the yeast secretory pathway pump responsible for high affinity transport of Mn2+ and Ca2+ into the Golgi, where these ions are sequestered and effectively removed from the cytoplasm. Phenotypic growth assays allow for convenient screening of side chains important for Ca2+ and Mn2+ transport. Earlier we demonstrated that mutant Q783A at the cytoplasmic interface of M6 could transport Ca2+, but not Mn2+. Scanning mutagenesis of side chains proximal to residue Gln-783 in membrane helices M2, M4, M5, and M6 revealed additional residues near the cytoplasmic interface, notably Leu-341 (M5), Phe-738 (M5), and Leu-785 (M6) that are sensitive to substitution. Importantly, we obtained evidence for a packing interaction between Val-335 in M4 and Gln-783 in M6 that is critical for Mn2+ transport. Thus, mutant V335G mimics the Mn2+ transport defect of Q783A and mutant V335I can effectively suppress the Mn2+-defective phenotype of Q783A. These changes in ion selectivity were confirmed by cation-dependent ATP hydrolysis using purified enzyme. Other substitutions at these sites are tolerated individually, but not in combination. Exchange of side chains at 335 and 783 also results in ion selectivity defects, suggesting that the packing interaction may be conformation-sensitive. Homology models of M4, M5, and M6 of PMR1 have been generated, based on the structures of the sarcoplasmic reticulum Ca2+-ATPase. The models are supported by data from mutagenesis and reveal that Gln-783 and Val-335 show conformation-sensitive packing at the cytoplasmic interface. We suggest that this region may constitute a gate for access of Mn2+ ions.

  15. Use of X-ray diffraction, molecular simulations, and spectroscopy to determine the molecular packing in a polymer-fullerene bimolecular crystal

    Energy Technology Data Exchange (ETDEWEB)

    Miller, Nichole Cates; Gysel, Roman; Sweetnam, Sean; McGehee, Michael D. [Department of Materials Science and Engineering, Stanford University, Stanford, CA (United States); Cho, Eunkyung [School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA (United States); School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA (United States); Junk, Matthias J.N.; Chmelka, Bradley F. [Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA (United States); Risko, Chad; Kim, Dongwook; Bredas, Jean-Luc [School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA (United States); Miller, Chad E. [Department of Materials Science and Engineering, Stanford University, Stanford, CA (United States); Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA (United States); Richter, Lee J.; Kline, R. Joseph [National Institute of Standards and Technology, Gaithersburg, MD (United States); Heeney, Martin; McCulloch, Iain [Department of Chemistry, Imperial College London (United Kingdom); Amassian, Aram [King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Thuwal (Saudi Arabia); Acevedo-Feliz, Daniel; Knox, Christopher [King Abdullah University of Science and Technology (KAUST), Visualization Core Laboratory, Thuwal (Saudi Arabia); Hansen, Michael Ryan; Dudenko, Dmytro [Max Planck Institute for Polymer Research, Mainz (Germany); Toney, Michael F. [Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA (United States)

    2012-11-27

    The molecular packing in a polymer: fullerene bimolecular crystal is determined using X-ray diffraction (XRD), molecular mechanics (MM) and molecular dynamics (MD) simulations, 2D solid-state NMR spectroscopy, and IR absorption spectroscopy. The conformation of the electron-donating polymer is significantly disrupted by the incorporation of the electron-accepting fullerene molecules, which introduce twists and bends along the polymer backbone and 1D electron-conducting fullerene channels. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  16. Use of X-ray diffraction, molecular simulations, and spectroscopy to determine the molecular packing in a polymer-fullerene bimolecular crystal

    KAUST Repository

    Miller, Nichole Cates

    2012-09-05

    The molecular packing in a polymer: fullerene bimolecular crystal is determined using X-ray diffraction (XRD), molecular mechanics (MM) and molecular dynamics (MD) simulations, 2D solid-state NMR spectroscopy, and IR absorption spectroscopy. The conformation of the electron-donating polymer is significantly disrupted by the incorporation of the electron-accepting fullerene molecules, which introduce twists and bends along the polymer backbone and 1D electron-conducting fullerene channels. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. The crystal structure of sulfamethoxazole, interaction with DNA, DFT calculation, and molecular docking studies

    Science.gov (United States)

    Das, Dipankar; Sahu, Nilima; Roy, Suman; Dutta, Paramita; Mondal, Sudipa; Torres, Elena L.; Sinha, Chittaranjan

    2015-02-01

    Sulfamethoxazole (SMX) [4-amino-N-(5-methyl-1,2-oxazol-3-yl)benzenesulfonamide] is structurally established by single crystal X-ray diffraction measurement. The crystal packing shows H-bonded 2D polymer through N(7)sbnd H(7A)---O(2), N(7)sbnd H(7B)---O(3), N(1)sbnd H(1)---N(2), C(5)sbnd H(5)---O(3)sbnd S(1) and N(7)sbnd (H7A)---O(2)sbnd S(1). Density Functional Theory (DFT) and Time Dependent-DFT (TD-DFT) computations of optimized structure of SMX determine the electronic structure and has explained the electronic spectral transitions. The interaction of SMX with CT-DNA has been studied by absorption spectroscopy and the binding constant (Kb) is 4.37 × 104 M-1. The in silico test of SMX with DHPS from Escherichia coli and Streptococcus pneumoniae helps to understand drug metabolism and accounts the drug-molecule interactions. The molecular docking of SMX-DNA also helps to predict the interaction feature.

  18. The crystal structure of sulfamethoxazole, interaction with DNA, DFT calculation, and molecular docking studies.

    Science.gov (United States)

    Das, Dipankar; Sahu, Nilima; Roy, Suman; Dutta, Paramita; Mondal, Sudipa; Torres, Elena L; Sinha, Chittaranjan

    2015-02-25

    Sulfamethoxazole (SMX) [4-amino-N-(5-methyl-1,2-oxazol-3-yl)benzenesulfonamide] is structurally established by single crystal X-ray diffraction measurement. The crystal packing shows H-bonded 2D polymer through N(7)-H(7A)-O(2), N(7)-H(7B)-O(3), N(1)-H(1)-N(2), C(5)-H(5)-O(3)-S(1) and N(7)-(H7A)-O(2)-S(1). Density Functional Theory (DFT) and Time Dependent-DFT (TD-DFT) computations of optimized structure of SMX determine the electronic structure and has explained the electronic spectral transitions. The interaction of SMX with CT-DNA has been studied by absorption spectroscopy and the binding constant (Kb) is 4.37×10(4)M(-1). The in silico test of SMX with DHPS from Escherichia coli and Streptococcus pneumoniae helps to understand drug metabolism and accounts the drug-molecule interactions. The molecular docking of SMX-DNA also helps to predict the interaction feature.

  19. Using Latex Balls and Acrylic Resin Plates to Investigate the Stacking Arrangement and Packing Efficiency of Metal Crystals

    Science.gov (United States)

    Ohashi, Atsushi

    2015-01-01

    A high-school third-year or undergraduate first-semester general chemistry laboratory experiment introducing simple-cubic, face-centered cubic, body-centered cubic, and hexagonal closest packing unit cells is presented. Latex balls and acrylic resin plates are employed to make each atomic arrangement. The volume of the vacant space in each cell is…

  20. Optimization of cooling and heat pump systems through interaction between PackCalc and BSim; Optimering af koele- og varmepumpeanlaeg gennem samspil mellem PackCalc og BSim

    Energy Technology Data Exchange (ETDEWEB)

    Johnsen, K. [Aalborg Univ., Statens Byggeforskningsinstitut (SBi), Hoersholm (Denmark); Olsen, Lars [Teknologisk Institut, Taastrup (Denmark); Barky, T. [Ramboell, Copenhagen (Denmark); Juel Skovrup, M. [IPU, Kgs. Lyngby (Denmark)

    2012-08-15

    The purpose of the project was: To develop a PC-tool, which can help show the economic consequences of different design of systems and choices of components and control strategy in relations to heat pump and air-conditioning systems in buildings. The tool should also assist in relating the economic consequences to the achieved indoor climate in the building. The resulting tool is a combination (and extension) of two previous existing tools: 1) Pack Calculation II for simulating refrigeration and heat pump systems. 2) BSim for detailed simulation of buildings. By combining the two tools it has been possible to: 3) Enable BSim users to get an insight in the economic and indoor climate consequences of their choice of technical system (heat pump and air-conditioning). 4) Enable PackCalc users to get a much more detailed overview - through BSim simulations - of the load situation when dimensioning refrigeration systems and heat pumps. (Author)

  1. 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.

  2. Crystal structures of the all-cysteinyl-coordinated D14C variant of Pyrococcus furiosus ferredoxin: [4Fe–4S] ↔ [3Fe–4S] cluster conversion

    DEFF Research Database (Denmark)

    Løvgreen, Monika Nøhr; Martic, Maja; Windahl, Michael S.

    2011-01-01

    molecules have different crystal packing and intramolecular disulfide bond conformation. The crystal packing reveals a β-sheet interaction between A molecules in adjacent asymmetric units, whereas B molecules are packed as monomers in a less rigid position next to the A–A extended β-sheet dimers...

  3. Theory of nonlocal soliton interaction in nematic liquid crystals

    DEFF Research Database (Denmark)

    Rasmussen, Per Dalgaard; Bang, Ole; Krolikowski, Wieslaw

    2005-01-01

    We investigate interactions between spatial nonlocal bright solitons in nematic liquid crystals using an analytical “effective particle” approach as well as direct numerical simulations. The model predicts attraction of out-of-phase solitons and the existence of their stable bound state....... This nontrivial property is solely due to the nonlocal nature of the nonlinear response of the liquid crystals. We further predict and verify numerically the critical outwards angle and degree of nonlocality which determine the transition between attraction and repulsion of out-of-phase solitons....

  4. Crystal Structure of Prp5p Reveals Interdomain Interactions that Impact Spliceosome Assembly

    Directory of Open Access Journals (Sweden)

    Zhi-Min Zhang

    2013-12-01

    Full Text Available The DEAD-box adenosine triphosphatase (ATPase Prp5p facilitates U2 small nuclear ribonucleoprotein particle (snRNP binding to the intron branch site region during spliceosome assembly. We present crystal structures of S. cerevisiae Prp5p alone and in complex with ADP at 2.12 Å and 1.95 Å resolution. The three-dimensional packing of Prp5p subdomains differs strikingly from that so far observed in other DEAD-box proteins: two RecA-like subdomains adopt an “open state” conformation stabilized by extensive interactions involving sequences that flank the two subdomains. This conformation is distinct from that required for ATP hydrolysis. Consistent with this, Prp5p mutations that destabilize interdomain interactions exhibited increased ATPase activity in vitro and inhibited splicing of suboptimal branch site substrates in vivo, whereas restoration of interdomain interactions reversed these effects. We conclude that the Prp5p open state conformation is biologically relevant and that disruption of the interdomain interaction facilitates a large-scale conformational change of Prp5p during U2 snRNP-branch site recognition.

  5. HEXAGONAL CLOSE-PACKED C-60

    NARCIS (Netherlands)

    de Boer, Jan; van Smaalen, Sander; Petricek, Vaclav; Dusek, Michal P.; Verheijen, Marcel A.; Meijer, G.

    1994-01-01

    C60 crystals were grown from purified powder material with a multiple sublimation technique. In addition to crystals wit a cubic close-packed (ccp) arrangement, crystals were found with a hexagonal close-packed (hcp) structure. Detailed crystallographic evidence is given, including complete refineme

  6. Crystal structures of four δ-keto esters and a Cambridge Structural Database analysis of cyano-halogen interactions.

    Science.gov (United States)

    Kamal, Kulsoom; Maurya, Hardesh K; Gupta, Atul; Vasudev, Prema G

    2015-10-01

    The revived interest in halogen bonding as a tool in pharmaceutical cocrystals and drug design has indicated that cyano-halogen interactions could play an important role. The crystal structures of four closely related δ-keto esters, which differ only in the substitution at a single C atom (by H, OMe, Cl and Br), are compared, namely ethyl 2-cyano-5-oxo-5-phenyl-3-(piperidin-1-yl)pent-2-enoate, C19H22N2O3, (1), ethyl 2-cyano-5-(4-methoxyphenyl)-5-oxo-3-(piperidin-1-yl)pent-2-enoate, C20H24N2O4, (2), ethyl 5-(4-chlorophenyl)-2-cyano-5-oxo-3-(piperidin-1-yl)pent-2-enoate, C19H21ClN2O3, (3), and the previously published ethyl 5-(4-bromophenyl)-2-cyano-5-oxo-3-(piperidin-1-yl)pent-2-enoate, C19H21BrN2O3, (4) [Maurya, Vasudev & Gupta (2013). RSC Adv. 3, 12955-12962]. The molecular conformations are very similar, while there are differences in the molecular assemblies. Intermolecular C-H...O hydrogen bonds are found to be the primary interactions in the crystal packing and are present in all four structures. The halogenated derivatives have additional aromatic-aromatic interactions and cyano-halogen interactions, further stabilizing the molecular packing. A database analysis of cyano-halogen interactions using the Cambridge Structural Database [CSD; Groom & Allen (2014). Angew. Chem. Int. Ed. 53, 662-671] revealed that about 13% of the organic molecular crystals containing both cyano and halogen groups have cyano-halogen interactions in their packing. Three geometric parameters for the C-X...N[triple-bond]C interaction (X = F, Cl, Br or I), viz. the N...X distance and the C-X...N and C-N...X angles, were analysed. The results indicate that all the short cyano-halogen contacts in the CSD can be classified as halogen bonds, which are directional noncovalent interactions.

  7. Interactions of Organic Additives with Ionic Crystal Hydrates

    Science.gov (United States)

    Füredi-Milhofer, H.; Sikirić, M.; Tunik, L.; Filipović-Vinceković, N.; Garti, N.

    The interactions of two groups of hydrated model crystals, calcium hydrogenphosphate dihydrate (DCPD) vs. octacalcium phosphate (OCP) and calcium oxalate monohydrate (COM) vs. calcium oxalate dihydrate (COD) with different organic additives are considered. DCPD precipitates as platelet-like crystals with the dominant faces shielded by hydrated layers and charged lateral faces. In the second system COM has charged surfaces, while all faces of COD are covered with layers containing water molecules. The organic molecules tested include negatively charged, flexible and rigid small and macromolecules (glutamic and aspartic acid, citrate, hexaammonium polyphosphate, phytate and polyaspartate) and anionic surfactants (sodium dodecyl sulphate, SDS, sodium diisooctyl sulfosuccinate, AOT, sodium cholate NaC and disodium oleoamido PEG-2 sulfosuccinate, PEG). Two types of effects have been demonstrated: (1) Effect on crystal growth morphology: Flexible organic molecules with high charge density and anionic surfactants affected the growth morphology of DCPD and COM by selectively interacting with the charged lateral faces while rigid molecules (phytate, polyaspartate) specifically recognized the dominant (010) face of DCPD due to structural and stereochemical compatibility. (2) Effect on phase composition: Anionic surfactants at concentrations above the cmc promoted growth of OCP and COD respectively by selectively adsorbing at, and inhibiting growth oif nuclei of DCPD and/or COM, which were dominant in the respective control systems. The effect was especially pronounced in the calcium oxalate precipitation system, where in some cases complete reversal of the phase composition occurred. The important role of the hydrated layer, as part of the structure of the investigated crystal hydrates, in the above crystal additive interactions is discussed.

  8. Interfacial dislocation motion and interactions in single-crystal superalloys

    Energy Technology Data Exchange (ETDEWEB)

    Liu, B. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Raabe, D. [Max Planck Inst. fur Eisenforshung. Dusseldorf (Germany); Roters, F. [Max Planck Inst. fur Eisenforshung. Dusseldorf (Germany); Arsenlis, A. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2014-10-01

    The early stage of high-temperature low-stress creep in single-crystal superalloys is characterized by the rapid development of interfacial dislocation networks. Although interfacial motion and dynamic recovery of these dislocation networks have long been expected to control the subsequent creep behavior, direct observation and hence in-depth understanding of such processes has not been achieved. Incorporating recent developments of discrete dislocation dynamics models, we simulate interfacial dislocation motion in the channel structures of single-crystal superalloys, and investigate how interfacial dislocation motion and dynamic recovery are affected by interfacial dislocation interactions and lattice misfit. Different types of dislocation interactions are considered: self, collinear, coplanar, Lomer junction, glissile junction, and Hirth junction. The simulation results show that strong dynamic recovery occurs due to the short-range reactions of collinear annihilation and Lomer junction formation. The misfit stress is found to induce and accelerate dynamic recovery of interfacial dislocation networks involving self-interaction and Hirth junction formation, but slow down the steady interfacial motion of coplanar and glissile junction forming dislocation networks. The insights gained from these simulations on high-temperature low-stress creep of single-crystal superalloys are also discussed.

  9. Colloidal interactions and transport in nematic liquid crystals.

    Science.gov (United States)

    Tatarkova, S A; Burnham, D R; Kirby, A K; Love, G D; Terentjev, E M

    2007-04-13

    We describe a new nematic liquid-crystal colloid system which is characterized by both charge stabilization of the particles and an interaction force. We estimate the effective charge of the particles by electrophoretic measurements and find that in such systems the director anchoring energy W is very low and the particles have little director distortion around them. The interaction force is created by producing a radial distribution of the nematic order parameter around a locally isotropic region created by ir laser heating. We theoretically describe this as being due to the induced flexoelectric polarization, the quadrupolar symmetry of which provides the required long-range force acting on charged particles.

  10. Direction-specific interactions control crystal growth by oriented attachment

    DEFF Research Database (Denmark)

    Li, Dongsheng; Nielsen, Michael H; Lee, Jonathan R.I.

    2012-01-01

    initiated at the contact point. Interface elimination proceeds at a rate consistent with the curvature dependence of the Gibbs free energy. Measured translational and rotational accelerations show that strong, highly direction-specific interactions drive crystal growth via oriented attachment....... using a fluid cell to directly observe oriented attachment of iron oxyhydroxide nanoparticles. The particles undergo continuous rotation and interaction until they find a perfect lattice match. A sudden jump to contact then occurs over less than 1 nanometer, followed by lateral atom-by-atom addition...

  11. Crystallization of copper(II) sulfate based minerals and MOF from solution: Chemical insights into the supramolecular interactions

    Indian Academy of Sciences (India)

    M Singh; D Kumar; J Thomas; A Ramanan

    2010-09-01

    Crystallization of solids, molecular or non-molecular from solution is a supramolecular reaction. Nucleation of a lattice structure at supersaturation can be conceived to result from a critical nucleus, a high energy intermediate (supramolecular transition state). Conceptualization of a structure for the critical nucleus in terms of aggregation of tectons through non-covalent interactions provides chemical insights into the architecture of a solid. The retrosynthetic analysis of copper-based minerals and materials offers an elegant description for the crystal packing. It addresses the influence of the geometry, functionality and reactivity of copper tecton(s) in directing a specific supramolecular aggregation. The mechanistic approach provides guiding principles to chemists to account for the experimentally crystallized solids and a platform to practice structure-synthesis correlation. Rationalization of the same composition with different atomic arrangements (polymorphs), compositional variation leading to different pseudopolymorphs, degree of hydration (anhydrous to hydrated), water clusters, role of solvent, etc. can all be justified on molecular basis. Also, the method gives predictive components including directions to synthesize new solids. In a nutshell, the paper is an attempt to generalize the crystallization of inorganic solids from solution by recognizing supramolecular interactions between metal tectons and gain insights for designing new MOF.

  12. Nature of packs used in propellant modeling.

    Science.gov (United States)

    Maggi, F; Stafford, S; Jackson, T L; Buckmaster, J

    2008-04-01

    In recent years we have constructed closely packed spheres using the Lubachevsky-Stillinger algorithm to generate morphological models of heterogeneous solid propellants. Improvements to the algorithm now allow us to create large polydisperse packs on a laptop computer, and to create monodisperse packs with packing fractions greater than 70% which display significant crystal order. The use of these models in the physical context motivates efforts to examine in some detail the nature of the packs, including certain statistical properties. We compare packing fractions for binary packs with long-known experimental data. Also, we discuss the near-neighbor number and the radial distribution function (RDF) for monodisperse packs and make comparisons with experimental data. We also briefly discuss the RDF for bidisperse packs. We also consider bounded monodisperse packs, and pay particular attention to the near-wall structure where we identify significant order.

  13. Crystal structures of MBi{sub 2}Br{sub 7} (M = Rb, Cs) - filled variants of AX{sub 7} sphere packing

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Jen-Hui; Wolff, Alexander [Fachrichtung Chemie und Lebensmittelchemie, Technische Universitaet Dresden, 01062 Dresden (Germany); Ruck, Michael [Fachrichtung Chemie und Lebensmittelchemie, Technische Universitaet Dresden, 01062 Dresden (Germany); Max-Planck-Institut fuer Chemische Physik fester Stoffe, Noethnitzer Str. 40, 01187 Dresden (Germany)

    2016-03-15

    The reinvestigation of the pseudo-binary systems MBr-BiBr{sub 3} (M = Rb, Cs) revealed two new phases with composition MBi{sub 2}Br{sub 7}. Both compounds are hygroscopic and show brilliant yellow color. The crystal structures were solved from X-ray single crystal diffraction data. The isostructural compounds adopt a new structure type in the triclinic space group P anti 1. The lattice parameters are a = 755.68(3) pm, b = 952.56(3) pm, c = 1044.00(4) pm, α = 76.400(2) , β = 84.590(2) , γ = 76.652(2) for RbBi{sub 2}Br{sub 7} and a = 758.71(5) pm, b = 958.23(7) pm, c = 1060.24(7) pm, α = 76.194(3) , β = 83.844(4) , γ = 76.338(3) for CsBi{sub 2}Br{sub 7}. The crystal structures consist of M{sup +} cations in anticuboctahedral coordination by bromide ions and bromidobismuthate(III) layers {sup 2}{sub ∞}[Bi{sub 2}Br{sub 7}]{sup -}. The 2D layers comprise pairs of BiBr{sub 6} octahedra sharing a common edge. The Bi{sub 2}Br{sub 10} double octahedra are further connected by common vertices. The bismuth(III) atoms increase their mutual distance in the double octahedra by off-centering so that the BiBr{sub 6} octahedra are distorted. The CsBi{sub 2}Br{sub 7} type can be interpreted as a common hexagonal close sphere packing of M and Br atoms, in which 1/4 of the octahedral voids are filled by Bi atoms. The structure type was systematically analyzed and compared with alternative types of common packings. The existence of a compound with the suggested composition CsBiBr{sub 4} could not be verified experimentally. (Copyright copyright 2016 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  14. Layering, melting, and recrystallization of a close-packed micellar crystal under steady and large-amplitude oscillatory shear flows

    Energy Technology Data Exchange (ETDEWEB)

    López-Barrón, Carlos R., E-mail: carlos.r.lopez-barron@exxonmobil.com [ExxonMobil Chemical Company, Baytown Technology and Engineering Complex, Baytown, Texas 77520 (United States); Wagner, Norman J. [Center for Neutron Science, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716 (United States); Porcar, Lionel [Institute Laue-Langevin, BP 156, F38042 Grenoble Cedex 9 (France)

    2015-05-15

    The rheology and three-dimensional microstructure of a concentrated viscoelastic solution of the triblock copolymer poly(ethylene oxide){sub 106}-poly(propylene oxide){sub 68}-poly(ethylene oxide){sub 106} (Pluronic F127) in the protic ionic liquid ethylammonium nitrate are measured by small angle neutron scattering (SANS) under flow in three orthogonal planes. This solution's shear-thinning viscosity is due to the formation of two-dimensional hexagonal close-packed (HCP) sliding layer structure. Shear-melting of the crystalline structure is observed without disruption of the self-assembled micelles, resulting in a change in flow properties. Spatially resolved measurements in the 1–2 plane reveal that both shear-melting and sliding are not uniform across the Couette gap. Melting and recrystallization of the HCP layers occur cyclically during a single large amplitude oscillatory shear (LAOS) cycle, in agreement with the “stick-slip” flow mechanism proposed by Hamley et al. [Phys. Rev. E 58, 7620–7628 (1998)]. Analysis of 3D “structural” Lissajous curves show that the cyclic melting and sliding are direct functions of the strain rate amplitude and show perfect correlation with the cyclic stress response during LAOS. Both viscosity and structural order obey the Delaware–Rutgers rule. Combining rheology with in situ spatiotemporally resolved SANS is demonstrated to elucidate the structural origins of the nonlinear rheology of complex fluids.

  15. Packing in protein cores

    Science.gov (United States)

    Gaines, J. C.; Clark, A. H.; Regan, L.; O'Hern, C. S.

    2017-07-01

    Proteins are biological polymers that underlie all cellular functions. The first high-resolution protein structures were determined by x-ray crystallography in the 1960s. Since then, there has been continued interest in understanding and predicting protein structure and stability. It is well-established that a large contribution to protein stability originates from the sequestration from solvent of hydrophobic residues in the protein core. How are such hydrophobic residues arranged in the core; how can one best model the packing of these residues, and are residues loosely packed with multiple allowed side chain conformations or densely packed with a single allowed side chain conformation? Here we show that to properly model the packing of residues in protein cores it is essential that amino acids are represented by appropriately calibrated atom sizes, and that hydrogen atoms are explicitly included. We show that protein cores possess a packing fraction of φ ≈ 0.56 , which is significantly less than the typically quoted value of 0.74 obtained using the extended atom representation. We also compare the results for the packing of amino acids in protein cores to results obtained for jammed packings from discrete element simulations of spheres, elongated particles, and composite particles with bumpy surfaces. We show that amino acids in protein cores pack as densely as disordered jammed packings of particles with similar values for the aspect ratio and bumpiness as found for amino acids. Knowing the structural properties of protein cores is of both fundamental and practical importance. Practically, it enables the assessment of changes in the structure and stability of proteins arising from amino acid mutations (such as those identified as a result of the massive human genome sequencing efforts) and the design of new folded, stable proteins and protein-protein interactions with tunable specificity and affinity.

  16. Molecular Structure and Crystal Packing of n-Type Semiconducting Material 3′,3′-(1,4-Phenylene)bis{2′-(4′′-trifluoromethyl)phenyl}acrylonitrile

    OpenAIRE

    Tetsuji Moriguchi; Shuichi Nagamatsu; Tatsuo Okauchi; Akihiko Tsuge; Wataru Takashima; Shuji Hayase

    2014-01-01

    The exact molecular structure and the crystal packing of the n-type semiconducting material 3′,3′-(1,4-phenylene)bis{2′-(4′′-trifluoromethyl)phenyl}acrylonitrile was determined by a single crystal X-ray diffraction with twin treatment technique. The air-stable product was crystallized from dichloromethane-hexane mixed solution. The solid-state structure is the example of a typical π-π stacking with side intermolecular CN–H short contact networks.

  17. Darmstadton Hunting in the Interaction $\\gamma$-Crystal

    CERN Multimedia

    2002-01-01

    From several years, indications of the existence of sharp lines, presenting all features of light neutral particles, particles have been found in heavy ions-atoms interaction at the GSI (Darmstadt).\\\\ \\\\ This experiment aims to produce these particles in $\\gamma$~interaction with the strong field of a crystal near the direction of an axis.\\\\ \\\\ The small divergence tagged $\\gamma$~beam is obtained from a 150~GeV e$^-$~beam. The angular measurements are performed by $\\mu$strip detector, at large distance ($\\approx$80~m of vacuum pipe shielded against the earth magnetic field). Energy measurements are performed by magnetic analysis and independently by lead glass calorimeters.\\\\ \\\\ The setup is fitted to the search of such particles in the lifetimes ranges:\\\\ \\\\ &lbrk. 10$^{-1}

  18. Cationic cobaltammine as anion receptor: Synthesis, characterization, single crystal X-ray structure and packing analysis of hexaamminecobalt(III) chloride ( R, R)-tartrate monohydrate

    Science.gov (United States)

    Bala, Ritu; Sharma, Raj Pal; Venugopalan, Paloth; Harrison, William T. A.

    2007-03-01

    In an effort to utilize the [Co(NH 3) 6] 3+ cation as a new anion receptor (binding agent) for dihydroxy dicarboxylate anion i.e., tartrate, orange single crystals of hexaamminecobalt(III) chloride ( R, R)-tartrate monohydrate, [Co(NH 3) 6]Cl(C 4H 4O 6)·H 2O, were obtained by reacting hexaamminecobalt(III) chloride with potassium-sodium tartrate tetrahydrate in a 1:1 molar ratio in hot water. The single crystal X-ray structure determination of [Co(NH 3) 6]Cl(C 4H 4O 6)·H 2O revealed that a distinctive network of hydrogen bonding interactions (N-H⋯O, N-H⋯Cl -, O-H⋯O) stabilize the crystal lattice. This is the first complex salt of hexaamminecobalt(III) with dihydroxy dicarboxylate anion i.e., tartrate.

  19. Aqueous solubility prediction: do crystal lattice interactions help?

    Science.gov (United States)

    Salahinejad, Maryam; Le, Tu C; Winkler, David A

    2013-07-01

    Aqueous solubility is a very important physical property of small molecule drugs and drug candidates but also one of the most difficult to predict accurately. Aqueous solubility plays a major role in drug delivery and pharmacokinetics. It is believed that crystal lattice interactions are important in solubility and that including them in solubility models should improve the accuracy of the models. We used calculated values for lattice energy and sublimation enthalpy of organic molecules as descriptors to determine whether these would improve the accuracy of the aqueous solubility models. Multiple linear regression employing an expectation maximization algorithm and a sparse prior (MLREM) method and a nonlinear Bayesian regularized artificial neural network with a Laplacian prior (BRANNLP) were used to derive optimal predictive models of aqueous solubility of a large and highly diverse data set of 4558 organic compounds over a normal ambient temperature range of 20-30 °C (293-303 K). A randomly selected test set and compounds from a solubility challenge were used to estimate the predictive ability of the models. The BRANNLP method showed the best statistical results with squared correlation coefficients of 0.90 and standard errors of 0.645-0.665 log(S) for training and test sets. Surprisingly, including descriptors that captured crystal lattice interactions did not significantly improve the quality of these aqueous solubility models.

  20. Close shell interactions in 3-ethoxycarbonyl-4-hydroxy-6-methoxymethyleneoxy-1-methyl-2-quinolone: 100 K single crystal neutron diffraction study and ab initio calculations

    Science.gov (United States)

    Pozzi, C. G.; Fantoni, A. C.; Goeta, A. E.; Wilson, C. C.; Autino, J. C.; Punte, G.

    2005-10-01

    The molecular and crystal structures of the title compound have been determined from a single crystal neutron diffraction experiment at 100 K. A comparison between the main geometrical features and related properties of the in-crystal and the ab initio optimized free molecule structures has shown that crystal packing induces a significant distortion in the molecular geometry. Packing instead would only have a moderate effect on the observed intramolecular resonance assisted hydrogen bond. Supermolecular ab initio molecular orbital calculations have been performed on the six different dimers one molecule forms with its nine nearest neighbours. The obtained results clearly show that dispersion contributions dominate in the most strongly interacting dimers, in good qualitative accord with the predictions made by using different empirical potentials. A qualitative description of the most prominent inductive effects determined from the electron density deformation upon dimer formation is presented. Topological analyses of the dimers charge densities have been performed in the framework of the Bader's AIM theory and all the intermolecular bond critical points have been identified. An attempt to determine some of the interaction energies only from topological quantities made evident the practical limitations of such an approach.

  1. Self-interaction chromatography as a tool for optimizing conditions for membrane protein crystallization.

    Science.gov (United States)

    Gabrielsen, Mads; Nagy, Lisa A; DeLucas, Lawrence J; Cogdell, Richard J

    2010-01-01

    The second virial coefficient, or B value, is a measurement of how well a protein interacts with itself in solution. These interactions can lead to protein crystallization or precipitation, depending on their strength, with a narrow range of B values (the 'crystallization slot') being known to promote crystallization. A convenient method of determining the B value is by self-interaction chromatography. This paper describes how the light-harvesting complex 1-reaction centre core complex from Allochromatium vinosum yielded single straight-edged crystals after iterative cycles of self-interaction chromatography and crystallization. This process allowed the rapid screening of small molecules and detergents as crystallization additives. Here, a description is given of how self-interaction chromatography has been utilized to improve the crystallization conditions of a membrane protein.

  2. Textures and melt-crystal-gas interactions in granites

    Directory of Open Access Journals (Sweden)

    Jean-Louis Vigneresse

    2015-09-01

    Full Text Available Felsic intrusions present ubiquitous structures. They result from the differential interactions between the magma components (crystal, melt, gas phase while it flows or when the flow is perturbed by a new magma injection. The most obvious structure consists in fabrics caused by the interactions of rotating grains in a flowing viscous melt. New magma inputs through dikes affect the buk massif flow, considered as global within each mineral facies. A review of the deformation and flow types developing in a magma chamber identifis the patterns that could be expected. It determines their controlling parameters and summarizes the tools for their quantification. Similarly, a brief review of the rheology of a complex multi-phase magma identifies and suggests interactions between the different components. The specific responses each component presents lead to instability development. In particular, the change in vorticity orientation, associated with the switch between monoclinic to triclinic flow is a cause of many instabilities. Those are preferentially local. Illustrations include fabric development, shear zones and flow banding. They depend of the underlying rheology of interacting magmas. Dikes, enclaves, schlieren and ladder dikes result from the interactions between the magma components and changing boundary conditions. Orbicules, pegmatites, unidirectional solidification textures and miarolitic cavities result from the interaction of the melt with a gaseous phase. The illustrations examine what is relevant to the bulk flow, local structures or boundary conditions. In each case a field observation illustrates the instability. The discussion reformulates instability observations, suggesting new trails for ther description and interpretation in terms of local departure to a bulk flow. A brief look at larger structures and at their evolution tries to relate these instabilities on a broader scale. The helical structures of the Říčany pluton, Czech

  3. Textures and melt-crystal-gas interactions in granites

    Institute of Scientific and Technical Information of China (English)

    Jean-Louis Vigneresse

    2015-01-01

    Felsic intrusions present ubiquitous structures. They result from the differential interactions between the magma components (crystal, melt, gas phase) while it flows or when the flow is perturbed by a new magma injection. The most obvious structure consists in fabrics caused by the interactions of rotating grains in a flowing viscous melt. New magma inputs through dikes affect the buk massif flow, considered as global within each mineral facies. A review of the deformation and flow types developing in a magma chamber identifis the patterns that could be expected. It determines their controlling parameters and summarizes the tools for their quantification. Similarly, a brief review of the rheology of a complex multi-phase magma identifies and suggests interactions between the different components. The specific re-sponses each component presents lead to instability development. In particular, the change in vorticity orientation, associated with the switch between monoclinic to triclinic flow is a cause of many in-stabilities. Those are preferentially local. Illustrations include fabric development, shear zones and flow banding. They depend of the underlying rheology of interacting magmas. Dikes, enclaves, schlieren and ladder dikes result from the interactions between the magma components and changing boundary conditions. Orbicules, pegmatites, unidirectional solidification textures and miarolitic cavities result from the interaction of the melt with a gaseous phase. The illustrations examine what is relevant to the bulk flow, local structures or boundary conditions. In each case a field observation illustrates the instability. The discussion reformulates instability observations, suggesting new trails for ther description and interpretation in terms of local departure to a bulk flow. A brief look at larger structures and at their evolution tries to relate these instabilities on a broader scale. The helical structures of the ?Rí?cany pluton, Czech Republic and by

  4. A triclinic crystal structure of the carboxy-terminal domain of HIV-1 capsid protein with four molecules in the asymmetric unit reveals a novel packing interface

    Science.gov (United States)

    Lampel, Ayala; Yaniv, Oren; Berger, Or; Bacharach, Eran; Gazit, Ehud; Frolow, Felix

    2013-01-01

    The Gag precursor is the major structural protein of the virion of human immunodeficiency virus-1 (HIV-1). Capsid protein (CA), a cleavage product of Gag, plays an essential role in virus assembly both in Gag-precursor multimerization and in capsid core formation. The carboxy-terminal domain (CTD) of CA contains 20 residues that are highly conserved across retroviruses and constitute the major homology region (MHR). Genetic evidence implies a role for the MHR in interactions between Gag precursors during the assembly of the virus, but the structural basis for this role remains elusive. This paper describes a novel triclinic structure of the HIV-1 CA CTD at 1.6 Å resolution with two canonical dimers of CA CTD in the asymmetric unit. The canonical dimers form a newly identified packing interface where interactions of four conserved MHR residues take place. This is the first structural indication that these MHR residues participate in the putative CTD–CTD interactions. These findings suggest that the molecules forming this novel interface resemble an intermediate structure that participates in the early steps of HIV-1 assembly. This interface may therefore provide a novel target for antiviral drugs. PMID:23722834

  5. Strong optomechanical interactions in a sliced photonic crystal nanobeam

    Science.gov (United States)

    Leijssen, Rick; Verhagen, Ewold

    2015-11-01

    Coupling between mechanical and optical degrees of freedom is strongly enhanced by using subwavelength optical mode profiles. We realize an optomechanical system based on a sliced photonic crystal nanobeam, which combines such highly confined optical fields with a low-mass mechanical mode. Analyzing the transduction of motion and effects of radiation pressure we find the system exhibits a photon-phonon coupling rate g0 /2π ≈ 11.5 MHz, exceeding previously reported values by an order of magnitude. We show that the large optomechanical interaction enables detecting thermal motion with detection noise below that at the standard quantum limit, even in broad bandwidth devices, important for both sensor applications as well as measurement-based quantum control.

  6. Phonon interactions with methyl radicals in single crystals

    Directory of Open Access Journals (Sweden)

    James W. Wells

    2017-04-01

    Full Text Available The high temperature ESR spectra’s anomalous appearance at very low temperatures for the methyl radical created in single crystals is explained by magnetic dipole interactions with neighboring protons. These protons acting via phonon vibrations induce resonant oscillations with the methyl group to establish a very temperature sensitive ‘‘relaxation’’ mode that allows the higher energy ‘‘E’’ state electrons with spin 12 to ‘‘decay’’ into ‘‘A’’ spin 12 states. Because of the amplitude amplification with temperature, the ‘‘E’’ state population is depleted and the ‘‘A’’ state population augmented to produce the high temperature ESR spectrum. This phenomenon is found to be valid for all but the very highest barriers to methyl group tunneling. In support, a time dependent spin population study shows this temperature evolution in the state populations under this perturbation.

  7. Packing Smart

    Centers for Disease Control (CDC) Podcasts

    2011-08-22

    In this podcast for kids, the Kidtastics talk about packing a lunch that's not boring and is full of the power and energy kids need to make it through the day.  Created: 8/22/2011 by National Center for Emerging and Zoonotic Infectious Diseases (NCEZID).   Date Released: 8/22/2011.

  8. Power Packing

    Centers for Disease Control (CDC) Podcasts

    2011-08-16

    In this podcast for kids, the Kidtastics talk about how to pack a lunch safely, to help keep you from getting sick.  Created: 8/16/2011 by National Center for Emerging and Zoonotic Infectious Diseases (NCEZID).   Date Released: 8/16/2011.

  9. Strong optomechanical interactions in a sliced photonic crystal nanobeam

    CERN Document Server

    Leijssen, Rick

    2015-01-01

    Cavity optomechanical systems can be used for sensitive detection of mechanical motion and to control mechanical resonators, down to the quantum level. The strength with which optical and mechanical degrees of freedom interact is defined by the photon-phonon coupling rate $g_0$, which is especially large in nanoscale systems. Here, we demonstrate an optomechanical system based on a sliced photonic crystal nanobeam, that combines subwavelength optical confinement with a low-mass mechanical mode. Analyzing the transduction of motion and effects of radiation pressure we find a coupling rate $g_0$/2{\\pi} = 11.5 MHz, exceeding previously reported values by an order of magnitude. Using this interaction we detect the resonator's motion with a noise imprecision below that at the standard quantum limit, even though the system has optical and mechanical quality factors smaller than $10^3$. The broad bandwidth is useful for application in miniature sensors, and for measurement-based control of the resonator's motional s...

  10. Hydrodynamic interactions in freely suspended liquid crystal films

    Science.gov (United States)

    Kuriabova, Tatiana; Powers, Thomas R.; Qi, Zhiyuan; Goldfain, Aaron; Park, Cheol Soo; Glaser, Matthew A.; Maclennan, Joseph E.; Clark, Noel A.

    2016-11-01

    Hydrodynamic interactions play an important role in biological processes in cellular membranes, a large separation of length scales often allowing such membranes to be treated as continuous, two-dimensional (2D) fluids. We study experimentally and theoretically the hydrodynamic interaction of pairs of inclusions in two-dimensional, fluid smectic liquid crystal films suspended in air. Such smectic membranes are ideal systems for performing controlled experiments as they are mechanically stable, of highly uniform structure, and have well-defined, variable thickness, enabling experimental investigation of the crossover from 2D to 3D hydrodynamics. Our theoretical model generalizes the Levine-MacKintosh theory of point-force response functions and uses a boundary-element approach to calculate the mobility matrix for inclusions of finite extent. We describe in detail the theoretical and computational approach previously outlined in Z. Qi et al., Phys. Rev. Lett. 113, 128304 (2014), 10.1103/PhysRevLett.113.128304 and extend the method to study the mutual mobilities of inclusions with asymmetric shapes. The model predicts well the observed mutual mobilities of pairs of circular inclusions in films and the self-mobility of a circular inclusion in the vicinity of a linear boundary.

  11. Interaction mechanism of non-metallic particles with crystallization front

    Directory of Open Access Journals (Sweden)

    Żak P. L.

    2017-03-01

    Full Text Available The process of steel solidification in the CCS mould is accompanied by a number of phenomena relating to the formation of non-metallic phase, as well as the mechanism of its interaction with the existing precipitations and the advancing crystallization front. In the solidification process the non-metallic inclusions may be absorbed or repelled by the moving front. As a result a specific distribution of non-metallic inclusions is obtained in the solidified ingot, and their distribution is a consequence of these processes. The interaction of a non-metallic inclusion with the solidification front was analyzed for alumina, for different values of the particle radius. The simulation was performed with the use of own computer program. Each time a balance of forces acting on a particle in its specific position was calculated. On this basis the change of position of alumina particle in relation to the front was defined for a specific radius and original location of the particle with respect to the front.

  12. Supramolecular self-assembly of a coumarine-based acylthiourea synthon directed by π-stacking interactions: Crystal structure and Hirshfeld surface analysis

    Science.gov (United States)

    Saeed, Aamer; Ashraf, Saba; Flörke, Ulrich; Delgado Espinoza, Zuly Yuliana; Erben, Mauricio F.; Pérez, Hiram

    2016-05-01

    The structure of 1-(2-oxo-2H-chromene-3-carbonyl)-3-(2-methoxy-phenyl)thiourea (1) has been determined by single-crystal X-ray crystallography. This compound crystallizes in the monoclinic space group P21/c with a = 7.455 (2) Å, b = 12.744 (3) Å, c = 16.892 (4) Å, β = 90.203 (6)° and Z = 4. Both, the coumarin and the phenyl rings are nearly coplanar with the central 1-acylthiourea group, with the Cdbnd O and Cdbnd S bonds adopting an opposite orientation. Intramolecular N-H···O, C-H···O, and C-H···S hydrogen bonds are favored by the planar conformation. The molecules are packed through C-H···O, C-H···S and C-H···C hydrogen bonds, and two π···π interactions with offset arrangement. Inter-centroid distance of 3.490 (2) Å, slip angles of 18.5 and 20.9°, and vertical displacements of 1.10 and 1.24 Å are the stacking parameters corresponding to the stronger π···π interaction. Hirshfeld surface analysis was performed for visualizing, exploring and quantifying intermolecular interactions in the crystal lattice of compound 1, and compared with two closely related species. Shape index and Curvedness surfaces indicated π-stacking with different features in opposed sides of the molecule. Fingerprint plot showed C···C contacts with similar contributions to the crystal packing in comparison with those associated to hydrogen bonds. Enrichment ratios for H···H, O···H, S···H and C···C contacts revealed a high propensity to form in the crystal.

  13. Mechanical interaction between gas bubbles and micro-crystals in magma

    Science.gov (United States)

    Dinger, Florian; Bobrowski, Nicole; Bredemeyer, Stefan; Arellano, Santiago; Platt, Ulrich; Wagner, Thomas

    2017-04-01

    The magnitude of volcanic gas emissions from low viscosity magmas is controlled by many factors. The buoyancy driven ascent of gas bubbles in the volcanic conduit is one of them. During the ascent the bubbles may collide with micro-crystals, slide along the crystal faces, and finally leave the crystal at the crystal tip. We investigate the mechanical consequences of this interaction in a static volume of magma assuming constant pressure, temperature and chemical composition and neglecting thermodynamic processes between bubbles and crystals. Explicitly, we focus on tabular crystals whose extensions are about one order of magnitude larger than the bubbles. The mechanical interaction changes the motion of both the bubbles and the crystals. The buoyancy force of the bubbles results in a torque on the crystal which ultimately orients the long axis of the crystal to the vertical direction. On the other hand, bubbles change their ascent path and velocity if they slide along a crystal face. This change in the bubble motion may have two opposing impacts on the magnitude of volcanic emissions: First, the reduced ascent velocity results in a bubble accumulation and thus enhanced bubble coalescence rate in the proximity of crystals. Second, the crystals align the bubbles in rise channels starting at the crystal tips while no bubbles access the magma volume immediately located above the crystal cross section, which we call "crystal shadow". Now, volatile degassing from supersaturated magma is a diffusive short-distance process which accelerate in the proximity of pre-existing gas bubbles. We thus infer that the orientation of the crystals influences the bulk volatile degassing rate and thus the volcanic gas emission rate due to the crystal shadow. The mechanical model suggests that all crystals get erected by the bubble-induced torque within time periods in the order of weeks to months. This has to be compared to the crystal nucleation rate in order to obtain a steady state

  14. Evaluation of the Kinetic Performance Differences between Hydrophilic-Interaction Liquid Chromatography and Reversed-Phase Liquid Chromatography under Conditions of Identical Packing Structure.

    Science.gov (United States)

    Song, Huiying; Desmet, Gert; Cabooter, Deirdre

    2015-12-15

    A protocol using trifluoroacetic acid at a temperature of 60 °C is developed for the adequate removal of the stationary phase of reversed-phase liquid chromatography (RPLC) columns. This procedure allows for studying the same column first under RPLC and subsequently under hydrophilic-interaction liquid chromatography (HILIC) conditions to isolate intrinsic differences between mass transfer properties in HILIC and RPLC from differences in packing quality. The established procedure allows for a complete removal of the stationary phase (confirmed by retention studies and thermogravimetry analyses) while leaving the structure of the packing unaffected (witnessed by an unchanged external porosity and pressure drop). Accurate plate height analysis comparing compounds at the same zone retention factor indicates a significant difference in reduced c-term (typically 40-80% larger under HILIC conditions), despite the columns otherwise being identical. Correcting for the known contributions of longitudinal diffusion (b-term) and mass transfer (cm- and cs-term) to focus on band broadening originating from eddy dispersion, similar strong differences are observed (differences of some h = 0.3 up to 1.2). These findings show that the interior structure and retention mechanism of the particles have a very strong effect on the observed eddy dispersion, a factor typically ascribed to phenomena occurring outside the particles. This also implies that comparing the quality of packings of different particle types is virtually impossible without the availability of a sound model to correct for the intraparticle effect on the observed eddy dispersion.

  15. GeoCrystal: graphic-interactive access to geodata archives

    Science.gov (United States)

    Goebel, Stefan; Haist, Joerg; Jasnoch, Uwe

    2002-03-01

    Recently there is spent a lot of effort to establish information systems and global infrastructures enabling both data suppliers and users to describe (-> eCommerce, metadata) as well as to find appropriate data. Examples for this are metadata information systems, online-shops or portals for geodata. The main disadvantages of existing approaches are insufficient methods and mechanisms leading users to (e.g. spatial) data archives. This affects aspects concerning usability and personalization in general as well as visual feedback techniques in the different steps of the information retrieval process. Several approaches aim at the improvement of graphical user interfaces by using intuitive metaphors, but only some of them offer 3D interfaces in the form of information landscapes or geographic result scenes in the context of information systems for geodata. This paper presents GeoCrystal, which basic idea is to adopt Venn diagrams to compose complex queries and to visualize search results in a 3D information and navigation space for geodata. These concepts are enhanced with spatial metaphors and 3D information landscapes (library for geodata) wherein users can specify searches for appropriate geodata and are enabled to graphic-interactively communicate with search results (book metaphor).

  16. Valve Packing

    Science.gov (United States)

    1992-01-01

    "S Glass" yarn was originally developed by NASA for high temperature space and aeronautical applications. When John Crane, Inc. required material that would withstand temperatures higher than 1,200 degrees Fahrenheit, they contacted Owens-Corning, which had developed a number of applications for the material. John Crane combines the yarn with other components to make Style 287-I packing. The product can be used in chemical processing operations, nuclear power stations, petroleum products, etc. Advantages include increased service life and reduced maintenance costs.

  17. Protein packing quality using Delaunay complexes

    DEFF Research Database (Denmark)

    Fonseca, Rasmus; Winter, Pawel; Karplus, Kevin

    2011-01-01

    A new method for estimating the packing quality of protein structures is presented. Atoms in high quality protein crystal structures are very uniformly distributed which is difficult to reproduce using structure prediction methods. Packing quality measures can therefore be used to assess structures...... of low quality and even to refine them. Previous methods mainly use the Voronoi cells of atoms to assess packing quality. The presented method uses only the lengths of edges in the Delaunay complex which is faster to compute since volumes of Voronoi cells are not evaluated explicitly. This is a novel...... application of the Delaunay complex that can improve the speed of packing quality computations. Doing so is an important step for, e.g., integrating packing measures into structure refinement methods. High- and low-resolution X-ray crystal structures were chosen to represent well- and poorly-packed structures...

  18. Roles of electrostatics and conformation in protein-crystal interactions.

    Directory of Open Access Journals (Sweden)

    Paul V Azzopardi

    Full Text Available In vitro studies have shown that the phosphoprotein osteopontin (OPN inhibits the nucleation and growth of hydroxyapatite (HA and other biominerals. In vivo, OPN is believed to prevent the calcification of soft tissues. However, the nature of the interaction between OPN and HA is not understood. In the computational part of the present study, we used molecular dynamics simulations to predict the adsorption of 19 peptides, each 16 amino acids long and collectively covering the entire sequence of OPN, to the {100} face of HA. This analysis showed that there is an inverse relationship between predicted strength of adsorption and peptide isoelectric point (P<0.0001. Analysis of the OPN sequence by PONDR (Predictor of Naturally Disordered Regions indicated that OPN sequences predicted to adsorb well to HA are highly disordered. In the experimental part of the study, we synthesized phosphorylated and non-phosphorylated peptides corresponding to OPN sequences 65-80 (pSHDHMDDDDDDDDDGD and 220-235 (pSHEpSTEQSDAIDpSAEK. In agreement with the PONDR analysis, these were shown by circular dichroism spectroscopy to be largely disordered. A constant-composition/seeded growth assay was used to assess the HA-inhibiting potencies of the synthetic peptides. The phosphorylated versions of OPN65-80 (IC(50 = 1.93 microg/ml and OPN220-235 (IC(50 = 1.48 microg/ml are potent inhibitors of HA growth, as is the nonphosphorylated version of OPN65-80 (IC(50 = 2.97 microg/ml; the nonphosphorylated version of OPN220-235 has no measurable inhibitory activity. These findings suggest that the adsorption of acidic proteins to Ca2+-rich crystal faces of biominerals is governed by electrostatics and is facilitated by conformational flexibility of the polypeptide chain.

  19. Evaluating the interactions of organic compounds with multi-walled carbon nanotubes by self-packed HPLC column and linear solvation energy relationship

    Energy Technology Data Exchange (ETDEWEB)

    Chu, Yingqian; Li, Xuehua, E-mail: lixuehua@dlut.edu.cn; Xie, Hongbin; Fu, Zhiqiang; Yang, Xianhai; Qiao, Xianliang; Cai, Xiyun; Chen, Jingwen

    2013-12-15

    Highlights: • The HPLC-based approach using CNTs as stationary phase is introduced. • The interactions of nine compounds to MWCNTs are evaluated by retention factors. • The LSER theory is adopted to probe the interactions of the compounds with MWCNTs. • π-/n-Electrons-dependent polarizable interaction plays a key role for adsorption. -- Abstract: Understanding the interactions between organic pollutants and carbon nanotubes (CNTs) is critical for fate assessment of both CNTs and organic pollutants. In this study, the chromatographic approach was introduced based on CNTs as stationary phase for the evaluation of such interactions. The pristine multi-walled carbon nanotubes (MWCNTs) were packed into columns of high-pressure liquid chromatography (HPLC) and the retention factors (k′) were determined to characterize the adsorption affinity of organic compounds onto MWCNTs. Nine compounds were tested. The results showed that their ln k′ values followed the order: benzene < toluene < phenol < chlorobenzene < bromobenzene < aniline < sulfamethoxazole < sulfadiazine ≈ sulfadimidine. The linear solvation energy relationship (LSER) theory was adopted to correlate ln k′ with the molecular solvatochromic parameters. We found that ln k′ of the studied compounds correlate positively with molecular polarizability (E) significantly, suggesting that the π-/n-electrons-dependent polarizable interactions play a major role for the adsorption. Moreover, the thermodynamic parameters calculated from van’t Hoff equations revealed that the interactions between the compounds and MWCNTs were spontaneous and exothermic processes.

  20. Strong Optomechanical Interaction in Hybrid Plasmonic-Photonic Crystal Nanocavities with Surface Acoustic Waves.

    Science.gov (United States)

    Lin, Tzy-Rong; Lin, Chiang-Hsin; Hsu, Jin-Chen

    2015-09-08

    We propose dynamic modulation of a hybrid plasmonic-photonic crystal nanocavity using monochromatic coherent acoustic phonons formed by ultrahigh-frequency surface acoustic waves (SAWs) to achieve strong optomechanical interaction. The crystal nanocavity used in this study consisted of a defective photonic crystal beam coupled to a metal surface with a nanoscale air gap in between and provided hybridization of a highly confined plasmonic-photonic mode with a high quality factor and deep subwavelength mode volume. Efficient photon-phonon interaction occurs in the air gap through the SAW perturbation of the metal surface, strongly coupling the optical and acoustic frequencies. As a result, a large modulation bandwidth and optical resonance wavelength shift for the crystal nanocavity are demonstrated at telecommunication wavelengths. The proposed SAW-based modulation within the hybrid plasmonic-photonic crystal nanocavities beyond the diffraction limit provides opportunities for various applications in enhanced sound-light interaction and fast coherent acoustic control of optomechanical devices.

  1. Strength of Drug–Polymer Interactions: Implications for Crystallization in Dispersions

    Energy Technology Data Exchange (ETDEWEB)

    Mistry, Pinal; Suryanarayanan, Raj

    2016-09-07

    We investigated the influence of the strength of drug–polymer interactions on the crystallization behavior of a model drug in amorphous solid dispersions (ASDs). Ketoconazole ASDs were prepared with each poly(acrylic acid), poly(2-hydroxyethyl methacrylate), and polyvinylpyrrolidone. Over a wide temperature range in the supercooled region, the α-relaxation time was obtained, which provided a measure of molecular mobility. Isothermal crystallization studies were performed in the same temperature interval using either a synchrotron (for low levels of crystallinity) or a laboratory X-ray (for crystallization kinetics) source. The stronger the drug–polymer interaction, the longer was the delay in crystallization onset time, indicating an increase in physical stability. Stronger drug–polymer interactions also translated to a decrease in the magnitude of the crystallization rate constant. In amorphous ketoconazole as well as in the dispersions, the coupling coefficient, a measure of the extent of coupling between relaxation and crystallization times was ~0.5. This value was unaffected by the strength of drug–polymer interactions. On the basis of these results, the crystallization times in ASDs were predicted at temperatures very close to Tg, using the coupling coefficient experimentally determined for amorphous ketoconazole. The predicted and experimental crystallization times were in good agreement, indicating the usefulness of the model.

  2. Mixed spin Ising model with four-spin interaction and random crystal field

    Energy Technology Data Exchange (ETDEWEB)

    Benayad, N., E-mail: n.benayad@fsac.ac.ma [Groupe de Mecanique Statistique, Laboratoire de physique theorique et appliquee, Faculte des sciences-Aien Chock, Universite Hassan II-Casablanca, B.P 5366 Maarif, Casablanca 20100 (Morocco); Laboratoire de physique des hautes energies et de la matiere condensee, Faculte des sciences-Aien Chock, Universite Hassan II-Casablanca, B.P 5366 Maarif, Casablanca 20100 (Morocco); Ghliyem, M. [Groupe de Mecanique Statistique, Laboratoire de physique theorique et appliquee, Faculte des sciences-Aien Chock, Universite Hassan II-Casablanca, B.P 5366 Maarif, Casablanca 20100 (Morocco); Laboratoire de physique des hautes energies et de la matiere condensee, Faculte des sciences-Aien Chock, Universite Hassan II-Casablanca, B.P 5366 Maarif, Casablanca 20100 (Morocco)

    2012-01-01

    The effects of fluctuations of the crystal field on the phase diagram of the mixed spin-1/2 and spin-1 Ising model with four-spin interactions are investigated within the finite cluster approximation based on a single-site cluster theory. The state equations are derived for the two-dimensional square lattice. It has been found that the system exhibits a variety of interesting features resulting from the fluctuation of the crystal field interactions. In particular, for low mean value D of the crystal field, the critical temperature is not very sensitive to fluctuations and all transitions are of second order for any value of the four-spin interactions. But for relatively high D, the transition temperature depends on the fluctuation of the crystal field, and the system undergoes tricritical behaviour for any strength of the four-spin interactions. We have also found that the model may exhibit reentrance for appropriate values of the system parameters.

  3. Influence of Molecular Interaction on Crystallization Behavior of Glycine from Mother Liquor

    Institute of Scientific and Technical Information of China (English)

    TAO Chang-yuan; LI Ming-song; FAN Xing; LIU Zuo-hua; DU Jun

    2011-01-01

    The mother liquor for preparing industrial HCN was investigated,to analyze the side-products' structure and influence of molecular interactions of side-products with glycine and solvent on the glycine's crystallization process.The side-products(SPs)were super-branched oligmers with plenty of hydrophilic groups,which could affect the crystallization process by interactions such as hydrogen bond.Alcohol-water mixed solvent with different polyols could be used to weaken the SPs-glycine interaction and strengthen the SPs-water interaction,which help to improve the crystallization efficiency and purity.After optimization,SPs' mass fraction in glycine could be reduced by 80%and the morphology of crystal particles could also be improved.

  4. Interaction of light with impurities in lithium niobate crystals

    Energy Technology Data Exchange (ETDEWEB)

    Schwesyg, Judith Renate Marie-Luise

    2011-06-06

    Congruent lithium niobate (LiNbO{sub 3}) and 5-mol% MgO-doped LiNbO{sub 3} (MgO:LN) crystals are widely used as nonlinear-optical crystals in frequency-conversion devices due to their large nonlinear-optic coefficients. These devices usually require high optical pump powers, but absorption of photons by impurities limits their usability due to heat accumulation that leads to thermo-optic refractive index changes. These refractive index changes distort the beam shape and disturb the phase-matching condition. Furthermore pyroelectric fields can build up. In this thesis the residual optical absorption in congruent LiNbO{sub 3} (CLN) and MgO:LN crystals is studied. Absorption spectra of CLN and MgO:LN crystals between 400-2000 nm reveal a residual absorption up to 0.04 cm{sup -1}. This absorption is mainly caused by transition metal impurities. Between 2300-2800 nm unknown hydrogen absorption bands in CLN and MgO:LN are revealed on the order of 0.001 cm{sup -1}. High-temperature annealing is applied to the CLN and MgO:LN crystals, which decreases optical absorption by up to one order of magnitude. As an application, the operation of a 1550-nm pumped singly-resonant CW optical parametric oscillator, resonant around 2600 nm, using a low-loss, periodically-poled, annealed CLN crystal is demonstrated. Another issue that affects CLN is photorefractive damage (PRD), i.e. light-induced refractive index changes. In contrast, MgO:LN crystals do not suffer from PRD even at high optical intensities. However, it is shown in this thesis that PRD can occur within seconds in MgO:LN, using green laser light at light intensity levels as low as 100 mW/cm{sup 2}, if the crystal is heated by several degrees Celsius during or before illumination. Photorefractive damage does not occur in CLN crystals under the same conditions. We show that the pyroelectric effect together with an elevated photoconductivity compared to that of CLN causes this beam distortion and that this effect also

  5. Aharonov-Casher effect in exchange interactions in a Wigner crystal.

    Science.gov (United States)

    Tserkovnyak, Yaroslav; Kindermann, Markus

    2009-03-27

    We theoretically study the effects of spin-orbit coupling on spin exchange in a low-density Wigner crystal. In addition to the familiar antiferromagnetic Heisenberg exchange, we find general anisotropic interactions in spin space if the exchange paths allowed by the crystal structure form loops in real space. In particular, it is shown that the two-electron exchange interaction can acquire ferromagnetic character.

  6. Enol-enamine tautomerism in crystals of 1,3-bis(pyridin-2-yl) propan-2-one: a combined crystallographic and quantum-chemical investigation of the effect of packing on tautomerization processes.

    Science.gov (United States)

    Godsi, Oded; Turner, Boaz; Suwinska, Kinga; Peskin, Uri; Eichen, Yoav

    2004-10-20

    The enolpyridine, OH-ketoenamime, NH equilibrium in crystals of 1,3-bis(pyridin-2-yl)propan-2-one was studied using temperature-dependent single-crystal X-ray diffraction. The relative population of the different tautomers was found to be sensitive to the temperature in the range of 100-300 K, illustrating the small thermodynamic difference between these two tautomers. This energy resemblance is partially attributed to the molecular packing in the crystal, where the molecules are arranged in the form of dimers. Ab initio electronic energy calculations (HF/6-31G** and MP2/6-31G**) reveal the effect of dimerization in the crystal on the electronic energy levels. Several tautomeric states were identified in the dimer of 1,3-bis(pyridin-2-yl)propan-2-one. A model is proposed in which four of these dimer states are populated in the crystal at ambient temperatures. The crystallographic data were treated according to this four-state dimer model, suggesting that the free energy of the OH-NH dimers is higher than that of the OH-OH dimers by 120 +/- 10 cal mol(-1) and that the NH-NH dimers are yet higher in free energy by 50 +/- 10 cal mol(-1).

  7. Static magnetic susceptibility, crystal field and exchange interactions in rare earth titanate pyrochlores.

    Science.gov (United States)

    Malkin, B Z; Lummen, T T A; van Loosdrecht, P H M; Dhalenne, G; Zakirov, A R

    2010-07-14

    The experimental temperature dependence (T = 2-300 K) of single crystal bulk and site susceptibilities of rare earth titanate pyrochlores R(2)Ti(2)O(7) (R = Sm, Eu, Gd, Tb, Dy, Ho, Er, Yb) is analyzed in the framework of crystal field theory and a mean field approximation. Analytical expressions for the site and bulk susceptibilities of the pyrochlore lattice are derived taking into account long range dipole-dipole interactions and anisotropic exchange interactions between the nearest neighbor rare earth ions. The sets of crystal field parameters and anisotropic exchange coupling constants have been determined and their variations along the lanthanide series are discussed.

  8. Influence of supramolecular structures in crystals on parallel stacking interactions between pyridine molecules.

    Science.gov (United States)

    Janjić, Goran V; Ninković, Dragan B; Zarić, Snezana D

    2013-08-01

    Parallel stacking interactions between pyridines in crystal structures and the influence of hydrogen bonding and supramolecular structures in crystals on the geometries of interactions were studied by analyzing data from the Cambridge Structural Database (CSD). In the CSD 66 contacts of pyridines have a parallel orientation of molecules and most of these pyridines simultaneously form hydrogen bonds (44 contacts). The geometries of stacked pyridines observed in crystal structures were compared with the geometries obtained by calculations and explained by supramolecular structures in crystals. The results show that the mean perpendicular distance (R) between pyridine rings with (3.48 Å) and without hydrogen bonds (3.62 Å) is larger than that calculated, because of the influence of supramolecular structures in crystals. The pyridines with hydrogen bonds show a pronounced preference for offsets of 1.25-1.75 Å, close to the position of the calculated minimum (1.80 Å). However, stacking interactions of pyridines without hydrogen bonds do not adopt values at or close to that of the calculated offset. This is because stacking interactions of pyridines without hydrogen bonds are less strong, and they are more susceptible to the influence of supramolecular structures in crystals. These results show that hydrogen bonding and supramolecular structures have an important influence on the geometries of stacked pyridines in crystals.

  9. The pursuit of perfect packing

    CERN Document Server

    Weaire, Denis

    2000-01-01

    In 1998 Thomas Hales dramatically announced the solution of a problem that has long teased eminent mathematicians: what is the densest possible arrangement of identical spheres? The Pursuit of Perfect Packing recounts the story of this problem and many others that have to do with packing things together. The examples are taken from mathematics, physics, biology, and engineering, including the arrangement of soap bubbles in foam, atoms in a crystal, the architecture of the bee''s honeycomb, and the structure of the Giant''s Causeway. Using an informal style and with key references, the book also includes brief accounts of the lives of many of the scientists who devoted themselves to problems of packing over many centuries, together with wry comments on their efforts. It is an entertaining introduction to the field for both specialists and the more general public.

  10. Interaction of excitons with optical phonons in layer crystals

    Science.gov (United States)

    Nitsovich, Bohdan M.; Zenkova, C. Y.; Kramar, N. K.

    2002-02-01

    The investigation is concerned with layer crystals of the GaSe, InSe, GaTe, MoS2-type and other inorganic semiconductors, whose phonon spectrum has a great number of peculiarities, among them the availability of low-energy optical phonons. In this case the dispersion of these phonons can be essential and vary in character. The mass operator of the exciton-phonon system and the light absorption coefficient for different dispersion laws of optical phonons have been calculated. The influence of the sign of the phonon 'effective mass' on the exciton absorption band of layer crystals, which causes the opposite in sign dynamics of the absorption maximum shift, and the change of the absorption curve asymmetry have been determined.

  11. Intermolecular interactions of oligothienoacenes: Do S⋯S interactions positively contribute to crystal structures of sulfur-containing aromatic molecules?

    Science.gov (United States)

    Tsuzuki, Seiji; Orita, Hideo; Sato, Naoki

    2016-11-07

    Intermolecular interactions in the crystals of tetra- and penta-thienoacene were studied using ab initio molecular orbital calculations for evaluating the magnitude of characteristic S⋯S interactions with great attention paid to their origin. The interactions between the π-stacked neighboring molecules are significantly greater than those between the neighboring molecules exhibiting the S⋯S contact, although it has sometimes been claimed that the S⋯S interactions play important roles in adjusting the molecular arrangement of sulfur-containing polycyclic aromatic molecules in the crystals owing to short S⋯S contacts. The coupled cluster calculations with single and double substitutions with noniterative triple excitation interaction energies at the basis set limit estimated for the π-stacked and S⋯S contacted neighboring molecules in the tetrathienoacene crystal are -11.17 and -4.27 kcal/mol, respectively. Those for π-stacked molecules in the pentathienoacene crystal is -14.38 kcal/mol, while those for S⋯S contacted molecules are -7.02 and -6.74 kcal/mol. The dispersion interaction is the major source of the attraction between the π-stacked and S⋯S contacted molecules, while the orbital-orbital interactions are repulsive: The orbital-orbital interactions, which are significant for charge carrier transport properties, are not much more than the results of the short S⋯S contact caused by the strong dispersion interactions. Besides, the intermolecular interaction energy calculated for a trithienoacene dimer has strong orientation dependence.

  12. The Magnetic Ordering in Diluted Crystal Magnets with Indirect Exchange Interaction

    OpenAIRE

    Belokon, V. I.; Nefedev, K. V.; Savunov, M. A.

    2006-01-01

    The closed system of equations for a determination of parameters distribution function for random interaction fields was calculated analytically. The estimations of critical concentrations for phase transitions in diluted crystal magnets with face centered cubic (fcc), volume centered cubic (vcc) and simple cubic (sc) lattices with interaction of Ruderman-Kittel-Kasua-Yosida between spins were made.

  13. Strong spin-orbit interaction of light on the surface of atomically thin crystals

    Science.gov (United States)

    Liu, Mengxia; Cai, Liang; Chen, Shizhen; Liu, Yachao; Luo, Hailu; Wen, Shuangchun

    2017-06-01

    The photonic spin Hall effect (SHE) can be regarded as a direct optical analogy of the SHE in electronic systems where a refractive index gradient plays the role of an electric potential. However, it has been demonstrated that the effective refractive index fails to adequately explain the light-matter interaction in atomically thin crystals. In this paper, we examine the spin-orbit interaction on the surface of the freestanding atomically thin crystals. We find that it is not necessary to involve the effective refractive index to describe the spin-orbit interaction and the photonic SHE in the atomically thin crystals. The strong spin-orbit interaction and giant photonic SHE are predicted, which can be explained as the large polarization rotation of plane-wave components in order to satisfy the transversality of photon polarization.

  14. Crystallization processes derived from the interaction of urine and dolostone

    Science.gov (United States)

    Cámara, Beatriz; Alvarez de Buergo, Monica; Fort, Rafael

    2015-04-01

    (these 3 sections, a) b) c) represent the first one centimeter of the specimen from the bottom); d) and the fourth and top section, which shows no influence by the effect of urine capillary absorption. The obtained results showed, from bottom to top, the following crystallized salts: a) abundant prismatic crystals enriched in P and Ca (calcium phosphate); b) amorphous round-shaped potassium sulfate crystals and cubic sodium chloride crystals embedded in an organic matrix; d) cubic sodium chloride crystals are dominant. In the unaffected area, no other crystals were detected different from the carbonate minerals forming the rock. These results are in accordance to which has already been published by the authors in granitic materials (Cámara et al 2014). Acknowledgements: to Geomateriales 2 programme (S2013/MIT-2914) funded by the Community of Madrid. Cámara B., Alvarez de Buergo, M.; Fort, R.; Ascaso, C. de los Rios, A.; Gomez-Heras, M. 2014. Another source of soluble salts in urban environments due to recent social behaviour pattern in historical centres. In: Science, Technology and Cultural Heritage (edited by M.A. Rogerio-Candelera), 89-94. CRC Press-Balkema, Taylor and Francis. ISBN 9781138027442 - CAT# K25502

  15. Interactions of biomacromolecules with reverse hexagonal liquid crystals: drug delivery and crystallization applications.

    Science.gov (United States)

    Libster, Dima; Aserin, Abraham; Garti, Nissim

    2011-04-15

    Recently, self-assembled lyotropic liquid crystals (LLCs) of lipids and water have attracted the attention of both scientific and applied research communities, due to their remarkable structural complexity and practical potential in diverse applications. The phase behavior of mixtures of glycerol monooleate (monoolein, GMO) was particularly well studied due to the potential utilization of these systems in drug delivery systems, food products, and encapsulation and crystallization of proteins. Among the studied lyotropic mesophases, reverse hexagonal LLC (H(II)) of monoolein/water were not widely subjected to practical applications since these were stable only at elevated temperatures. Lately, we obtained stable H(II) mesophases at room temperature by incorporating triacylglycerol (TAG) molecules into the GMO/water mixtures and explored the physical properties of these structures. The present feature article summarizes recent systematic efforts in our laboratory to utilize the H(II) mesophases for solubilization, and potential release and crystallization of biomacromolecules. Such a concept was demonstrated in the case of two therapeutic peptides-cyclosporin A (CSA) and desmopressin, as well as RALA peptide, which is a model skin penetration enhancer, and eventually a larger macromolecule-lysozyme (LSZ). In the course of the study we tried to elucidate relationships between the different levels of organization of LLCs (from the microstructural level, through mesoscale, to macroscopic level) and find feasible correlations between them. Since the structural properties of the mesophase systems are a key factor in drug release applications, we investigated the effects of these guest molecules on their conformations and the way these molecules partition within the domains of the mesophases. The examined H(II) mesophases exhibited great potential as transdermal delivery vehicles for bioactive peptides, enabling tuning the release properties according to their chemical

  16. Crystal packing and hydrogen bonding in platinum(II) nucleotide complexes: X-ray crystal structure of [Pt(MeSCH(2)CH(2)SMe)(5'-GMP-N7)(2)].6H(2)O.

    Science.gov (United States)

    Djuran, Milos I; Milinkovic, Snezana U; Habtemariam, Abraha; Parsons, Simon; Sadler, Peter J

    2002-02-01

    We have synthesised the complex [Pt(CH(3)SCH(2)CH(2)SCH(3))(5'-GMP-N7)(2)].6H(2)O (1), where 5'-GMP is 5'-guanosine monophosphate, and determined its X-ray crystal structure. Pt(II) adopts a square-planar geometry in which the bases are coordinated head-to-tail (HT) in the Delta configuration. The nucleotide conformation in this complex is almost identical to that in the previously reported complex [Pt(en)(5'-GMP-N7)(2)].9H(2)O (2), in which there is outer sphere macrochelation via intramolecular H-bonding between the monoanionic phosphate groups and the coordinated ethylenediamine (en) NH. It is therefore apparent that intermolecular interactions rather than intramolecular H-bonding determines the orientation of the sugar-phosphate side-chain in these Pt(II) bisnucleotide complexes in the solid state.

  17. Coordination and Crystallization Molecules: Their Interactions Affecting the Dimensionality of Metalloporphyrinic SCFs

    Directory of Open Access Journals (Sweden)

    Arkaitz Fidalgo-Marijuan

    2015-04-01

    Full Text Available Synthetic metalloporphyrin complexes are often used as analogues of natural systems, and they can be used for the preparation of new Solid Coordination Frameworks (SCFs. In this work, a series of six metalloporphyrinic compounds constructed from different meso substituted metalloporphyrins (phenyl, carboxyphenyl and sulfonatophenyl have been structurally characterized by means of single crystal X-ray diffraction, IR spectroscopy and elemental analysis. The compounds were classified considering the dimensionality of the crystal array, referred just to coordination bonds, into 0D, 1D and 2D compounds. This way, the structural features and relationships of those crystal structures were analyzed, in order to extract conclusions not only about the dimensionality of the networks but also about possible applications of the as-obtained compounds, focusing the interest on the interactions of coordination and crystallization molecules. These interactions provide the coordination bonds and the cohesion forces which produce SCFs with different dimensionalities.

  18. Crystal Structure of the DFNKF Segment of Human Calcitonin Unveils Aromatic Interactions between Phenylalanines.

    Science.gov (United States)

    Bertolani, Arianna; Pizzi, Andrea; Pirrie, Lisa; Gazzera, Lara; Morra, Giulia; Meli, Massimiliano; Colombo, Giorgio; Genoni, Alessandro; Cavallo, Gabriella; Terraneo, Giancarlo; Metrangolo, Pierangelo

    2017-02-10

    Although intensively studied, the high-resolution crystal structure of the peptide DFNKF, the core-segment of human calcitonin, has never been described. Here we report how the use of iodination as a strategy to promote crystallisation and facilitate phase determination, allowed us to solve, for the first time, the single-crystal X-ray structure of a DFNKF derivative. Computational studies suggest that both the iodinated and the wild-type peptides populate very similar conformations. Furthermore, the conformer found in the solid-state structure is one of the most populated in solution, making the crystal structure a reliable model for the peptide in solution. The crystal structure of DFNKF(I) confirms the overall features of the amyloid cross-β spine and highlights how aromatic-aromatic interactions are important structural factors in the self-assembly of this peptide. A detailed analysis of such interactions is reported.

  19. On the theory of interaction potentials in ionic crystals

    Science.gov (United States)

    Acevedo, Roberto; Soto-Bubert, Andrés

    2008-11-01

    The aim of this research work is to report a more comprehensive and detailed study of both, the intermolecular and intramolecular potencial functions with reference to the various families of the elpasolite type crystals. The cohesive energy has been thought as a sum of three terms; the long range (Coulombic), the Born and the van der Waals contributions to the total energy. The Born-Mayer-Buckingham potential1 has been employed in all of these current studies and a number of convergence tests are analyzed from a formal viewpoint. Our work has been focused to the following systems: Cs2NaLnF6, Cs2NaLnCl6, Cs2NaLnBr6, Rb2NaLnF6 and Cs2KLnF6 in the Fm3m space group. A substantial amount of theoretical models have been analyzed and several computing simulations have been undertaken to estimate the reticular energies and the corresponding heat of formation for these crystals. To achieve this goal, a Born-Haber thermodynamic cycle has been introduced in our model. It is shown that the calculated energy values are reasonable and follow the expected trend along the lanthanide series in the periodic chart. We also discuss the advantages and disadvantages of the current and proposed generalized model. The most likely sources for improvement are discussed in detail. New convergence tests as well as some master equations have been introduced to study the various diagonal contributions to the total energy.

  20. Colloid-in-Liquid Crystal Gels that Respond to Biomolecular Interactions

    OpenAIRE

    Agarwal, Ankit; Sidiq, Sumyra; Setia, Shilpa; Bukusoglu, Emre; de Pablo, Juan J.; Pal, Santanu Kumar; Abbott, Nicholas L.

    2013-01-01

    This paper advances the design of stimuli-responsive materials based on colloidal particles dispersed in liquid crystals (LCs). Specifically, we report that thin films of colloid-in-liquid crystal (CLC) gels can undergo easily visualized ordering transitions in response to reversible and irreversible (enzymatic) biomolecular interactions occurring at aqueous interfaces of the gels. In particular, we demonstrate that LC ordering transitions can propagate across the entire thickness of the gels...

  1. Results on the Coherent Interaction of High Energy Electrons and Photons in Oriented Single Crystals

    CERN Document Server

    Apyan, A; Badelek, B; Ballestrero, S; Biino, C; Birol, I; Cenci, P; Connell, S H; Eichblatt, S; Fonseca, T; Freund, A; Gorini, B; Groess, R; Ispirian, K; Ketel, T; Kononets, Y V; López, A; Mangiarotti, A; Van Rens, B; Sellschop, J P Friedel; Shieh, M; Sona, P; Strakhovenko, V M; Uggerhøj, Erik; Uggerhøj, U; Ünel, G; Velasco, M; Vilakazi, Z Z; Wessely, O; Kononets, Yu.V.

    2005-01-01

    The CERN-NA-59 experiment examined a wide range of electromagnetic processes for multi-GeV electrons and photons interacting with oriented single crystals. The various types of crystals and their orientations were used for producing photon beams and for converting and measuring their polarisation. The radiation emitted by 178 GeV unpolarised electrons incident on a 1.5 cm thick Si crystal oriented in the Coherent Bremsstrahlung (CB) and the String-of-Strings (SOS) modes was used to obtain multi-GeV linearly polarised photon beams. A new crystal polarimetry technique was established for measuring the linear polarisation of the photon beam. The polarimeter is based on the dependence of the Coherent Pair Production (CPP) cross section in oriented single crystals on the direction of the photon polarisation with respect to the crystal plane. Both a 1 mm thick single crystal of Germanium and a 4 mm thick multi-tile set of synthetic Diamond crystals were used as analyzers of the linear polarisation. A birefringence ...

  2. Optomechanical and Photothermal Interactions in Suspended Photonic Crystal Membranes

    CERN Document Server

    Woolf, David N; Iwase, Eiji; Khan, Mughees; Rodriguez, Alejandro W; Deotare, Parag; Bulu, Irfan; Johnson, Steven G; Capasso, Federico; Loncar, Marko

    2012-01-01

    We present here an optomechanical system fabricated with novel stress management techniques that allow us to suspend an ultrathin defect-free silicon photonic-crystal membrane above a Silicon-on-Insulator (SOI) substrate with a gap that is tunable to below 200 nm. Our devices are able to generate strong attractive and repulsive optical forces over a large surface area with simple in- and outcoupling and feature the strongest repulsive optomechanical coupling in any geometry to date (gOM/2{\\pi} ~ -65 GHz/nm). The interplay between the optomechanical and photo-thermal-mechanical dynamics is explored, and the latter is used to achieve cooling and amplification of the mechanical mode, demonstrating that our platform is well-suited for applications in low-power mass, force, and refractive index sensing as well as and optomechanical accelerometry.

  3. On the theory of interaction potentials in ionic crystals

    Energy Technology Data Exchange (ETDEWEB)

    Acevedo, Roberto [Departamento de Ciencia de los Materiales, Facultad de Ciencias Fisicas y Matematicas, Beauchef 850, Santiago (Chile); Soto-Bubert, Andres [Instituto de Ciencias Basicas, Facultad de Ingenieria, Universidad Diego Portales, Avenida Ejercito 441, Santiago (Chile)], E-mail: roberto.acevedo@umayor.cl

    2008-11-01

    The aim of this research work is to report a more comprehensive and detailed study of both, the intermolecular and intramolecular potencial functions with reference to the various families of the elpasolite type crystals. The cohesive energy has been thought as a sum of three terms; the long range (Coulombic), the Born and the van der Waals contributions to the total energy. The Born-Mayer-Buckingham potential{sup 1} has been employed in all of these current studies and a number of convergence tests are analyzed from a formal viewpoint. Our work has been focused to the following systems: Cs{sub 2}NaLnF{sub 6}, Cs{sub 2}NaLnCl{sub 6}, Cs{sub 2}NaLnBr{sub 6}, Rb{sub 2}NaLnF{sub 6} and Cs{sub 2}KLnF{sub 6} in the Fm3m space group. A substantial amount of theoretical models have been analyzed and several computing simulations have been undertaken to estimate the reticular energies and the corresponding heat of formation for these crystals. To achieve this goal, a Born-Haber thermodynamic cycle has been introduced in our model. It is shown that the calculated energy values are reasonable and follow the expected trend along the lanthanide series in the periodic chart. We also discuss the advantages and disadvantages of the current and proposed generalized model. The most likely sources for improvement are discussed in detail. New convergence tests as well as some master equations have been introduced to study the various diagonal contributions to the total energy.

  4. Relation between stabilization energy, crystal field coefficient and themagnetic exchange interaction for Tb3+ ion

    Institute of Scientific and Technical Information of China (English)

    ZHANG Xiangmu; MA Wenjuan; CUI Shuwen; WANG Lihua

    2006-01-01

    Based on a single ion model, Hamiltonian of the simplest form about magnetocrystalline anisotropy for Tb3+ ion was solved by using the numerical method. The relation between the stabilization energy, crystal field coefficient B20 and the magnetic exchange interaction was studied as temperature approaches to 0K. The results show that the stabilization energy contributed by Tb3+ is linear with crystal field coefficient B20 approximately, but it is insensitive to the change of magnetic exchange interaction for the strong magnetic substancessuch as TbCo5, Tb2Co17 and Tb2Fe14B compounds.

  5. Directional Control of Plasmon-Exciton interaction with Plexcitonic Crystals

    Science.gov (United States)

    Balci, Sinan; Karademir, Ertugrul; Kocabas, Coskun; Aydinli, Atilla

    2015-03-01

    Plexcitons are strongly coupled plasmon excitons modes. In this work, we developed a platform, consisting of one and two dimensional corrugated surface patterns coated with a thin metal film and a dye solution. This system shows a controlled coupling action based on the excitation direction of SPP modes. Our scheme is based on the control of wavelengths of the forbidden SPP modes. Three kinds of patterns have been tested; a one dimensional uniform, a triangular, and a square lattice type crystals. For all three cases, lowest wavelength of the band gap is observed in Γ to M direction. For triangular and square lattice cases, band gap center oscillates between two finite values for every 60° and 90°s, respectively. We utilized this behavior to control SPP and J-aggregate coupling. We observe directional dependence of Rabi splitting energy varying between 0 meV and 60 meV . Square lattice gives the ability to tune a larger band gap, whereas triangular lattice gives higher number of symmetry points. Simulations show that, an 80 nm deep triangular lattice with 280 nm periodicity can result in omnidirectional decoupling of plexcitons. TUBITAK, Grants 110T790, 110T589, and 112T091.

  6. Interaction of a crack with crystal defects in solids

    Energy Technology Data Exchange (ETDEWEB)

    Narita, N. [Kyushu Inst. of Tech., Kitakyushu (Japan). Dept. of Materials Science and Engineering; Higashida, K.

    1997-06-01

    The modifications of stress states near a crack tip by interstitial impurities and by dislocations are analyzed using 2-D and 3-D potential methods. In the case of interstitial impurities, the local stress intensity k{sub D} due to impurities is much affected by their location and is altered from crack tip shielding to anti-shielding as their location changes from behind a crack tip to the front. If impurities are mobile, their forward redistribution is induced by crack fields to increase k{sub D} values. The tetragonal strain of impurities also enhances the increase of the k{sub D} values. In dislocation-crack systems, two kinds of screw dislocation arrays are observed on each different slip plane ahead of a crack tip in MgO thin crystals and they mainly induce the mode I stress intensity of shielding type as a result of the mutual cancellation of the other modes. The effect of crack tip shielding/anti-shielding on crack extension is discussed in connection with the experimental observation of fracture toughness. (orig.). 7 refs.

  7. Influence of Acoustic Field Structure on Polarization Characteristics of Acousto-optic Interaction in Crystals

    Science.gov (United States)

    Muromets, A. V.; Trushin, A. S.

    Influence of acoustic field structure on polarization characteristics of acousto-optic interaction is investigated. It is shown that inhomogeneity of acoustic field and mechanism of ultrasound excitation causes changes in values of acousto-optic figure of merit for ordinary and extraordinary light beams in comparison with theoretic values. The theoretic values were derived under assumption that acoustic wave is homogeneous. Experimental analysis was carried out in acousto-optic cell based on lithium niobate crystal where the acoustic wave propagates at the angle 13 degrees to Z axis of the crystal. We used three different methods of ultrasound generation in the crystal: by means of external piezotransducer, by interdigital transducer and by two sets of electrodes placed on top of the crystal surface. In the latter case, the first pair of the electrodes was directed along X crystal axis, while the second pair of the electrodes was directed orthogonally to X crystal axis and the direction of ultrasound. Obtained values for diffraction efficiencies for ordinary and extraordinary polarized optical beams were qualitatively different which may be caused by spatial inhomogeneity of the generated acoustic waves in the crystal. Structure of acoustic field generated by these sets of electrodes was examined by laser probing. We performed the analysis of the acoustic field intensity using acousto-optic method. A relation of diffraction efficiencies for ordinary and extraordinary light waves was measured during each iteration of the laser probing.

  8. Direct visualization of spruce budworm antifreeze protein interacting with ice crystals: basal plane affinity confers hyperactivity.

    Science.gov (United States)

    Pertaya, Natalya; Marshall, Christopher B; Celik, Yeliz; Davies, Peter L; Braslavsky, Ido

    2008-07-01

    Antifreeze proteins (AFPs) protect certain organisms from freezing by adhering to ice crystals, thereby preventing their growth. All AFPs depress the nonequilibrium freezing temperature below the melting point; however AFPs from overwintering insects, such as the spruce budworm (sbw) are 10-100 times more effective than most fish AFPs. It has been proposed that the exceptional activity of these AFPs depends on their ability to prevent ice growth at the basal plane. To test the hypothesis that the hyperactivity of sbwAFP results from direct affinity to the basal plane, we fluorescently tagged sbwAFP and visualized it on the surface of ice crystals using fluorescence microscopy. SbwAFP accumulated at the six prism plane corners and the two basal planes of hexagonal ice crystals. In contrast, fluorescently tagged fish type III AFP did not adhere to the basal planes of a single-crystal ice hemisphere. When ice crystals were grown in the presence of a mixture of type III AFP and sbwAFP, a hybrid crystal shape was produced with sbwAFP bound to the basal planes of truncated bipyramidal crystals. These observations are consistent with the blockage of c-axial growth of ice as a result of direct interaction of sbwAFP with the basal planes.

  9. Optical vibration modes and electron-phonon interaction in ternary mixed crystals of polar semiconductors

    Institute of Scientific and Technical Information of China (English)

    Liang Xi-Xia; Ban Shi-Liang

    2004-01-01

    @@ Optical vibrations of the lattice and the electron-phonon interaction in polar ternary mixed crystals are studied in the framework of the continuum model of Born and Huang and the random-element-isodisplacement model. A normal-coordinate system to describe the optical vibration in ternary mixed crystals is correctly adopted to derive a new Frohlich-like Hamiltonian for the electron-phonon interaction including the unit-cell volume variation influence.The numerical results for the phonon modes, the electron-phonon coupling constants and the polaronic energies for several typical materials are obtained. It is verified that the nonlinearity of the electron-phonon coupling effects with the composition is essential and the unit-cell volume effects cannot be neglected for most ternary mixed crystals.

  10. Influence of deuteration and fluorination on the supramolecular architecture of pyridine N-oxide crystals.

    Science.gov (United States)

    Shishkin, Oleg V; Shishkina, Svitlana V; Maleev, Andrey V; Zubatyuk, Roman I; Vasylyeva, Vera; Merz, Klaus

    2013-03-18

    To understand how deuterium and fluorine substituents influence the supramolecular architecture of pyridine N-oxide crystals, the crystal structure of 3-fluoropyridine N-oxide (PNO-3F) was determined and the crystal packing motives of non-deuterated pyridine-N-oxide (PNO), partial-deuterated pyridine-N-oxide (PNO-D) and PNO-3F were analyzed based on ab initio quantum-chemical calculations of the intermolecular interaction energy, using the MP2/6-311G(d,p) method. The appearance of the weak-directing substituents deuterium and fluorine leads to significant changes in the crystal organization of the isotropic packing of PNO molecules.

  11. Interaction between Functional Domains of Bacillus thuringiensis Insecticidal Crystal Proteins

    Science.gov (United States)

    Rang, Cécile; Vachon, Vincent; de Maagd, Ruud A.; Villalon, Mario; Schwartz, Jean-Louis; Bosch, Dirk; Frutos, Roger; Laprade, Raynald

    1999-01-01

    Interactions among the three structural domains of Bacillus thuringiensis Cry1 toxins were investigated by functional analysis of chimeric proteins. Hybrid genes were prepared by exchanging the regions coding for either domain I or domain III among Cry1Ab, Cry1Ac, Cry1C, and Cry1E. The activity of the purified trypsin-activated chimeric toxins was evaluated by testing their effects on the viability and plasma membrane permeability of Sf9 cells. Among the parental toxins, only Cry1C was active against these cells and only chimeras possessing domain II from Cry1C were functional. Combination of domain I from Cry1E with domains II and III from Cry1C, however, resulted in an inactive toxin, indicating that domain II from an active toxin is necessary, but not sufficient, for activity. Pores formed by chimeric toxins in which domain I was from Cry1Ab or Cry1Ac were slightly smaller than those formed by toxins in which domain I was from Cry1C. The properties of the pores formed by the chimeras are therefore likely to result from an interaction between domain I and domain II or III. Domain III appears to modulate the activity of the chimeric toxins: combination of domain III from Cry1Ab with domains I and II of Cry1C gave a protein which was more strongly active than Cry1C. PMID:10388684

  12. Crystallization kinetics of colloidal binary mixtures with depletion attraction.

    Science.gov (United States)

    Kozina, Anna; Díaz-Leyva, Pedro; Palberg, Thomas; Bartsch, Eckhard

    2014-12-21

    In this work the crystallization kinetics of colloidal binary mixtures with attractive interaction potential (Asakura-Oosawa) has been addressed. Parameters such as fraction of crystals, linear crystal dimension and crystal packing have been quantified in order to understand how the crystal formation is driven in terms of the depth of the attractive potential and the composition of the binary mixture (described by the number ratio). It was found that inside the eutectic triangle, crystallization is mainly governed by nucleation and the crystal packing is close to the close-packing of hard spheres. Moving out from the eutectic triangle towards small component results in the crystallization of small spheres. Enrichment of the eutectic mixture with large component results in the crystallization of both large and small spheres, however, the kinetics are completely different from those of the eutectic composition. Crosslinked polystyrene microgels with nearly hard sphere interactions were used as model systems. Attraction was introduced by addition of linear polystyrene. The time evolution of crystallization has been followed by static light scattering.

  13. Interaction between submicron COD crystals and renal epithelial cells

    Directory of Open Access Journals (Sweden)

    Peng H

    2012-08-01

    cells plays an important role in the formation of early-stage kidney stones.Keywords: cell modulation, crystal adhesion, calcium oxalate dihydrate, kidney stone, pathological mineralization

  14. Mechanical interactions between ice crystals and red blood cells during directional solidification.

    Science.gov (United States)

    Ishiguro, H; Rubinsky, B

    1994-10-01

    Experiments in which red blood cells were frozen on a directional solidification stage under a microscope show that there is a mechanical interaction between ice crystals and cells in which cells are pushed and deformed by the ice crystals. The mechanical interaction occurs during freezing of cells in physiological saline and is significantly inhibited by the addition of 20% v/v glycerol to the solution. The addition of osmotically insignificant quantities of antifreeze proteins from the winter flounder or ocean pout to the physiological saline with 20% v/v glycerol generates strong mechanical interactions between the ice and the cells. The cells were destroyed during freezing in physiological saline, survived freezing in physiological saline with glycerol, and were completely destroyed by the addition of antifreeze proteins to the solution with glycerol. The difference in cell survival through freezing and thawing appears to be related, in part, to the habit of ice crystal growing in the suspension of red blood cells and the nature of mechanical interaction between the ice crystal and the cells. This suggests that mechanical damage may be a factor during cryopreservation of cells.

  15. Thick monolithic scintillation crystals for TOF-PET with depth-of-interaction measurement

    NARCIS (Netherlands)

    Vinke, Ruud; van Dam, Herman T.; Seifert, Stefan; Beekman, Freek J.; Lohner, Herbert; Schaart, Dennis R.; Dendooven, Peter

    2010-01-01

    Positron emission tomography (PET) detectors based on monolithic scintillation crystals show excellent intrinsic spatial resolution and allow depth-of-interaction (DOI) reconstruction using a single photosensor array. The inclusion of time-of-flight (TOF) information in the image reconstruction

  16. Crystal structure of the PDZ domain of mouse Dishevelled 1 and its interaction with CXXC5.

    Science.gov (United States)

    Lee, Inhwan; Choi, Sooho; Yun, Ji-Hye; Seo, Seolhwa; Choi, Sehee; Choi, Kang-Yell; Lee, Weontae

    2016-12-05

    Dishevelled (Dvl) plays a crucial role in Wnt signaling by interacting with membrane-bound receptors and downstream molecules through its PDZ domain. CXXC5 is one of the key molecules that interacts with Dvl and negatively regulates the Wnt/β-catenin pathway in osteoblast differentiation. Recently, the Dvl-CXXC5 interaction has been identified as an excellent target for osteoporosis treatment. Therefore, it is desirable to have detailed structural information for the Dvl-CXXC5 interaction. Although solution structures of the Dvl1 PDZ domain have been reported, a high-resolution crystal structure would provide detailed sidechain information that is essential for drug development. Here, we determined the first crystal structure of the Dvl-1 PDZ domain at a resolution of 1.76 Å, and compared it with its previously reported solution structure. The Dvl1 PDZ domain crystal belonged to the space group H32 with unit-cell parameters a = b = 72.837, c = 120.616, α = ß = 90.00, γ = 120.00. The crystal structure of Dvl1 PDZ shared its topology with the previously reported structure determined by nuclear magnetic resonance (NMR); however, the crystal structure was quite different from the solution structure in both the secondary structural region and the ligand-binding pocket. Molecular modeling based on NMR and X-ray crystallographic data yielded detailed information about the Dvl1/CXXC5 interaction, which will be useful for designing inhibitors.

  17. Dependence of magnetization on crystal fields and exchange interactions in magnetite

    Energy Technology Data Exchange (ETDEWEB)

    Ouaissa, Mohamed, E-mail: m.ouaissa@yahoo.fr [Laboratoire de Génie Physique et Environnement, Faculté des Sciences, Université Ibn Tofail, Campus Universitaire BP 133, Kénitra 14000 (Morocco); Benyoussef, Abdelilah [Laboratory of Magnetism and Physics of High Energy, Faculty of Science, Mohammed V-Agdal University, Rabat (Morocco); Abo, Gavin S. [Department of Electrical and Computer Engineering and MINT Center, The University of Alabama, Tuscaloosa, AL 35487 (United States); Ouaissa, Samia; Hafid, Mustapha [Laboratoire de Génie Physique et Environnement, Faculté des Sciences, Université Ibn Tofail, Campus Universitaire BP 133, Kénitra 14000 (Morocco); Belaiche, Mohammed [Laboratoire de Magnétisme, Matériaux Magnétiques, Microonde et Céramique, Ecole Normale Supérieure, Université Mohammed V-Agdal, B.P. 9235, Océan, Rabat (Morocco)

    2015-11-15

    In this work, we study the magnetization of magnetite (Fe{sub 3}O{sub 4}) with different exchange interactions and crystal fields using variational method based on the Bogoliubov inequality for the Gibbs free energy within the mean field theory. The magnetic behavior was investigated in the absence and presence of crystal fields. The investigations also revealed that the transition temperature depends on the crystal fields of the octahedral and tetrahedral sites. Magnetite exhibits ferrimagnetic phase with second order transition to paramagnetic phase at 850 K. This result is confirmed using the mean field theory within the Heisenberg model. Important factors that can affect the magnetic behavior of the system are exchange interactions and crystal field. Indeed, a new magnetic behavior was observed depending on these parameters. A first order phase transition from ferrimagnetic to ferromagnetic was found at low temperature, and a second order transition from ferromagnetic to paramagnetic was observed at high temperature. - Highlights: • Magnetization of magnetite versus temperature was studied by mean field theory. • The critical temperature of magnetite (Fe{sub 3}O{sub 4}) was approximately obtained. • Effect of sublattice crystal fields on the magnetization of Fe{sub 3}O{sub 4} was investigated.

  18. Depth of interaction resolution of LuAP and LYSO crystals

    CERN Document Server

    Trummer, J; Lecoq, P

    2009-01-01

    The Crystal Clear Collaboration (CCC) has built a prototype of a novel positron emission tomograph dedicated to functional breast imaging, the ClearPEM. One aim of the ClearPEM is to be able to depict small tumours with a diameter of 2–3 mm in the breast and axilla region. To achieve such a spatial resolution one needs to know the position of the photon interaction in the crystal—the depth of interaction (DOI) with a precision of a least 2 mm. The main component of the detector are 20 mm long LYSO crystals read out at both ends with avalanche photo diodes (APD). The method to determine the DOI in the ClearPEM is via light sharing between the two end faces of the crystal. In this work 20 mm long LuAP and LYSO crystals were used to study the spatial resolution of the DOI in the crystal. The influence of the surface state (polished and unpolished) and wrapping on the DOI resolution and the light yield were also investigated.

  19. Body-centered cubic dissipative crystal formation in a dispersive and diffractive optical parametric oscillator.

    Science.gov (United States)

    Tlidi, M; Pieroux, D; Mandel, Paul

    2003-09-15

    We show that coupling diffraction and chromatic dispersion lead to body-centered cubic and hexagonally packed cylinders of dissipative optical crystals in a degenerate optical parametric oscillator. The stabilization of these crystals is a direct consequence of the interaction between the modulational and the quasi-neutral modes.

  20. The diffraction of X-rays by close-packed polytypic crystals containing single stacking faults. Pt. 3. Measurements of diffraction effects caused by stacking faults in plate or film form samples

    Energy Technology Data Exchange (ETDEWEB)

    Michalski, E. [Military Acad. of Technol., Warsaw (Poland). Inst. of Tech. Phys.; Piecek, W. [Military Acad. of Technol., Warsaw (Poland). Inst. of Tech. Phys.; Demianiuk, M. [Military Acad. of Technol., Warsaw (Poland). Inst. of Tech. Phys.

    1995-07-01

    A theory that describes the diffraction effects from stacking faults in close-packed polytypic crystal structures was developed in two previous papers of this series. In this paper, attention is paid to the measurement of these diffraction effects for the cases where needle-shaped or rod-like specimens cannot be made from the given sample (e.g. thin films) or when single-crystal samples should not be destroyed for preparing such specimens. For this purpose, methods of measurement based on standard X-ray diffraction equipment such as oscillation or Weissenberg cameras and a powder diffraction diffractometer have been developed A complete description of the limitation of the area of the reciprocal lattice that can intersect the Ewald sphere has been provided. Examples of the results obtained by these methods are given. The diffractometer two-dimensional scanning method, which allows an undistorted reciprocal lattice to be recorded and higher precision and results more convenient for mathematical treatment than in photographic methods to be obtained, seems to be especially interesting. (orig.).

  1. Direct evidence of the molecular interaction propagation in the phase transition of liquid crystals

    Science.gov (United States)

    Katayama, Kenji; Sato, Takahiro; Kuwahara, Shota

    2016-09-01

    The molecular interaction sometimes propagates in a collective manner, reaching for a long distance on the order of millimeters. Such interactions have been well known in the field of strongly-correlated electron systems in a beautiful crystal interleaved by donor and acceptor layers, induced by photo-stimulus. The other examples can be found in liquid crystals (LCs), which could be found in many places in nature such as bio-membrane. Different from crystals, LCs features "softness", which enables it to be a curved structure such as a cell. In LCs, even a small molecular change would trigger the overall structural change by the propagation of the molecular interaction. Here we will show, for the first time, how long and how fast the molecular interaction propagates in LCs. The patterned phase transition was induced in a LC, causing the phase transition propagation in a controlled way and the propagation was measured with an time-resolved optical technique, called the transient grating. A LC sample doped with azobenzene was put into a thermally controlled LC cell. A grating pattern of a pulse light with 355 nm was impinged to the LC cell, and the light was absorbed by the dyes, releasing heat or photomechanical motion. We could observe the fringe spacing dependence on the phase transition response, which indicates that phase transition was delayed as the fringe spacing due to the delay by the phase transition propagation. This is the first direct evidence of the molecular interaction propagation of the LC molecules.

  2. Modelling of the crystallization front – particles interactions in ZnAl/(SiCp composites

    Directory of Open Access Journals (Sweden)

    M. Szucki

    2015-04-01

    Full Text Available The presented work focuses on solid particle interactions with the moving crystallization front during a solidification of the metal matrix composite. The current analyses were made for silicon carbide particles and ZnAl alloy with different additions of aluminium. It was found, that the chemical composition of the metal matrix influences the behaviour of SiC particles. At the same time calculations of the forces acting on a single particle near the crystallization front were performed. For each alloy type the critical conditions that determine whether particle will be absorbed or pushed, were specified.

  3. Phase transitions and exchange interactions in the SmCr3(BO3)4 crystal

    Science.gov (United States)

    Dobretsova, E. A.; Boldyrev, K. N.; Popova, M. N.; Gavrilkin, S. Yu.; Mukhin, A. A.; Ivanov, V. Yu.; Mal'tsev, V. V.; Leonyuk, N. I.; Malkin, B. Z.

    2016-12-01

    Spectroscopic investigation and specific heat and magnetic susceptibility measurements of SmCr3(BO3)4 crystals were performed. The spectra of the Sm3+ and Cr3+ ions in samarium chromium borate were calculated and parameters of the exchange interactions between the nearest chromium ions, chromium and samarium ions were determined. Three phase transitions were observed at the temperatures T1 = 7.8 ± 0.5 K, T2 = 6.7 ± 0.5 K, and T3 = 4.3 ± 0.2 K, their nature is discussed. The crystal structures with different space symmetry groups R32 and C2/c were found to coexist in a SmCr3(BO3)4 single crystal.

  4. Crystal structures and intermolecular interactions of two novel antioxidant triazolyl-benzimidazole compounds

    Energy Technology Data Exchange (ETDEWEB)

    Karayel, A., E-mail: matchlessjimmy@163.com, E-mail: yccaoh@hotmail.com; Özbey, S. [Hacettepe University, Physics Engineering Department (Turkey); Ayhan-Kılcıgil, G.; Kuş, C. [Ankara University, Department of Pharmaceutical Chemistry, Faculty of Pharmacy (Turkey)

    2015-12-15

    The crystal structures of 5-(2-(p-chlorophenylbenzimidazol-1-yl-methyl)-4-(3-fluorophenyl)-2, 4-dihydro-[1,2,4]-triazole-3-thione (G6C) and 5-(2-(p-chlorophenylbenzimidazol-1-yl-methyl)-4-(2-methylphenyl)-2, 4-dihydro-[1,2,4]-triazole-3-thione (G4C) have been determined by single-crystal X-ray diffraction. Benzimidazole ring systems in both molecules are planar. The triazole part is almost perpendicular to the phenyl and the benzimidazole parts of the molecules in order to avoid steric interactions between the rings. The crystal structures are stabilized by intermolecular hydrogen bonds between the amino group of the triazole and the nitrogen atom of benzimidazole of a neighboring molecule.

  5. Enhancing ubiquitin crystallization through surface-entropy reduction.

    Science.gov (United States)

    Loll, Patrick J; Xu, Peining; Schmidt, John T; Melideo, Scott L

    2014-10-01

    Ubiquitin has many attributes suitable for a crystallization chaperone, including high stability and ease of expression. However, ubiquitin contains a high surface density of lysine residues and the doctrine of surface-entropy reduction suggests that these lysines will resist participating in packing interactions and thereby impede crystallization. To assess the contributions of these residues to crystallization behavior, each of the seven lysines of ubiquitin was mutated to serine and the corresponding single-site mutant proteins were expressed and purified. The behavior of these seven mutants was then compared with that of the wild-type protein in a 384-condition crystallization screen. The likelihood of obtaining crystals varied by two orders of magnitude within this set of eight proteins. Some mutants crystallized much more readily than the wild type, while others crystallized less readily. X-ray crystal structures were determined for three readily crystallized variants: K11S, K33S and the K11S/K63S double mutant. These structures revealed that the mutant serine residues can directly promote crystallization by participating in favorable packing interactions; the mutations can also exert permissive effects, wherein crystallization appears to be driven by removal of the lysine rather than by addition of a serine. Presumably, such permissive effects reflect the elimination of steric and electrostatic barriers to crystallization.

  6. Atom–atom interactions around the band edge of a photonic crystal waveguide

    Science.gov (United States)

    Hood, Jonathan D.; Goban, Akihisa; Asenjo-Garcia, Ana; Lu, Mingwu; Yu, Su-Peng; Chang, Darrick E.; Kimble, H. J.

    2016-01-01

    Tailoring the interactions between quantum emitters and single photons constitutes one of the cornerstones of quantum optics. Coupling a quantum emitter to the band edge of a photonic crystal waveguide (PCW) provides a unique platform for tuning these interactions. In particular, the cross-over from propagating fields E(x)∝e±ikxx outside the bandgap to localized fields E(x)∝e−κx|x| within the bandgap should be accompanied by a transition from largely dissipative atom–atom interactions to a regime where dispersive atom–atom interactions are dominant. Here, we experimentally observe this transition by shifting the band edge frequency of the PCW relative to the D1 line of atomic cesium for N¯=3.0±0.5 atoms trapped along the PCW. Our results are the initial demonstration of this paradigm for coherent atom–atom interactions with low dissipation into the guided mode. PMID:27582467

  7. Atom-atom interactions around the band edge of a photonic crystal waveguide.

    Science.gov (United States)

    Hood, Jonathan D; Goban, Akihisa; Asenjo-Garcia, Ana; Lu, Mingwu; Yu, Su-Peng; Chang, Darrick E; Kimble, H J

    2016-09-20

    Tailoring the interactions between quantum emitters and single photons constitutes one of the cornerstones of quantum optics. Coupling a quantum emitter to the band edge of a photonic crystal waveguide (PCW) provides a unique platform for tuning these interactions. In particular, the cross-over from propagating fields [Formula: see text] outside the bandgap to localized fields [Formula: see text] within the bandgap should be accompanied by a transition from largely dissipative atom-atom interactions to a regime where dispersive atom-atom interactions are dominant. Here, we experimentally observe this transition by shifting the band edge frequency of the PCW relative to the [Formula: see text] line of atomic cesium for [Formula: see text] atoms trapped along the PCW. Our results are the initial demonstration of this paradigm for coherent atom-atom interactions with low dissipation into the guided mode.

  8. Vibronic interaction in crystals with the Jahn-Teller centers in the elementary energy bands concept

    Directory of Open Access Journals (Sweden)

    D.M. Bercha

    2015-09-01

    Full Text Available The order-disorder type phase transition caused by the vibronic interaction (collective Jahn-Teller effect in a monoclinic CuInP2S6 crystal is analyzed. For this purpose, a trigonal protostructure model of CuInP2S6 is created, through a slight change in the crystal lattice parameters of the CuInP2S6 paraelectric phase. In parallel to the group-theoretical analysis, the DFT-based ab initio band structure calculations of the CuInP2S6 protostructure, para-, and ferriphases are performed. Using the elementary energy bands concept, a part of the band structure from the vicinity of the forbidden energy gap, which is created by the d-electron states of copper has been related with a certain Wyckoff position where the Jahn-Teller's centers are localized. A construction procedure of the vibronic potential energy matrix is generalized for the case of crystal using the elementary energy bands concept and the group theoretical method of invariants. The procedure is illustrated by the creation of the adiabatic potentials of the Γ5-Γ5 vibronic coupling for the protostructure and paraphase of the CuInP2S6 crystal. A structure of the obtained adiabatic potentials is analyzed, followed by conclusions on their transformation under a phase transition and the discussion on the possibility for the spontaneous polarization to arise in this crystal.

  9. Structural variation and uniformity among tetraloop-receptor interactions and other loop-helix interactions in RNA crystal structures.

    Directory of Open Access Journals (Sweden)

    Li Wu

    Full Text Available Tetraloop-receptor interactions are prevalent structural units in RNAs, and include the GAAA/11-nt and GNRA-minor groove interactions. In this study, we have compiled a set of 78 nonredundant loop-helix interactions from X-ray crystal structures, and examined them for the extent of their sequence and structural variation. Of the 78 interactions in the set, only four were classical GAAA/11-nt motifs, while over half (48 were GNRA-minor groove interactions. The GNRA-minor groove interactions were not a homogeneous set, but were divided into five subclasses. The most predominant subclass is characterized by two triple base pair interactions in the minor groove, flanked by two ribose zipper contacts. This geometry may be considered the "standard" GNRA-minor groove interaction, while the other four subclasses are alternative ways to form interfaces between a minor groove and tetraloop. The remaining 26 structures in the set of 78 have loops interacting with mostly idiosyncratic receptors. Among the entire set, a number of sequence-structure correlations can be identified, which may be used as initial hypotheses in predicting three-dimensional structures from primary sequences. Conversely, other sequence patterns are not predictive; for example, GAAA loop sequences and GG/CC receptors bind to each other with three distinct geometries. Finally, we observe an example of structural evolution in group II introns, in which loop-receptor motifs are substituted for each other while maintaining the larger three-dimensional geometry. Overall, the study gives a more complete view of RNA loop-helix interactions that exist in nature.

  10. Electron-phonon interaction in three-, two- and one-dimensional ternary mixed crystals

    Science.gov (United States)

    Hou, Junhua; Fan, Yunpeng

    2016-05-01

    The electron-phonon (e-p) interaction in three-dimensional (3D), two-dimensional (2D) and one-dimensional (1D) ternary mixed crystals is studied. The e-p interaction Hamiltonians including the unit cell volume variation in ternary mixed crystals are obtained by using the modified random-element-isodisplacement model and Born-Huang method. The polaronic self-trapping energy and renormalized effective mass of GaAsxSb1-x, GaPxAs1-x and GaPxSb1-x compounds are numerically calculated. It is confirmed theoretically that the nonlinear variation of the self-trapping energy and effective mass with the composition is essential and the unit cell volume effects cannot be neglected except the weak e-p coupling. The dimensional effect cannot also be ignored.

  11. Engineering chiral light--matter interaction in photonic crystal waveguides with slow light

    CERN Document Server

    Mahmoodian, Sahand; Söllner, Immo; Stobbe, Søren; Lodahl, Peter

    2016-01-01

    We design photonic crystal waveguides with efficient chiral light--matter interfaces that can be integrated with solid-state quantum emitters. By using glide-plane-symmetric waveguides, we show that chiral light-matter interaction can exist even in the presence of slow light with slow-down factors of up to $100$ and therefore the light--matter interaction exhibits both strong Purcell enhancement and chirality. This allows for near-unity directional $\\beta$-factors for a range of emitter positions and frequencies. Additionally, we design an efficient mode adapter to couple light from a standard nanobeam waveguide to the glide-plane symmetric photonic crystal waveguide. Our work sets the stage for performing future experiments on a solid-state platform.

  12. Study of 3-D stress development in parent and twin pairs of a hexagonal close-packed polycrystal: Part II - Crystal plasticity finite element modeling

    DEFF Research Database (Denmark)

    Abdolvand, Hamidreza; Majkut, Marta; Oddershede, Jette

    2015-01-01

    -of-mass positions and volumes as measured by three-dimensional X-ray diffraction (3DXRD) microscopy. The constructed microstructure is meshed with different element densities and for different numbers of grains. Then a selected group of twin and parent pairs are studied. It is shown that the measured average stress...... each grain, stresses in the parent and twin are quite different if they are plotted in the global coordinate system. However, if the stress tensor is rotated into the local coordinate system of the twin habit plane, all the stress components averaged over the presented population are close, except......Stress heterogeneity within each individual grain of polycrystalline Zircaloy-2 is studied using a crystal plasticity finite element (CPFE) model. For this purpose, the weighted Voronoi tessellation method is used to construct 3D geometries of more than 2600 grains based on their center...

  13. Synthesis of 2,6-diaminopyridine substituted -oxoketene ,-acetals: Crystal structure and hydrogen bonding interactions

    Indian Academy of Sciences (India)

    Okram Mukherjee Singh; Laishram Ronibala Devi; Neeladri Das

    2013-09-01

    Polyaza -oxoketene ,-acetals can exist as either enamino or imino tautomeric forms. Based on the spectroscopic data and structural analysis of one of the ,-acetals, the stereochemistry was unambiguously assigned as an all--configuration. The crystal structure confirms the enamino structure and shows extensive use of C-H…X (X = N, O, and S) weak hydrogen bonding interactions, thereby generating a 3-dimensional network in solid state.

  14. Electronically configured battery pack

    Energy Technology Data Exchange (ETDEWEB)

    Kemper, D.

    1997-03-01

    Battery packs for portable equipment must sometimes accommodate conflicting requirements to meet application needs. An electronically configurable battery pack was developed to support two highly different operating modes, one requiring very low power consumption at a low voltage and the other requiring high power consumption at a higher voltage. The configurable battery pack optimizes the lifetime and performance of the system by making the best use of all available energy thus enabling the system to meet its goals of operation, volume, and lifetime. This paper describes the cell chemistry chosen, the battery pack electronics, and tradeoffs made during the evolution of its design.

  15. Use of Pom Pons to Illustrate Cubic Crystal Structures.

    Science.gov (United States)

    Cady, Susan G.

    1997-01-01

    Describes a method that uses olefin pom pons to illustrate cubic crystal structure. Facilitates hands-on examination of different packing arrangements such as hexagonal close-packed and cubic close-packed structures. (JRH)

  16. TLC Pack Unpacked

    Science.gov (United States)

    Oberhofer, Margret; Colpaert, Jozef

    2015-01-01

    TLC Pack stands for Teaching Languages to Caregivers and is a course designed to support migrants working or hoping to work in the caregiving sector. The TLC Pack resources range from A2 to B2 level of the Common European Framework of Reference for Languages (CEFR), and will be made available online in the six project languages: Dutch, English,…

  17. Helix 3 acts as a conformational hinge in Class A GPCR activation: An analysis of interhelical interaction energies in crystal structures.

    Science.gov (United States)

    Lans, Isaias; Dalton, James A R; Giraldo, Jesús

    2015-12-01

    A collection of crystal structures of rhodopsin, β2-adrenergic and adenosine A2A receptors in active, intermediate and inactive states were selected for structural and energetic analyses to identify the changes involved in the activation/deactivation of Class A GPCRs. A set of helix interactions exclusive to either inactive or active/intermediate states were identified. The analysis of these interactions distinguished some local conformational changes involved in receptor activation, in particular, a packing between the intracellular domains of transmembrane helices H3 and H7 and a separation between those of H2 and H6. Also, differential movements of the extracellular and intracellular domains of these helices are apparent. Moreover, a segment of residues in helix H3, including residues L/I3.40 to L3.43, is identified as a key component of the activation mechanism, acting as a conformational hinge between extracellular and intracellular regions. Remarkably, the influence on the activation process of some glutamic and aspartic acidic residues and, as a consequence, the influence of variations on local pH is highlighted. Structural hypotheses that arose from the analysis of rhodopsin, β2-adrenergic and adenosine A2A receptors were tested on the active and inactive M2 muscarinic acetylcholine receptor structures and further discussed in the context of the new mechanistic insights provided by the recently determined active and inactive crystal structures of the μ-opioid receptor. Overall, the structural and energetic analyses of the interhelical interactions present in this collection of Class A GPCRs suggests the existence of a common general activation mechanism featuring a chemical space useful for drug discovery exploration.

  18. Correlation between crystallization behaviour and interfacial interactions in plasticized PLA/POSS nanocomposites

    Science.gov (United States)

    Kodal, Mehmet; Şirin, Hümeyra; Özkoç, Güralp

    2016-03-01

    In this study, the correlation between crystallization behavior and surface chemistry of polyhedral oligomeric silsesquioxanes (POSS) for plasticized poly(lactic acid) (PLA)/POSS nanocomposites was investigated. Four different kinds of POSS particles having different chemical structures were used. Poly(ethylene glycol) (PEG, 8000 g/mol) was utilized as the plasticiser. The nanocomposites were melt-compounded in an Xplore Instruments 15 cc twin screw microcompounder at 180°C barrel temperature and 100 rpm screw speed. Non-isothermal crystallization behaviour of PLA/PEG/POSS nanocomposites were evaluated from common kinetic models such as Avrami and Avrami-Ozawa and Kissinger by using the thermal data obtained from differantial scanning calorimetry (DSC). A polarized optical microscope (POM) equipped with a hot-stage was used to examine the morphology during the crystal growth. In order to investigate the interfacial interactions between POSS particles and plasticized PLA, thermodynamic work of adhesion approach was adopted using the experimentally determined surface energies. A strong correlation was obtained between interfacial chemistry and the nucleation rate in plasticized PLA/POSS nanocomposites. It was found that the polar interactions were the dominating factor which determines the nucleation activity of the POSS particles.

  19. Dynamic interaction between suspended particles and defects in a nematic liquid crystal.

    Science.gov (United States)

    Grollau, S; Abbott, N L; de Pablo, J J

    2003-05-01

    Insertion of spherical particles into a uniform nematic liquid crystal gives rise to the formation of topological defects. In the present work, we investigate how a spherical particle accompanied by its topological defects interacts with neighboring disclination lines. We perform two- and three-dimensional dynamic simulations to analyze the effect of a particle on the annihilation process of two disclination lines. The dynamics of the liquid crystal is described by a time-dependent evolution equation on the symmetric traceless order parameter that includes some of the salient features of liquid crystalline materials: excluded volume effects, or equivalently, short-range order elasticity and long-range order elasticity. At the surface of the particle, the liquid crystal is assumed to exhibit strong homeotropic anchoring. The particle is located between two disclination lines of topological charges +1/2 and -1/2. Two-dimensional simulations indicate that the topological defects bound to the particle mediate an interaction between the two disclination lines which increases the attraction between them. This result is confirmed by three-dimensional simulations that provide a complete description of the director field and of the order parameter around the particle. These simulations indicate that a spherical particle between two disclination lines can be surrounded by a Saturn ring, and suggest that the dynamic behavior of disclination lines could be used to report the structure of a defect around the particle.

  20. Analyses of crystal field and exchange interaction of Dy3Ga5O12 under extreme conditions

    Institute of Scientific and Technical Information of China (English)

    Wang Wei; Qi Xin; Yue Yuan

    2011-01-01

    This paper theoretically investigates the effects of crystal field and exchange interaction field on magnetic properties in dysprosium gallium garnet under extreme conditions (low temperatures and high magnetic fields) based on quantum theory. Here, five sets of crystal field parameters are discussed and compared. It demonstrates that, only considering the crystal field effect, the experiments can not be successfully explained. Thus, referring to the molecular field theory,an effective exchange field associated with the Dy-Dy exchange interaction is further taken into account. Under special consideration of crystal field and the exchange interaction field, it obtains an excellent agreement between the theoretical results and experiments, and further confirms that the exchange interaction field between rare-earth ions has great importance to magnetic properties in paramagnetic rare-earth gallium garnets.

  1. Crystal structure of pseudoguainolide

    Directory of Open Access Journals (Sweden)

    Noureddine Beghidja

    2015-03-01

    Full Text Available The lactone ring in the title molecule, C15H22O3 (systematic name: 3,4a,8-trimethyldodecahydroazuleno[6,5-b]furan-2,5-dione, assumes an envelope conformation with the methine C atom adjacent to the the methine C atom carrying the methyl substituent being the flap atom. The other five-membered ring adopts a twisted conformation with the twist being about the methine–methylene C—C bond. The seven-membered ring is based on a twisted boat conformation. No specific interactions are noted in the the crystal packing.

  2. Probing the interaction between nanoparticles and lipid membranes by quartz crystal microbalance with dissipation monitoring

    Science.gov (United States)

    Yousefi, Nariman; Tufenkji, Nathalie

    2016-12-01

    There is increasing interest in using quartz crystal microbalance with dissipation monitoring (QCM-D) to investigate the interaction of nanoparticles (NPs) with model surfaces. The high sensitivity, ease of use and the ability to monitor interactions in real-time has made it a popular technique for colloid chemists, biologists, bioengineers and biophysicists. QCM-D has been recently used to probe the interaction of NPs with supported lipid bilayers (SLBs) as model cell membranes. The interaction of NPs with SLBs is highly influenced by the quality of the lipid bilayers. Unlike many surface sensitive techniques, using QCM-D, the quality of SLBs can be assessed in real-time, hence QCM-D studies on SLB-NP interactions are less prone to the artefacts arising from bilayers that are not well formed. The ease of use and commercial availability of a wide range of sensor surfaces also have made QCM-D a versatile tool for studying NP interactions with lipid bilayers. In this review, we summarize the state-of-the-art on QCM-D based techniques for probing the interactions of NPs with lipid bilayers.

  3. Direct calculation of the lattice Green function with arbitrary interactions for general crystals.

    Science.gov (United States)

    Yasi, Joseph A; Trinkle, Dallas R

    2012-06-01

    Efficient computation of lattice defect geometries such as point defects, dislocations, disconnections, grain boundaries, interfaces, and free surfaces requires accurate coupling of displacements near the defect to the long-range elastic strain. Flexible boundary condition methods embed a defect in infinite harmonic bulk through the lattice Green function. We demonstrate an efficient and accurate calculation of the lattice Green function from the force-constant matrix for general crystals with an arbitrary basis by extending a method for Bravais lattices. New terms appear due to the presence of optical modes and the possible loss of inversion symmetry. By separately treating poles and discontinuities in reciprocal space, numerical accuracy is controlled at all distances. We compute the lattice Green function for a two-dimensional model with broken symmetry to elucidate the role of different coupling terms. The algorithm is generally applicable in two and three dimensions to crystals with arbitrary number of atoms in the unit cell, symmetry, and interactions.

  4. Designing spin-spin interactions with one and two dimensional ion crystals in planar micro traps

    CERN Document Server

    Welzel, J; Abarbanel, C; Wineman-Fisher, V; Wunderlich, C; Folman, R; Schmidt-Kaler, F

    2011-01-01

    We discuss the experimental feasibility of quantum simulation with trapped ion crystals, using magnetic field gradients. We describe a micro structured planar ion trap, which contains a central wire loop generating a strong magnetic gradient of about 20 T/m in an ion crystal held about 160 \\mu m above the surface. On the theoretical side, we extend a proposal about spin-spin interactions via magnetic gradient induced coupling (MAGIC) [Johanning, et al, J. Phys. B: At. Mol. Opt. Phys. 42 (2009) 154009]. We describe aspects where planar ion traps promise novel physics: Spin-spin coupling strengths of transversal eigenmodes exhibit significant advantages over the coupling schemes in longitudinal direction that have been previously investigated. With a chip device and a magnetic field coil with small inductance, a resonant enhancement of magnetic spin forces through the application of alternating magnetic field gradients is proposed. Such resonantly enhanced spin-spin coupling may be used, for instance, to create...

  5. Non-Covalent Interactions in the Crystal Structure of Methyl 4-Hydroxy-3-Nitrobenzoate

    Directory of Open Access Journals (Sweden)

    Jim Simpson

    2012-06-01

    Full Text Available Methyl 4-hydroxy-3-nitrobenzoate, (I, C8H7NO5, crystallizes with two unique molecules, A and B, in the asymmetric unit of the triclinic unit cell. The space group was assigned as P-1, with lattice parameters a = 0.72831(15, b = 1.0522(2, c = 1.1410(2 nm, α = 83.38(3, β = 80.83(3, γ = 82.02(3°, Z = 4, V = 0.8510(3 nm3, Mr = 197.15, Dc = 1.539 g/m3, µ= 0.131 mm−1, F(000 = 408, R = 0.1002 and wR = 0.2519. In the crystal structure, 12 hydrogen bonding and two p-stacking interactions link the molecules into infinite stacked sheets parallel to (101.

  6. Propagation and interaction of cos-Gaussian beams in photorefractive crystals

    Science.gov (United States)

    Jiang, Qichang; Su, Yanli; Nie, Hexian; Ma, Ziwei; Li, Yonghong

    2017-07-01

    Investigate numerically the propagation and interaction of cos-Gaussian beams in a biased photorefractive crystal by the finite difference method. The results show that the single cos-Gaussian beam can evolve into Y-type breathing solitons when the self-focusing nonlinearity is small, and the soliton properties can be controlled by adjusting the nonlinear parameter or cos modulation parameter. The distance between two components of Y-type breathing solitons will decrease with increasing the nonlinear parameter or decreasing the cos modulation parameter. The breathing soliton with two weak sidebands can form when the self-focusing nonlinearity is big. Moreover, two internal components of two cos-Gaussian beams have obvious interaction but two outside components have tiny interaction.

  7. Hyperfine and crystal field interactions in multiferroic HoCrO3

    Science.gov (United States)

    Kumar, C. M. N.; Xiao, Y.; Nair, H. S.; Voigt, J.; Schmitz, B.; Chatterji, T.; Jalarvo, N. H.; Brückel, Th

    2016-11-01

    We report a comprehensive specific heat and inelastic neutron scattering study to explore the possible origin of multiferroicity in HoCrO3. We have performed specific heat measurements in the temperature range 100 mK-290 K and inelastic neutron scattering measurements were performed in the temperature range 1.5-200 K. From the specific heat data we determined hyperfine splitting at 22.5(2) μeV and crystal field transitions at 1.379(5) meV, 10.37(4) meV, 15.49(9) meV and 23.44(9) meV, indicating the existence of strong hyperfine and crystal field interactions in HoCrO3. Further, an effective hyperfine field is determined to be 600(3) T. The quasielastic scattering observed in the inelastic scattering data and a large linear term γ =6.3(8) mJ mol-1  K-2 in the specific heat is attributed to the presence of short range exchange interactions, which is understood to be contributing to the observed ferroelectricity. Further the nuclear and magnetic entropies were computed to be, ˜17.2 Jmol-1 K-1 and  ˜34 Jmol-1 K-1, respectively. The entropy values are in excellent agreement with the limiting theoretical values. An anomaly is observed in the peak position of the temperature dependent crystal field spectra around 60 K, at the same temperature an anomaly in the pyroelectric current is reported. From this we could elucidate a direct correlation between the crystal electric field excitations of Ho3+ and ferroelectricity in HoCrO3. Our present study, along with recent reports, confirm that HoCrO3, and RCrO3 (R  =  rare earth) in general, possess more than one driving force for the ferroelectricity and multiferroicity.

  8. Elastic interactions and manipulation of wire-shaped inclusions in nematic liquid crystals

    Science.gov (United States)

    Lapointe, Clayton P.

    Anisotropic particles suspended in a nematic liquid crystal disturb the alignment of the liquid crystal molecules and experience small forces and torques mediated by the elasticity of the fluid. These elastic interactions depend upon the orientation of the particle relative to the alignment of the liquid crystal as well as the nature of the molecular-scale alignment at the surface of the particle. In this thesis, I present the results of video microscopy studies on elastic interactions on ferromagnetic nanowires suspended in the nematic liquid crystal 4-pentyl-4-cyanobiphenyl (5CB). In the first part, I describe measurements that characterize the orientation-dependent elastic torque on a nanowire with longitudinal anchoring in uniformly aligned 5CB, its temperature dependence, as well as the elastic repulsion of a nanowire from a flat wall. These measurements were found to be quantitatively consistent with theoretical predictions based on the elastic properties of 5CB. In the second part of this thesis, I demonstrate that distorting the liquid crystal from a state of uniform alignment results in converting the elastic torque on a nanowire into an orientation-dependant translational force that can be utilized to reversibly manipulate the positions of isolated nanowires as well as to assemble suspensions of them into pre-designed arrays on a substrate. First, I describe measurements of an orientation-dependent levitating force on a nanowire in a twisted nematic cell. This force can be used to position nanowires to pre-determined heights above the bottom substrate by controlling their orientation with an external magnetic field. I then describe a series of experiments in which in a liquid crystal cell with a pattern of micron-scale stripe domains was used to drive nanowires held at a fixed orientation with external magnetic fields selectively into the middle of the stripe domains. In the last part of this thesis, I discuss video microscopy experiments to probe the

  9. Graphitic packing removal tool

    Energy Technology Data Exchange (ETDEWEB)

    Meyers, K.E.; Kolsun, G.J.

    1996-12-31

    Graphitic packing removal tools are described for removal of the seal rings in one piece from valves and pumps. The packing removal tool has a cylindrical base ring the same size as the packing ring with a surface finish, perforations, knurling or threads for adhesion to the seal ring. Elongated leg shanks are mounted axially along the circumferential center. A slit or slits permit insertion around shafts. A removal tool follower stabilizes the upper portion of the legs to allow a spanner wrench to be used for insertion and removal.

  10. Optimal Packed String Matching

    DEFF Research Database (Denmark)

    Ben-Kiki, Oren; Bille, Philip; Breslauer, Dany

    2011-01-01

    In the packed string matching problem, each machine word accommodates – characters, thus an n-character text occupies n/– memory words. We extend the Crochemore-Perrin constantspace O(n)-time string matching algorithm to run in optimal O(n/–) time and even in real-time, achieving a factor – speedup...... over traditional algorithms that examine each character individually. Our solution can be efficiently implemented, unlike prior theoretical packed string matching work. We adapt the standard RAM model and only use its AC0 instructions (i.e., no multiplication) plus two specialized AC0 packed string...

  11. Molecular Dynamics Study of Interaction between Acrylamide Copolymers and Alumina Crystal

    Institute of Scientific and Technical Information of China (English)

    Feng-he Wang; Feng-yun Wang; Xue-dong Gong

    2012-01-01

    Four acrylamide polymer flocculants,anionic polyacrylamide P(AA-co-AM),cationic polyacrylamide P(DMB-co-AM),nonionic polyacrylamide P(AM),and hydrophobical polyacrylamide P(OA-co-AM) have been prepared by copolymerizing with acrylic acid,cationic monomer dimethylethyl (acryloxyethyl) ammonium bromide (DMB) and hydrophobical monomer octadecyl acrylate with acrylamide.The interactions between the flocculants with the (012) surface of alumina crystal (Al2O3) have been simulated by molecular dynamics method.All the polymers can bind tightly with Al2O3 crystal,the interaction between the O of polymers and Al of the (012) surface of Al2O3 is significantly strong.The order of binding energy is as follows:P(DMB-co-AM)>P(OA-co-AM)>P(AA-co-AM)>P(AM),implying a better flocculation performance of P(DMB-co-AM) than the others.Analysis indicates that binding energy is mainly determined by Coulomb interaction.Bonds are found between the O atoms of the polymers and the AI atoms of Al2O3.The polymers' structures deform when they combine with Al2O3 crystal,but the deformation energies are low and far less than non-bonding energies.Flocculation experiments in suspension medium of l%Kaolin show a transmittancy of 90.8% for 6 mg/L P(DMB-co-AM) and 73.0% for P(AM).The sequence of flocculation performance of four polymers is P(DMB-co-AM)>P(OA-co-AM)>P(AA-co-AM)>P(AM),which is in excellent agreement with the simulation results of binding energy.

  12. Tetrel Bonds in Infinite Molecular Chains by Electronic Structure Theory and Their Role for Crystal Stabilization.

    Science.gov (United States)

    George, Janine; Dronskowski, Richard

    2017-02-16

    Intermolecular bonds play a crucial role in the rational design of crystal structures, dubbed crystal engineering. The relatively new term tetrel bonds (TBs) describes a long-known type of such interactions presently in the focus of quantum chemical cluster calculations. Here, we energetically explore the strengths and cooperativity of these interactions in infinite chains, a possible arrangement of such tetrel bonds in extended crystals, by periodic density functional theory. In the chains, the TBs are amplified due to cooperativity by up to 60%. Moreover, we computationally take apart crystals stabilized by infinite tetrel-bonded chains and assess the importance of the TBs for the crystal stabilization. Tetrel bonds can amount to 70% of the overall interaction energy within some crystals, and they can also be energetically decisive for the taken crystal structure; their individual strengths also compete with the collective packing within the crystal structures.

  13. The effect of pressure on open-framework silicates: elastic behaviour and crystal-fluid interaction

    Science.gov (United States)

    Gatta, G. D.; Lotti, P.; Tabacchi, G.

    2017-08-01

    The elastic behaviour and the structural evolution of microporous materials compressed hydrostatically in a pressure-transmitting fluid are drastically affected by the potential crystal-fluid interaction, with a penetration of new molecules through the zeolitic cavities in response to applied pressure. In this manuscript, the principal mechanisms that govern the P-behaviour of zeolites with and without crystal-fluid interaction are described, on the basis of previous experimental findings and computational modelling studies. When no crystal-fluid interaction occurs, the effects of pressure are mainly accommodated by tilting of (quasi-rigid) tetrahedra around O atoms that behave as hinges. Tilting of tetrahedra is the dominant mechanism at low-mid P-regime, whereas distortion and compression of tetrahedra represent the mechanisms which usually dominate the mid-high P regime. One of the most common deformation mechanisms in zeolitic framework is the increase of channels ellipticity. The deformation mechanisms are dictated by the topological configuration of the tetrahedral framework; however, the compressibility of the cavities is controlled by the nature and bonding configuration of the ionic and molecular content, resulting in different unit-cell volume compressibility in isotypic structures. The experimental results pertaining to compression in "penetrating" fluids, and thus with crystal-fluid interaction, showed that not all the zeolites experience a P-induced intrusion of new monoatomic species or molecules from the P-transmitting fluids. For example, zeolites with well-stuffed channels at room conditions (e.g. natural zeolites) tend to hinder the penetration of new species through the zeolitic cavities. Several variables govern the sorption phenomena at high pressure, among those: the "free diameters" of the framework cavities, the chemical nature and the configuration of the extra-framework population, the partial pressure of the penetrating molecule in the

  14. Investigating Intermolecular Interactions in Crystalline Aspirin Using CDFT

    OpenAIRE

    Turner, Nicholas; Li, Tonglei; Zhang, Mingtao

    2013-01-01

    Drugs today are widely administered in their crystalline form, namely via tablets and capsules. The crystal structure of a drug molecule affects important drug qualities such as solubility, bioavailability, shelf life, and compaction properties. In order to form a basis for crystal structure prediction, it is necessary to first understand how intermolecular interactions cause molecules to pack in certain ways. Being able to predict and perhaps even control a drug molecule’s crystal structure ...

  15. Cocrystals of kaempferol, quercetin and myricetin with 4,4‧-bipyridine: Crystal structures, analyses of intermolecular interactions and antibacterial properties

    Science.gov (United States)

    Zhang, Yu-Nan; Yin, He-Mei; Zhang, Yu; Zhang, Da-Jun; Su, Xin; Kuang, Hai-Xue

    2017-02-01

    With an aim to explore the interactions of Osbnd H⋯N between hydroxyl moiety of the flavonoids and the pyridyl ring of N-containing aromatic amines, three flavonols with varying B-ring-hydroxyl groups (kaempferol, quercetin, and myricetin) were selected to combine with 4,4‧-bipyridine. As a result, three new cocrystals of flavonols were obtained with a solution evaporation approach. These three cocrystals were characterized by single crystal X-ray diffraction, XPRD, IR and NMR methods. The resulting cocrystals were kaempferol: 4,4‧-bipyridine (2:1) (KAE·BPY·2H2O), quercetin: 4,4‧-bipyridine (1:1.5) (QUE·BPY), and myricetin: 4,4‧-bipyridine (1:2) (MYR·BPY·H2O). Structural analyses show that an array of hydrogen bonds and π-π stacking interactions interconnect the molecules to form a two-dimensional (2D) supramolecular layer in KAE·BPY·2H2O, QUE·BPY, and MYR·BPY·H2O. In the three cocrystals, they present as three different synthons-ⅠR88(58), Ⅳ R44(42) and, Ⅶ R66(29) with 4,4‧-bipyridine, respectively-which may yield a strategy for constructing the supramolecule. Cocrystals of flavonols combined with N-containing aromatic amines, 7-OH, B-ring-hydroxyl number and/or the location of the flavonols to play a significant part in extending the dimensionality of the cocrystals. The resulting motif formation and crystal packing in these flavonols cocrystals has combined with N-containing aromatic amines. Additionally, the antibacterial properties of the three cocrystals against Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli) have been investigated.

  16. New Limits on Interactions between Weakly Interacting Massive Particles and Nucleons Obtained with CsI(Tl) Crystal Detectors

    CERN Document Server

    Kim, S C; Choi, J H; Kang, W G; Kim, B H; Kim, H J; Kim, K W; Kim, S K; Kim, Y D; Lee, J; Lee, J H; Lee, J K; Lee, M J; Lee, S J; Li, J; Li, J; Li, X R; Li, Y J; Myung, S S; Olsen, S L; Ryu, S; Seong, I S; So, J H; Yue, Q

    2012-01-01

    New limits are presented on the cross section for Weakly Interacting Massive Particle (WIMP) nucleon scattering in the KIMS CsI(T) detector array at the Yangyang Underground Laboratory. The exposure used for these results is 24524.3 kg\\cdotdays. Nuclei recoiling from WIMP interactions are identified by a pulse shape discrimination method. A low energy background due to alpha emitters on the crystal surfaces is identified and taken into account in the analysis. The detected numbers of nuclear recoils are consistent with zero and 90% confidence level upper limits on the WIMP interaction rates are set for electron equivalent energies from 3 keV to 11 keV. The 90% upper limit of NR event rate for 3.6-5.8 keV corresponding to 2-4 keV in NaI(T) is 0.0098 counts/kg/keV/day which is below the annual modulation amplitude reported by DAMA. This is incompatible with interpretations that enhance the modulation amplitude such as inelastic dark matter models. We establish the most stringent cross section limits on spin-dep...

  17. Crystal engineering: A brief overview

    Indian Academy of Sciences (India)

    Gautam R Desiraju

    2010-09-01

    Crystal structures of organic and metal-organic compounds have been determined in enormous numbers over the past century, and at the time of writing this review, the Cambridge Structural Database has just crossed the half million mark. The possibility of designing a particular crystal packing is, however, of more recent origin and the subject of crystal engineering has addressed this possibility, more or less systematically, during the past 30 years. Crystal engineering demands a detailed and thorough knowledge of intermolecular interactions, which act as the supramolecular glue that binds molecules into crystals. It also requires systematic strategies for the design of a crystal, the architectural blueprint as it were. Finally, this enterprise needs to be geared towards a useful property in that the crystal that is being designed is a functional one. All these features of the subject are directly or indirectly connected with the fact that there is a very large database of known crystal structures that is available to the crystal engineer. This review attempts to briefly survey the current scenario in this expanding subject.

  18. Evaluation of the exchange interaction and crystal fields in a prototype Dy2 SMM

    Science.gov (United States)

    Zhang, Qing; Sarachik, Myriam; Baker, Michael; Chen, Yizhang; Kent, Andrew; Pineda, Eufemio; McInnes, Eric

    In order to gain an understanding of the INS and magnetization data obtained for Dy2, the simplest member of a newly synthesized family of dysprosium-based molecular magnets, we report on calculations of the magnetic behavior of a Dy2 cluster with the formula [hqH2][Dy2(hq)4(NO3)3].MeOH. The molecular complex contains one high symmetry Dy(III) ion and one low symmetry Dy(III) ion. Our calculations suggest that exchange coupling between the two ions controls the behavior of the magnetization at low temperature, while the crystal field of the low symmetry Dy(III) ion controls the behavior at higher temperature. A point charge electrostatic model, based on crystallographic coordinates, provides a starting point for the determination of the crystal field. Parameters in these calculations are adjusted to provide best fits to inelastic neutron scattering data (INS) and low temperature magnetometry: the INS measurements access crystal field energies and low temperature magnetization probes the Dy-Dy exchange interaction. Work supported by ARO W911NF-13-1-1025 (CCNY) and NSF-DMR-1309202 (NYU).

  19. The Role of Many-Body Dispersion Interactions in Molecular Crystal Polymorphism

    Science.gov (United States)

    Leiserowitz, Leslie; Marom, Noa; Distasio, Robert A., Jr.; Atalla, Viktor; Levchenko, Sergey; Kapishnikov, Sergey; Chelikowsky, James R.; Tkatchenko, Alexandre

    2012-02-01

    Molecular crystals often have several polymorphs that are close in energy (few meV per molecule), but possess very different physical and chemical properties. Treating polymorphism from first principles has been a long standing problem because conventional density-functional theory (DFT) lacks a proper description of long-range dispersion interactions that govern the structure and energetics of molecular crystals. Here we assess the effect of the many-body dispersion (MBD) energy on the structure and relative energies of the polymorphs of benchmark molecular crystals: glycine, alanine, and para-diiodobenzene. This is accomplished by using the recently developed first-principles DFT+MBD method [A. Tkatchenko, R.A. DiStasio Jr., R. Car, M. Scheffler, submitted], based on the earlier Tkatchenko-Scheffler (TS) dispersion correction [PRL 102, 073005 (2009)]. We show that the non-additive MBD energy plays a crucial role in making qualitatively and quantitatively accurate predictions for the structure and relative energies of polymorphs.

  20. Quantum-trajectory Monte Carlo method for study of electron-crystal interaction in STEM.

    Science.gov (United States)

    Ruan, Z; Zeng, R G; Ming, Y; Zhang, M; Da, B; Mao, S F; Ding, Z J

    2015-07-21

    In this paper, a novel quantum-trajectory Monte Carlo simulation method is developed to study electron beam interaction with a crystalline solid for application to electron microscopy and spectroscopy. The method combines the Bohmian quantum trajectory method, which treats electron elastic scattering and diffraction in a crystal, with a Monte Carlo sampling of electron inelastic scattering events along quantum trajectory paths. We study in this work the electron scattering and secondary electron generation process in crystals for a focused incident electron beam, leading to understanding of the imaging mechanism behind the atomic resolution secondary electron image that has been recently achieved in experiment with a scanning transmission electron microscope. According to this method, the Bohmian quantum trajectories have been calculated at first through a wave function obtained via a numerical solution of the time-dependent Schrödinger equation with a multislice method. The impact parameter-dependent inner-shell excitation cross section then enables the Monte Carlo sampling of ionization events produced by incident electron trajectories travelling along atom columns for excitation of high energy knock-on secondary electrons. Following cascade production, transportation and emission processes of true secondary electrons of very low energies are traced by a conventional Monte Carlo simulation method to present image signals. Comparison of the simulated image for a Si(110) crystal with the experimental image indicates that the dominant mechanism of atomic resolution of secondary electron image is the inner-shell ionization events generated by a high-energy electron beam.

  1. The effect of additives interaction on the miscibility and crystal structure of two immiscible biodegradable polymers

    Directory of Open Access Journals (Sweden)

    Ahmed Mohamed El-Hadi

    2014-01-01

    Full Text Available Poly lactic acid (PLLA is a promising biopolymer, obtained from polymerization of lactic acid that is derived from renewable resources through fermentation. The characteristic brittleness of PLLA is attributed to slow crystallization rates, which results in the formation of the large spherulites. Its glass temperature is relative high, above room temperature and close to 60 ºC, and therefore its applications are limited. The additives poly((R-3-hydroxybutyrate (PHB, poly(vinyl acetate (PVAc and tributyl citrate (TBC were used as compatibilizers in the biodegradable polymer blend of (PLLA/PPC. Results from DSC and POM analysis indicated that the blends of PLLA and PPC are immiscible. However, the blends with additives are miscible. TBC as plasticizer was added to PLLA to reduce its Tg. PVAc was used as compatibilizer to improve the miscibility between PLLA and PPC. FT-IR showed about 7 cm-1 shift in the C=O peak in miscible blends due to physical interactions. POM experiments together with the results of DSC and WAXD showed that PHB enhances the crystallization behavior of PLLA by acting as bio nuclei and the crystallization process can occur more quickly. Consequently an increase was observed in the peak intensity in WAXD.

  2. Optimized packings with applications

    CERN Document Server

    Pintér, János

    2015-01-01

    This volume presents a selection of case studies that address a substantial range of optimized object packings (OOP) and their applications. The contributing authors are well-recognized researchers and practitioners. The mathematical modelling and numerical solution aspects of each application case study are presented in sufficient detail. A broad range of OOP problems are discussed: these include various specific and non-standard container loading and object packing problems, as well as the stowing of hazardous and other materials on container ships, data centre resource management, automotive engineering design, space station logistic support, cutting and packing problems with placement constraints, the optimal design of LED street lighting, robust sensor deployment strategies, spatial scheduling problems, and graph coloring models and metaheuristics for packing applications. Novel points of view related to model development and to computational nonlinear, global, mixed integer optimization and heuristic st...

  3. Nasal packing and stenting

    Directory of Open Access Journals (Sweden)

    Weber, Rainer K.

    2009-01-01

    Full Text Available Nasal packs are indispensable in ENT practice. This study reviews current indications, effectiveness and risks of nasal packs and stents. In endoscopic surgery, nasal packs should always have smooth surfaces to minimize mucosal damage, improve wound healing and increase patient comfort. Functional endoscopic endonasal sinus surgery allows the use of modern nasal packs, since pressure is no longer required. So called hemostatic/resorbable materials are a first step in this direction. However, they may lead to adhesions and foreign body reactions in mucosal membranes. Simple occlusion is an effective method for creating a moist milieu for improved wound healing and avoiding dryness. Stenting of the frontal sinus is recommended if surgery fails to produce a wide, physiologically shaped drainage path that is sufficiently covered by intact tissue.

  4. Layered circle packings

    Directory of Open Access Journals (Sweden)

    David Dennis

    2005-01-01

    Full Text Available Given a bounded sequence of integers {d0,d1,d2,…}, 6≤dn≤M, there is an associated abstract triangulation created by building up layers of vertices so that vertices on the nth layer have degree dn. This triangulation can be realized via a circle packing which fills either the Euclidean or the hyperbolic plane. We give necessary and sufficient conditions to determine the type of the packing given the defining sequence {dn}.

  5. Atom-atom interactions around the band edge of a photonic crystal waveguide

    Science.gov (United States)

    Hood, Jonathan D.; Goban, Akihisa; Asenjo-Garcia, Ana; Lu, Mingwu; Yu, Su-Peng; Chang, Darrick E.; Kimble, H. J.

    2016-09-01

    Tailoring the interactions between quantum emitters and single photons constitutes one of the cornerstones of quantum optics. Coupling a quantum emitter to the band edge of a photonic crystal waveguide (PCW) provides a unique platform for tuning these interactions. In particular, the cross-over from propagating fields E(x)∝e±ikxxE(x)∝e±ikxx outside the bandgap to localized fields E(x)∝e-κx|x|E(x)∝e-κx|x| within the bandgap should be accompanied by a transition from largely dissipative atom-atom interactions to a regime where dispersive atom-atom interactions are dominant. Here, we experimentally observe this transition by shifting the band edge frequency of the PCW relative to the D1D1 line of atomic cesium for N¯=3.0±0.5N¯=3.0±0.5 atoms trapped along the PCW. Our results are the initial demonstration of this paradigm for coherent atom-atom interactions with low dissipation into the guided mode.

  6. Packing of ganglioside-phospholipid monolayers

    DEFF Research Database (Denmark)

    Majewski, J.; Kuhl, T.L.; Kjær, K.

    2001-01-01

    DPPE monolayer and does not distort the hexagonal in-plane unit cell or out-of-plane two-dimensional (2-D) packing compared with a pure DPPE monolayer. The oligosaccharide headgroups were found to extend normally from the monolayer surface, and the incorporation of these glycolipids into DPPE...... monolayers did not affect hydrocarbon tail packing (fluidization or condensation of the hydrocarbon region). This is in contrast to previous investigations of lipopolymer-lipid mixtures, where the packing structure of phospholipid monolayers was greatly altered by the inclusion of lipids bearing hydrophilic...... polymer groups. Indeed, the lack of packing disruptions by the oligosaccharide groups indicates that protein-GM, interactions, including binding, insertion, chain fluidization, and domain formation (lipid rafts), can be studied in 2-D monolayers using scattering techniques....

  7. Crystal structure of syndesmos and its interaction with Syndecan-4 proteoglycan

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Heeyoun [Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120-749 (Korea, Republic of); Yoo, Jiho [Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 120-749 (Korea, Republic of); Lee, Inhwan [Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120-749 (Korea, Republic of); Kang, Ying Jin [Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 120-749 (Korea, Republic of); Cho, Hyun-Soo, E-mail: hscho8@yonsei.ac.kr [Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 120-749 (Korea, Republic of); Lee, Weontae, E-mail: wlee@spin.yonsei.ac.kr [Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120-749 (Korea, Republic of)

    2015-08-07

    Syndesmos, nucleoside diphosphate linked moiety X (nudix)-type motif 16-like 1 (Nudt16l1), is evolutionarily divergent from the Nudt16 family. Syndesmos, which is co-localized with syndecan-4 cytoplasmic domain (Syn4{sup cyto}) in focal contacts, interacts with various cell adhesion adaptor proteins to control cell signaling. We determined the X-ray crystal structure of syndesmos; it is composed of seven α-helices and seven β-strands. Although syndesmos has a molecular topology similar to that of nudix hydrolase proteins, the structure of the nudix motif differs from that of X29. The dimeric interface of syndesmos is composed of α-helix 4, 7 and β-strand 2, 7, which primarily form hydrophobic interactions. The binding interaction between syndesmos and syn4{sup cyto} was characterized as a low-affinity interaction (K{sub d} = 62 μM) by surface plasmon resonance (SPR) and nuclear magnetic resonance (NMR). The NMR resonances of Lys (177, 178, 179), Gly182, and Ser183 in the C1 region and Lys193 and Lys194 in the V region of syndecan-4 are perturbed upon syndesmos binding. Our results provide structural insight into the molecular function of syndesmos in the regulation of cell signaling via binding to syndecan-4. - Highlights: • Crystal structure of syndesmos has been determined as a dimer at 2.01 Å resolution. • The molecular topology of syndesmos resembles that of the Nudix hydrolase protein. • The structure of the Nudix motif of syndesmos is quite different from that of X29. • Syndesmos binds cytoplasmic domain of syndecan-4 proteoglycan with low affinity.

  8. Intermolecular interaction studies in ammonium squarate: crystal structure and vibrational spectra

    Science.gov (United States)

    Georgopoulos, Stéfanos L.; Diniz, Renata; Rodrigues, Bernardo L.; Yoshida, Maria I.; de Oliveira, Luiz Fernando C.

    2005-10-01

    Ammonium squarate salt [(NH 4) 2C 4O 4] crystallizes in the monoclinic space group P2 1/c. The crystal presents the squarate ions displayed in layers parallel to a crystallographic axis and forming hydrogen bonds interactions with NH4+ cations, localized between squarate anions layers. The squarate anion presents similar CC and CO bond distances which indicate a degree of electronic delocalization in the rings. A π-stacking interaction is observed between squarate rings separated by interplanar distance and centroid ring distance of respectively 3.41 and 3.71 Å. The electron delocalization was also observed in the vibrational spectra. The infrared spectrum shows a narrow band around 1530 cm -1, assigned to a coupled stretching mode of CO and CC groups, indicating the high symmetry of the squarate ion. The Raman spectrum also shows this effect in the 1000 to 1200 cm -1 region (related to CC stretching mode), where it is expected a decrease of the number of bands if compared to squarate ion in aqueous solution, where the symmetry is actually D4 h; in the (NH 4) 2C 4O 4 Raman spectrum just one strong band is observed at 1120 cm -1. All the vibrational results indicate the symmetry is very close to the one observed for the solvated ion in aqueous solution; once again the vibrational analysis appears as an important tool in recognizing the oxocarbon ion geometry in the solid state.

  9. Crystal structure of soluble MD-1 and its interaction with lipid IVa

    Science.gov (United States)

    Yoon, Sung-il; Hong, Minsun; Han, Gye Won; Wilson, Ian A.

    2010-01-01

    Lipopolysaccharide (LPS) of Gram-negative bacteria is a common pathogen-associated molecular pattern (PAMP) that induces potent innate immune responses. The host immune response against LPS is triggered by myeloid differentiation factor 2 (MD-2) in association with Toll-like receptor 4 (TLR4) on the cell surface. The MD-2/TLR4-mediated LPS response is regulated by the evolutionarily related complex of MD-1 and Toll-like receptor homolog RP105. Here, we report crystallographic and biophysical data that demonstrate a previously unidentified direct interaction of MD-1 with LPS. The crystal structure of chicken MD-1 (cMD-1) at 2.0 Å resolution exhibits a β-cup-like fold, similar to MD-2, that encloses a hydrophobic cavity between the two β-sheets. A lipid-like moiety was observed inside the cavity, suggesting the possibility of a direct MD-1/LPS interaction. LPS was subsequently identified as an MD-1 ligand by native gel electrophoresis and gel filtration analyses. The crystal structure of cMD-1 with lipid IVa, an LPS precursor, at 2.4 Å resolution revealed that the lipid inserts into the deep hydrophobic cavity of the β-cup-like structure, but with some important differences compared with MD-2. These findings suggest that soluble MD-1 alone, in addition to its complex with RP105, can regulate host LPS sensitivity. PMID:20534476

  10. Van der Waals interaction between microparticle and uniaxial crystal with application to hydrogen atoms and multiwall carbon nanotubes

    CERN Document Server

    Blagov, E V; Mostepanenko, V M

    2005-01-01

    The Lifshitz theory of the van der Waals force is extended for the case of an atom (molecule) interacting with a plane surface of an uniaxial crystal or with a long solid cylinder or cylindrical shell made of isotropic material or uniaxial crystal. For a microparticle near a semispace or flat plate made of an uniaxial crystal the exact expressions for the free energy of the van der Waals and Casimir-Polder interaction are presented. An approximate expression for the free energy of microparticle- cylinder interaction is obtained which becomes precise for microparticle-cylinder separations much smaller than cylinder radius. The obtained expressions are used to investigate the van der Waals interaction between hydrogen atoms (molecules) and graphite plates or multiwall carbon nanotubes. To accomplish this the behavior of graphite dielectric permittivities along the imaginary frequency axis is found using the optical data for the complex refractive index of graphite for the ordinary and extraordinary rays. It is ...

  11. The influence of the stereochemistry of alanine residue on the solid state conformation and crystal packing of opioid peptides containing D-Ala or L-Ala in message domain--XRD and NMR study.

    Science.gov (United States)

    Trzeciak-Karlikowska, Katarzyna; Bujacz, Anna; Ciesielski, Włodzimierz; Bujacz, Grzegorz D; Potrzebowski, Marek J

    2011-08-18

    In this work, an X-ray diffraction (XRD) and solid state NMR study of two tetrapeptides with different stereochemistry of alanine residue is presented using Tyr-(D-Ala)-Phe-Gly (1), an N-terminal sequence of opioid peptide dermorphin, and its biologically inactive analog Tyr-(L-Ala)-Phe-Gly (2). Single-crystal XRD proved that 1 crystallized under different conditions from exclusively one structure: a monoclinic crystal with P2(1) space group. In contrast, 2 very easily formed at least three crystallographic modifications, 2a (monoclinic P2(1)), 2b (orthorhombic P2(1)2(1)2) and 2c (tetragonal P4(1)2(1)2). Solid-state NMR spectroscopy was employed to investigate the structure and molecular dynamics of 1, 2a, and 2b. By employing different NMR experiments (dipolar dephasing and PILGRIM) and an analysis of the (13)C principal elements of the chemical shift tensor (CST), it was proven that the main skeleton of tetrapeptides is rigid, whereas significant differences in the molecular motion of the aromatic residues were observed. Comparing current data with those of previous studies (J. Phys. Chem. B2004, 108, 4535-4545 and Cryst. Growth Des. 2009, 9, 4050-4059), it can be assumed that an important preorganization mechanism anticipating the formation of peptide crystals containing D-Ala in sequence is the intramolecular CH-π interaction, which occurs for the amino acid with D stereochemistry. This effect may be responsible for the formation of only one crystallographic form of D-Ala peptides.

  12. Weak antibody-cyclodextrin interactions determined by quartz crystal microbalance and dynamic/static light scattering.

    Science.gov (United States)

    Härtl, Elisabeth; Dixit, Nitin; Besheer, Ahmed; Kalonia, Devendra; Winter, Gerhard

    2013-11-01

    In a quest to elucidate the mechanism by which hydroxypropyl β-cyclodextrin (HPβCD) stabilizes antibodies against shaking stress, two heavily debated hypotheses exist, namely that stabilization is due to HPβCD's surface activity, or due to specific interactions with proteins. In a previous study by Serno et al. (Pharm. Res. 30 (2013) 117), we could refute the first hypothesis by proving that, although HPβCD is slightly surface active, it does not displace the antibody at the air-water interface, and accordingly, its surface activity is not the underlying stabilizing mechanism. In the present study, we investigated the possibility of interactions between HPβCD and monoclonal antibodies as the potential stabilization mechanism using quartz crystal microbalance (QCM) and static as well as dynamic light scattering. In the presence of HPβCD, the adsorption of IgG antibodies in the native state (IgG A) and the unfolded state (IgG A and IgG B) on gold-coated quartz crystals was studied by QCM. Results show that HPβCD causes a reduction in protein adsorption in both the folded and the unfolded states, probably due to an interaction between the protein and the cyclodextrin, leading to a reduced hydrophobicity of the protein and consequently a lower extent of adsorption. These results were supported by investigation of the interaction between the native protein and HPβCD using static and dynamic light scattering experiments, which provide the protein-protein interaction parameters, B22 and kD, respectively. Both B22 and kD showed an increase in magnitude with increasing HPβCD-concentrations, indicating a rise in net repulsive forces between the protein molecules. This is further evidence for the presence of interactions between HPβCD and the studied antibodies, since an association of HPβCD on the protein surface leads to a change in the intermolecular forces between the protein molecules. In conclusion, this study provides evidence that the previously observed

  13. Magnetic dipolar interaction between correlated triplets created by singlet fission in tetracene crystals

    CERN Document Server

    Wang, Rui; Zhang, Bo; Liu, Yunlong; Wang, Xiaoyong; Xiao, Min

    2015-01-01

    Singlet fission (SF) can potentially break the Shockley-Queisser efficiency limit in single-junction solar cells by splitting one photo-excited singlet exciton (S1) into two triplets (2T1) in organic semiconductors. A dark multi-exciton (ME) state has been proposed as the intermediate connecting S1 to 2T1. However, the exact nature of this ME state, especially how the doubly-excited triplets interact, remains elusive. Here, we report a quantitative study on the magnetic dipolar interaction between SF-induced correlated triplets in tetracene crystals by monitoring quantum beats relevant to the ME sublevels at room temperature. The resonances of ME sublevels approached by tuning an external magnetic field are observed to be avoided, which agrees well with the theoretical predictions considering a magnetic dipolar interaction of ~ 0.008 GHz. Our work paves a way to quantify the magnetic dipolar interaction in organic materials and marks an important step towards understanding the underlying physics of the ME sta...

  14. Packing of nonoverlapping cubic particles: Computational algorithms and microstructural characteristics.

    Science.gov (United States)

    Malmir, Hessam; Sahimi, Muhammad; Tabar, M Reza Rahimi

    2016-12-01

    Packing of cubic particles arises in a variety of problems, ranging from biological materials to colloids and the fabrication of new types of porous materials with controlled morphology. The properties of such packings may also be relevant to problems involving suspensions of cubic zeolites, precipitation of salt crystals during CO_{2} sequestration in rock, and intrusion of fresh water in aquifers by saline water. Not much is known, however, about the structure and statistical descriptors of such packings. We present a detailed simulation and microstructural characterization of packings of nonoverlapping monodisperse cubic particles, following up on our preliminary results [H. Malmir et al., Sci. Rep. 6, 35024 (2016)2045-232210.1038/srep35024]. A modification of the random sequential addition (RSA) algorithm has been developed to generate such packings, and a variety of microstructural descriptors, including the radial distribution function, the face-normal correlation function, two-point probability and cluster functions, the lineal-path function, the pore-size distribution function, and surface-surface and surface-void correlation functions, have been computed, along with the specific surface and mean chord length of the packings. The results indicate the existence of both spatial and orientational long-range order as the the packing density increases. The maximum packing fraction achievable with the RSA method is about 0.57, which represents the limit for a structure similar to liquid crystals.

  15. Packing of nonoverlapping cubic particles: Computational algorithms and microstructural characteristics

    Science.gov (United States)

    Malmir, Hessam; Sahimi, Muhammad; Tabar, M. Reza Rahimi

    2016-12-01

    Packing of cubic particles arises in a variety of problems, ranging from biological materials to colloids and the fabrication of new types of porous materials with controlled morphology. The properties of such packings may also be relevant to problems involving suspensions of cubic zeolites, precipitation of salt crystals during CO2 sequestration in rock, and intrusion of fresh water in aquifers by saline water. Not much is known, however, about the structure and statistical descriptors of such packings. We present a detailed simulation and microstructural characterization of packings of nonoverlapping monodisperse cubic particles, following up on our preliminary results [H. Malmir et al., Sci. Rep. 6, 35024 (2016), 10.1038/srep35024]. A modification of the random sequential addition (RSA) algorithm has been developed to generate such packings, and a variety of microstructural descriptors, including the radial distribution function, the face-normal correlation function, two-point probability and cluster functions, the lineal-path function, the pore-size distribution function, and surface-surface and surface-void correlation functions, have been computed, along with the specific surface and mean chord length of the packings. The results indicate the existence of both spatial and orientational long-range order as the the packing density increases. The maximum packing fraction achievable with the RSA method is about 0.57, which represents the limit for a structure similar to liquid crystals.

  16. The experimental setup of the Interaction in Crystals for Emission of RADiation collaboration at Mainzer Mikrotron: Design, commissioning, and tests

    Energy Technology Data Exchange (ETDEWEB)

    Lietti, D., E-mail: Daniela.Lietti@cern.ch [Università degli Studi dell’Insubria, Via Valleggio 11, 22100 Como (Italy); Backe, H.; Lauth, W. [Institut für Kernphysik der Universität Mainz, D-55099 Mainz (Germany); Bagli, E.; Bandiera, L.; Germogli, G.; Guidi, V.; Mazzolari, A. [Università degli Studi di Ferrara, Via Saragat 1, 44100 Ferrara (Italy); INFN Sezione di Ferrara, Via Saragat 1, 44100 Ferrara (Italy); Berra, A.; Prest, M. [Università degli Studi dell’Insubria, Via Valleggio 11, 22100 Como (Italy); INFN Sezione di Milano Bicocca, Piazza della Scienza 3, 20126 Milano (Italy); Carturan, S.; De Salvador, D. [Università degli Studi di Padova, Via Marzolo 8, 35131 Padova (Italy); INFN Laboratori Nazionali di Legnaro, Viale dell’Università 2, 35020 Legnaro (Italy); Vallazza, E. [INFN Sezione di Trieste, Via Valerio 2, 34127 Trieste (Italy)

    2015-04-15

    Silicon/germanium flat/bent crystals are thin devices able to efficiently deflect charged particle GeV-energy beams up to a few hundreds of μrad; moreover, high intensity photons can be efficiently produced in the so-called Multi-Volume Reflection (MVR) and Multiple Volume Reflections in One Crystal (MVROC) conditions. In the last years, the research interest in this field has moved to the dynamic studies of light negative leptons in the low energy range: the possibility to deflect negative particles and to produce high intensity γ sources via the coherent interactions with crystals in the sub-GeV energy range has been proved by the ICE-RAD (Interaction in Crystals for Emission of RADiation) Collaboration at the MAinzer MIkrotron (MAMI, Germany). This paper describes the setup used by the ICE-RAD experiment for the crystals characterization (both in terms of deflection and radiation emission properties): a high precision goniometer is used to align the crystals with the incoming beam, while a silicon based profilometer and an inorganic scintillator reconstruct, respectively, the particle position and the photon spectra after the samples. The crystals manufacturing process and their characterization, the silicon profilometer commissioning at the CERN PS T9 beamline, and the commissioning of the whole setup installed at MAMI are presented.

  17. Liquid crystal tunable photonic crystal dye laser

    DEFF Research Database (Denmark)

    Buss, Thomas; Christiansen, Mads Brøkner; Smith, Cameron

    2010-01-01

    We present a dye-doped liquid crystal laser using a photonic crystal cavity. An applied electric field to the liquid crystal provides wavelength tunability. The photonic crystal enhances resonant interaction with the gain medium....

  18. Packing of elastic wires in flexible shells

    Science.gov (United States)

    Vetter, R.; Wittel, F. K.; Herrmann, H. J.

    2015-11-01

    The packing problem of long thin filaments that are injected into confined spaces is of fundamental interest for physicists and biologists alike. How linear threads pack and coil is well known only for the ideal case of rigid containers, though. Here, we force long elastic rods into flexible spatial confinement borne by an elastic shell to examine under which conditions recently acquired knowledge on wire packing in rigid spheres breaks down. We find that unlike in rigid cavities, friction plays a key role by giving rise to the emergence of two distinct packing patterns. At low friction, the wire densely coils into an ordered toroidal bundle with semi-ellipsoidal cross-section, while at high friction, it packs into a highly disordered, hierarchic structure. These two morphologies are shown to be separated by a continuous phase transition. Our findings demonstrate the dramatic impact of friction and confinement elasticity on filamentous packing and might drive future research on such systems in physics, biology and even medical technology toward including these mutually interacting effects.

  19. Battery Pack Thermal Design

    Energy Technology Data Exchange (ETDEWEB)

    Pesaran, Ahmad

    2016-06-14

    This presentation describes the thermal design of battery packs at the National Renewable Energy Laboratory. A battery thermal management system essential for xEVs for both normal operation during daily driving (achieving life and performance) and off-normal operation during abuse conditions (achieving safety). The battery thermal management system needs to be optimized with the right tools for the lowest cost. Experimental tools such as NREL's isothermal battery calorimeter, thermal imaging, and heat transfer setups are needed. Thermal models and computer-aided engineering tools are useful for robust designs. During abuse conditions, designs should prevent cell-to-cell propagation in a module/pack (i.e., keep the fire small and manageable). NREL's battery ISC device can be used for evaluating the robustness of a module/pack to cell-to-cell propagation.

  20. Superconducting switch pack

    Energy Technology Data Exchange (ETDEWEB)

    Srivastava, V.C.; Wollan, J.J.

    1990-07-24

    This patent describes a superconducting switch pack at least one switch element. The switch element including a length of superconductive wire having a switching portion and two lead portions, the switching portion being between the lead portions; means for supporting the switching portion in a plane in a common mold; hardened resin means encapsulating the switching portion in the plane in a solid body; wherein the solid body has an exterior surface which is planar and substantially parallel with and spaced apart from the plane in which the switching portion is positioned. The exterior surface being exposed to the exterior of the switch pack and the resin means filling the space between the exterior surface and the plane of the switching portion so as to provide uninterrupted thermal communication between the plane of the switching portion and the exterior of the switch pack; and a heater element in thermal contact with the switching portion.

  1. Crystallization of an engineered RUN domain of Rab6-interacting protein 1/DENND5

    Energy Technology Data Exchange (ETDEWEB)

    Fernandes, Humberto; Franklin, Edward; Khan, Amir R. (Trinity)

    2011-08-29

    Effectors of the Rab small GTPases are large multi-domain proteins which have proved difficult to express in soluble form in Escherichia coli. Generally, effectors are recruited to a distinct subcellular compartment by active (GTP-bound) Rabs, which are linked to membranes by one or two prenylated Cys residues at their C-termini. Following recruitment via their Rab-binding domain (RBD), effectors carry out various aspects of vesicle formation, transport, tethering and fusion through their other domains. Previously, successful purification of the RUN-PLAT tandem domains (residues 683-1061) of the 1263-residue Rab6-interacting protein 1 (R6IP1) required co-expression with Rab6, as attempts to solubly express the effector alone were unsuccessful. R6IP1 is also known as DENN domain-containing protein 5 (DENND5) and is expressed as two isoforms, R6IP1A/B (DENND5A/B), which differ by 24 amino acids at the N-terminus. Here, a deletion in R6IP1 was engineered to enable soluble expression and to improve the quality of the crystals grown in complex with Rab6. A large 23-residue loop linking two -helices in the RUN1 domain was removed and replaced with a short linker. This loop resides on the opposite face to the Rab6-binding site and is not conserved in the RUN-domain family. In contrast to wild-type R6IP1-Rab6 crystals, which took several weeks to grow to full size, the engineered R6IP1 (RPdel)-Rab6 crystals could be grown in a matter of days.

  2. Two studies of colloidal interactions: electric polarizability and protein crystallization. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Fraden, Seth; Hu, Yue

    2001-08-06

    (I)Electric polarizability. During this grant period, the focus was on five topics concerning electric field effects on colloids. The first topic focuses on electric interactions between charged colloids in the absence of external fields, and the remaining four deal with colloids in the presence of external fields. The topics are (1) calculation of the effect of confinement on the pair-potential between like-charged colloids, (2) experimental determination of the interparticle potential under the conditions of dielectric polarization, (3) measurement of the evolution of structure of ER fluids, (4) synthesis of novel colloids designed for ER studies, and (5) computer modeling of polarization of surface charge. (II) Protein crystallization. Studies of the phase behavior of mixtures of proteins and polymers were initiated. The motivation was to test recent theories that suggested that optimal conditions for protein crystallization could be obtained using such mixtures. Combined light scattering measurements of the virial coefficients and determination of the phase diagram of protein/polymer mixtures revealed that the theoretical picture needs to be substantially modified.

  3. Colloid-in-liquid crystal gels that respond to biomolecular interactions.

    Science.gov (United States)

    Agarwal, Ankit; Sidiq, Sumyra; Setia, Shilpa; Bukusoglu, Emre; de Pablo, Juan J; Pal, Santanu Kumar; Abbott, Nicholas L

    2013-08-26

    This paper advances the design of stimuli-responsive materials based on colloidal particles dispersed in liquid crystals (LCs). Specifically, thin films of colloid-in-liquid crystal (CLC) gels undergo easily visualized ordering transitions in response to reversible and irreversible (enzymatic) biomolecular interactions occurring at the aqueous interfaces of the gels. In particular, LC ordering transitions can propagate across the entire thickness of the gels. However, confinement of the LC to small domains with lateral sizes of ∼10 μm does change the nature of the anchoring transitions, as compared to films of pure LC, due to the effects of confinement on the elastic energy stored in the LC. The effects of confinement are also observed to cause the response of individual domains of the LC within the CLC gel to vary significantly from one to another, indicating that manipulation of LC domain size and shape can provide the basis of a general and facile method to tune the response of these LC-based physical gels to interfacial phenomena. Overall, the results presented in this paper establish that CLC gels offer a promising approach to the preparation of self-supporting, LC-based stimuli-responsive materials.

  4. Influence of spin-orbit interactions on the cubic crystal-field states of the d4 system*

    OpenAIRE

    Radwanski, R. J.; Ropka, Z.

    2002-01-01

    It has been shown that for the highly-correlated d4 electronic system the spin-orbit interactions produce, even in case of the cubic crystal-field interactions, a singlet ground state. Its magnetic moment grows rapidly with the applied magnetic field approaching 4 uB for the Eg state, but only 3 uB for the T2g state. The applicability of the present results to the Mn3+ ion in LaMnO3 is discussed. Keywords: crystal-field, spin-orbit, orbital moment. PACS: 71.70.E, 75.10.D

  5. Structural considerations on acridine/acridinium derivatives: Synthesis, crystal structure, Hirshfeld surface analysis and computational studies

    Science.gov (United States)

    Wera, Michał; Storoniak, Piotr; Serdiuk, Illia E.; Zadykowicz, Beata

    2016-02-01

    This article describes a detailed study of the molecular packing and intermolecular interactions in crystals of four derivatives of acridine, i.e. 9-methyl-, 9-ethyl, 9-bromomethyl- and 9-piperidineacridine (1, 2, 3 and 4, respectively) and three 10-methylacridinium salts containing the trifluoromethanesulphonate anion and 9-vinyl-, 9-bromomethyl, and 9-phenyl-10-methylacridinium cations (5, 6 and 7, respectively). The crystal structures of all of the compounds are stabilized by long-range electrostatic interactions, as well as by a network of short-range C-HṡṡṡO (in hydrates and salts 3 and 5-7, respectively), C-Hṡṡṡπ, π-π, C-Fṡṡṡπ and S-Oṡṡṡπ (in salts 5-7) interactions. Hirshfeld surface analysis shows that various intermolecular contacts play an important role in the crystal packing, graphically exhibiting the differences in spatial arrangements of the acridine/acridinium derivatives under scrutiny here. Additionally, computational methods have been used to compare the intermolecular interactions in the crystal structures of the investigated compounds. Computations have confirmed the great contribution of dispersive interactions for crystal lattice stability in the case of 9-substituted acridine and electrostatic interactions for the crystal lattice stability in the case of 9-substituted 10-methylacridinium trifluoromethanesulphonates. The value of crystal lattice energy and the electrostatic contribution in the crystal lattice energy of monohydrated acridine derivatives have confirmed that these compounds have behave as acridinium derivatives.

  6. DIY Fraction Pack.

    Science.gov (United States)

    Graham, Alan; Graham, Louise

    2003-01-01

    Describes a very successful attempt to teach fractions to year 5 pupils based on pupils making their own fraction pack. Children decided for themselves how to make the fractional slices used in the activity using colored cardboard sheets and templates of a paper circle consisting of 24 equal slices. (Author/NB)

  7. Supramolecular layers and versatile packing modes: The solid state behavior of ortho, ortho-linked bisphenols

    Science.gov (United States)

    Augustin, André U.; Katzsch, Felix; Prior, Stephen H.; Gruber, Tobias

    2017-05-01

    A series of ortho-ortho-linked bisphenols featuring electron-withdrawing groups (EWGs) attached to the phenolic rings is reported. Their respective molecular structures and packing behaviors have been studied by X-ray diffraction, comparatively discussed and put into relation with the unsubstituted mother compound. Except for the mother compound, the molecular structures of all bisphenols studied here exhibit distorted aromatic moieties. Hence, the substituents studied here prevent proximal positioning of phenolic units and the formation of strong Osbnd H⋯O hydrogen bonds. In the packing of the underivatized bisphenol we found a strand-like molecular arrangement featuring strong Osbnd H⋯O hydrogen bonds and extensive edge-to-face contacts (Csbnd H⋯π) between the bisphenol molecules. The introduction of EWGs to the aromatic moieties changes these intermolecular interactions into face-to-face contacts resulting either in bisphenol stacks or handshake-like motifs between two bisphenol molecules. In both cases, the Csbnd H⋯π interactions are more or less replaced by Csbnd H⋯O contacts as the prevalent non-covalent interaction. In the packing of two nitro bisphenols in their DMSO inclusion compounds an exciting layered arrangement is observed, which also matches with the pronounced foliated habitus of their crystals. Additionally, proton NMR was used to establish the binding coefficients between the respective bisphenols and DMSO in solution.

  8. Determination of specific binding interactions at L-cystine crystal surfaces with chemical force microscopy.

    Science.gov (United States)

    Mandal, Trinanjana; Ward, Michael D

    2013-04-17

    The pathogenesis of L-cystine kidney stones involves four critical steps: nucleation, crystal growth, crystal aggregation, and crystal adhesion to cells. Although inhibition of crystal growth by L-cystine "imposters" at L-cystine crystal surfaces has been suggested as a plausible route for the suppression of stones, understanding the factors that govern crystal-crystal aggregation and adhesion of crystals to epithelial cells also is essential for devising strategies to mitigate L-cystine stone formation. Chemical force microscopy performed with atomic force microscope tips decorated with functional groups commonly found in urinary constituents that likely mediate aggregation and attachment (e.g., COOH, NH2, SH, CH3, OH) revealed signatures that reflect differences in the chemical affinity of these groups for the (001) and {100} faces of the naturally occurring hexagonal form of L-cystine single crystals and the {110} faces of the non-native tetragonal form. These signatures can be explained by the different chemical compositions of the crystal faces, and they reveal a remarkable binding specificity of the thiol group for the sulfur-rich {100} and {110} faces of the hexagonal and tetragonal forms, respectively. Collectively, these observations suggest that alterations of the crystal habit and polymorph by crystal growth inhibitors may not affect crystal aggregation or adhesion to cells significantly.

  9. CELLmicrocosmos 2.2 MembraneEditor: a modular interactive shape-based software approach to solve heterogeneous membrane packing problems.

    Science.gov (United States)

    Sommer, Björn; Dingersen, Tim; Gamroth, Christian; Schneider, Sebastian E; Rubert, Sebastian; Krüger, Jens; Dietz, Karl-Josef

    2011-05-23

    New perspectives have been developed to understand the processes of modeling heterogeneous membranes. These are crucial steps prior to applying advanced techniques like molecular dynamic simulations of whole membrane systems. Lipid, protein, and membrane packing problems are addressed based on biochemical properties in combination with computational optimization techniques. The CELLmicrocosmos 2.2 MembraneEditor (CmME) is introduced as an appropriate framework to handle such problems by offering diverse algorithmic approaches. Its algorithm plug-in-interface enables modelers to generate problem-specific algorithms. Good solutions concerning runtime and lipid density are realized by focusing on the outer shapes of the PDB-based molecules. Application cases are presented like the publication-based modeling of inner and outer mitochondrial membrane-fragments, semiautomatic incorporation of proteins, and the assembly of rafts. Concerning geometrical aspects of the lipids, the achieved results are consistent with experimental observations related to lipid densities and distributions. Finally, two membranes simulated with GROMACS are analyzed and compared: the first is generated with conventional scripting techniques, the second with the CmME Distributor algorithm. The examples prove that CmME is a valuable and versatile tool for a broad set of applications in analysis and visualization of biomembranes.

  10. A Study of Drop-Microstructured Surface Interactions during Dropwise Condensation with Quartz Crystal Microbalance

    Science.gov (United States)

    Su, Junwei; Charmchi, Majid; Sun, Hongwei

    2016-10-01

    Dropwise condensation (DWC) on hydrophobic surfaces is attracting attention for its great potential in many industrial applications, such as steam power plants, water desalination, and de-icing of aerodynamic surfaces, to list a few. The direct dynamic characterization of liquid/solid interaction can significantly accelerate the progress toward a full understanding of the thermal and mass transport mechanisms during DWC processes. This work reports a novel Quartz Crystal Microbalance (QCM) based method that can quantitatively analyze the interaction between water droplets and micropillar surfaces during different condensation states such as filmwise, Wenzel, and partial Cassie states. A combined nanoimprinting lithography and chemical surface treatment approach was utilized to fabricate the micropillar based superhydrophobic and superhydrophilic surfaces on the QCM substrates. The normalized frequency shift of the QCM device together with the microscopic observation of the corresponding drop motion revealed the droplets growth and their coalescence processes and clearly demonstrated the differences between the three aforementioned condensation states. In addition, the transition between Cassie and Wenzel states was successfully captured by this method. The newly developed QCM system provides a valuable tool for the dynamic characterization of different condensation processes.

  11. Bile acid-surfactant interactions at the liquid crystal/aqueous interface.

    Science.gov (United States)

    He, Sihui; Liang, Wenlang; Cheng, Kung-Lung; Fang, Jiyu; Wu, Shin-Tson

    2014-07-14

    The interaction between bile acids and surfactants at interfaces plays an important role in fat digestion. In this paper, we study the competitive adsorption of cholic acid (CA) at the sodium dodecyl sulfate (SDS)-laden liquid crystal (LC)/aqueous interface formed with cyanobiphenyl (nCB, n = 5-8) and the mixture of 5CB with 4-(4-pentylcyclohexyl)benzonitrile (5PCH). We find that the critical concentration of CA required to displace SDS from the interface linearly decreases from 160 μM to 16 μM by reducing the alkyl chain length of nCB from n = 8 to n = 5 and from 16 μM to 1.5 μM by increasing the 5PCH concentration from 0 wt% to 19 wt% in the 5PCH-5CB binary mixture. Our results clearly demonstrate that the sensitivity of 5PCH-5CB mixtures for monitoring the interaction between CA and SDS at the LC/aqueous interface can be increased by one order of magnitude, compared to 5CB.

  12. Supramolecular [60]fullerene liquid crystals formed by self-organized two-dimensional crystals.

    Science.gov (United States)

    Zhang, Xiaoyan; Hsu, Chih-Hao; Ren, Xiangkui; Gu, Yan; Song, Bo; Sun, Hao-Jan; Yang, Shuang; Chen, Erqiang; Tu, Yingfeng; Li, Xiaohong; Yang, Xiaoming; Li, Yaowen; Zhu, Xiulin

    2015-01-02

    Fullerene-based liquid crystalline materials have both the excellent optical and electrical properties of fullerene and the self-organization and external-field-responsive properties of liquid crystals (LCs). Herein, we demonstrate a new family of thermotropic [60]fullerene supramolecular LCs with hierarchical structures. The [60]fullerene dyads undergo self-organization driven by π-π interactions to form triple-layer two-dimensional (2D) fullerene crystals sandwiched between layers of alkyl chains. The lamellar packing of 2D crystals gives rise to the formation of supramolecular LCs. This design strategy should be applicable to other molecules and lead to an enlarged family of 2D crystals and supramolecular liquid crystals.

  13. Arsenic species interactions with a porous carbon electrode as determined with an electrochemical quartz crystal microbalance

    Science.gov (United States)

    Morallón, Emilia; Arias-Pardilla, Joaquín; Calo, J.M.; Cazorla-Amorós, D.

    2009-01-01

    The interactions of arsenic species with platinum and porous carbon electrodes were investigated with an electrochemical quartz crystal microbalance (EQCM) and cyclic voltammetry in alkaline solutions. It is shown that the redox reactions in arsenic-containing solutions, due to arsenic reduction/deposition, oxidation/desorption, and electrocatalyzed oxidation by Pt can be readily distinguished with the EQCM. This approach was used to show that the arsenic redox reactions on the carbon electrode are mechanistically similar to that on the bare Pt electrode. This could not be concluded with just classical cyclic voltammetry alone due to the obfuscation of the faradaic features by the large capacitative effects of the carbon double layer. For the porous carbon electrode, a continual mass loss was always observed during potential cycling, with or without arsenic in the solution. This was attributed to electrogasification of the carbon. The apparent mass loss per cycle was observed to decrease with increasing arsenic concentration due to a net mass increase in adsorbed arsenic per cycle that increased with arsenic concentration, offsetting the carbon mass loss. Additional carbon adsorption sites involved in arsenic species interactions are created during electrogasification, thereby augmenting the net uptake of arsenic per cycle. It is demonstrated that EQCM, and in particular the information given by the behavior of the time derivative of the mass vs. potential, or massogram, is very useful for distinguishing arsenic species interactions with carbon electrodes. It may also prove to be effective for investigating redox/adsorption/desorption behavior of other species in solution with carbon materials as well. PMID:20161369

  14. Arsenic species interactions with a porous carbon electrode as determined with an electrochemical quartz crystal microbalance.

    Science.gov (United States)

    Morallón, Emilia; Arias-Pardilla, Joaquín; Calo, J M; Cazorla-Amorós, D

    2009-06-30

    The interactions of arsenic species with platinum and porous carbon electrodes were investigated with an electrochemical quartz crystal microbalance (EQCM) and cyclic voltammetry in alkaline solutions. It is shown that the redox reactions in arsenic-containing solutions, due to arsenic reduction/deposition, oxidation/desorption, and electrocatalyzed oxidation by Pt can be readily distinguished with the EQCM. This approach was used to show that the arsenic redox reactions on the carbon electrode are mechanistically similar to that on the bare Pt electrode. This could not be concluded with just classical cyclic voltammetry alone due to the obfuscation of the faradaic features by the large capacitative effects of the carbon double layer.For the porous carbon electrode, a continual mass loss was always observed during potential cycling, with or without arsenic in the solution. This was attributed to electrogasification of the carbon. The apparent mass loss per cycle was observed to decrease with increasing arsenic concentration due to a net mass increase in adsorbed arsenic per cycle that increased with arsenic concentration, offsetting the carbon mass loss. Additional carbon adsorption sites involved in arsenic species interactions are created during electrogasification, thereby augmenting the net uptake of arsenic per cycle.It is demonstrated that EQCM, and in particular the information given by the behavior of the time derivative of the mass vs. potential, or massogram, is very useful for distinguishing arsenic species interactions with carbon electrodes. It may also prove to be effective for investigating redox/adsorption/desorption behavior of other species in solution with carbon materials as well.

  15. The Six Pack Model

    DEFF Research Database (Denmark)

    Andersen, Henrik; Ritter, Thomas

    Ever seen a growth strategies fail because it was not connect ed to the firm’s customer base? Or a customer relationship strategy falters just because it was the wrong thing to do with that given customer? This article presents the six pack model, a tool that makes growth profitable and predictable....... Not all customers can and should grow – thus a firm needs to classify its customers in order to implement the right customer strategy....

  16. Supra-molecular inter-actions in a 1:1 co-crystal of acridine and 3-chloro-thio-phene-2-carb-oxy-lic acid.

    Science.gov (United States)

    Prajina, Olakkandiyil; Thomas Muthiah, Packianathan; Perdih, Franc

    2016-05-01

    In the title co-crystal, C5H3ClO2S·C13H9N, the components inter-act with each other via an O-H⋯N hydrogen bond. Acridine-acridine stacking, thio-phene-thio-phene stacking and acridine-thio-phene C-H⋯π inter-actions also occur in the crystal.

  17. Polymer-Ion Interaction Weakens the Strain-Rate Dependence of Extension-Induced Crystallization for Poly(ethylene oxide).

    Science.gov (United States)

    Hu, Tingting; Tian, Nan; Ali, Sarmad; Wang, Zhen; Chang, Jiarui; Huang, Ningdong; Li, Liangbin

    2016-03-01

    The crystallization of poly(ethylene oxide) (PEO)-sodium iodine (NaI) composites is investigated by differential scanning calorimetry (DSC), extensional rheology, and in situ small-angle X-ray scattering (SAXS) with the aim of demonstrating versatile roles played by polymer-ion interactions. In the isothermal quiescent crystallization process, a decrease in the crystal growth rate is observed for PEO-NaI and is attributed to slow chain movement caused by the coordination between cations and polymer. In situ SAXS on extensional flow-induced crystallization (FIC) exhibits enhanced kinetics and orientation for both PEO and PEO-NaI with increasing strain rate. However, an overall weaker strain-rate dependence of FIC is observed for PEO-NaI, which can be interpreted as a synergistic consequence of promoted nucleation under flow and impeded crystal growth by polymer-ion interaction. A possible microscopic mechanism is proposed to account for the experimental observation based on the formation of transient cross-linking points in PEO-NaI and their influence on the entanglement network of polymer under various flow fields. The disclosed strain-rate dependence and various ion effects on the behavior of PEO-salt composites contribute to a comprehensive understanding of polymer-ion solid polyelectrolytes.

  18. Crystallization process

    Science.gov (United States)

    Adler, Robert J.; Brown, William R.; Auyang, Lun; Liu, Yin-Chang; Cook, W. Jeffrey

    1986-01-01

    An improved crystallization process is disclosed for separating a crystallizable material and an excluded material which is at least partially excluded from the solid phase of the crystallizable material obtained upon freezing a liquid phase of the materials. The solid phase is more dense than the liquid phase, and it is separated therefrom by relative movement with the formation of a packed bed of solid phase. The packed bed is continuously formed adjacent its lower end and passed from the liquid phase into a countercurrent flow of backwash liquid. The packed bed extends through the level of the backwash liquid to provide a drained bed of solid phase adjacent its upper end which is melted by a condensing vapor.

  19. Tampering with molecular cohesion in crystals of hexaphenylbenzenes.

    Science.gov (United States)

    Gagnon, Eric; Halperin, Shira D; Métivaud, Valérie; Maly, Kenneth E; Wuest, James D

    2010-01-15

    Hexaphenylbenzene (HPB) and analogous compounds have properties of broad utility in science and technology, including conformationally well-defined molecular structures, high thermal stability, high HOMO-LUMO gaps, little self-association, inefficient packing, and high solubilities. Previous structural studies of HPB and its analogues have revealed persistent involvement of the central aromatic ring in strong C-H...pi interactions. These interactions can be blocked by adding simple ortho alkyl substituents to the peripheral phenyl groups. Comparison of the structures of HPB and a series of ortho-substituted derivatives has shown systematic changes in molecular cohesion and packing, as measured by packing indices, densities, solubilities, temperatures of sublimation, melting points, and ratios of H...H, C...H, and C...C contacts. These results illustrate how crystal engineering can guide the search for improved materials by identifying small but telling molecular alterations that thwart established patterns of association.

  20. AFM Studies of Salt Concentration Effects on the (110) Surface Structure of Tetragonal Lysozyme Crystals

    Science.gov (United States)

    Pusey, Marc Lee; Gorti, Sridhar; Forsythe, Elizabeth; Konnert, John

    2002-01-01

    Previous high resolution AFM studies of the (110) surface of tetragonal chicken egg white lysozyme crystals had shown that only one of two possible molecular surfaces is present, those constituting the completed 43 helices. These suggested that the crystal growth process was by the solution-phase assembly of the growth units, which then attach to the surface. However, the best fit for the imaged surfaces, vs. those predicted based upon the bulk crystallographic coordinates, were obtained when the packing about the 43 helices was "tightened up", while maintaining the underlying crystallographic unit cell spacing. This results in a widening of the gap between adjacent helices, and the top- most layer(s) may no longer be in contact. We postulated that the tightened packing about the helices is a result of the high salt concentrations in the bulk solution, used to crystallize the protein, driving hydrophobic interactions. Once the crystal surface is sufficiently buried by subsequent growth layers the ratio of salt to protein molecules decreases and the helices relax to their bulk crystallographic coordinates. The crystal surface helix structure is thus a reflection of the solution structure, and the tightness of the packing about the 43 helices would be a function of the bulk salt concentration. AFM images of the (110) surface of tetragonal lysozyme crystals grown under low (2%) and high (5%) NaCl concentrations reveal differences in the packing about the 43 helices consistent with the above proposal.

  1. Hair-inspired crystal growth of HOA in cavities of cellulose matrix via hydrophobic-hydrophilic interface interaction.

    Science.gov (United States)

    He, Meng; Kwok, Ryan T K; Wang, Zhenggang; Duan, Bo; Tang, Ben Zhong; Zhang, Lina

    2014-06-25

    As one of the most ordinary phenomena in nature, numerous pores on animal skins induce the growth of abundant hairs. In this study, cavities of a cellulose matrix were used as hard templates to lead the hair-inspired crystal growth of 12-hydroxyoctadecanoic acid (HOA) through hydrophobic-hydrophilic interface interaction, and short hair-like HOA crystals with a smooth surface were formed on cellulose films. In our findings, by using solvent evaporation induced crystallization, hydrophobic HOA grew along the hydrophilic cellulose pore wall to form regular vertical worm-like and pillar-like crystals with an average diameter of about 200 nm, depending on the experimental conditions and HOA concentration. The formation mechanism of the short hair-like HOA crystals as well as the structure and properties of the cellulose/HOA submicrometer composite films were studied. The pores of the cellulose matrix supplied not only cavities for the HOA crystals fixation but also hydrophilic shells to favor the vertical growth of the relatively hydrophobic HOA crystals. The cellulose/HOA submicrometer composite films exhibited high hydrophobicity, as a result of the formation of the solid/air composite surface. Furthermore, 4-(1,2,2-triphenylethenyl) benzoic acid, an aggregation-induced emission luminogen, was used to aggregate on the cellulose surface with HOA to emit and monitor the HOA crystal growth, showing bifunctional photoluminscence and self-cleaning properties. This work opens up a novel one-step pathway to design bio-inspired submicrometer materials by utilizing natural products, showing potential applications in self-cleaning optical devices.

  2. The Crystal Water Affect in the Interaction between the Tenebrio Molitor Alpha-Amylase and Its Inhibitor

    Directory of Open Access Journals (Sweden)

    Zhu Zhi-Fei

    2008-01-01

    Full Text Available Molecular dynamics simulation of the interaction between the Tenebrio molitor alpha-amylase and its inhibitor at different proportion of crystal water was carried out with OPLS force field by hyperchem 7.5 software. In the correlative study, the optimal temperature of wheat monomeric and dimeric protein inhibitors was from 273 K to 318 K. The the average temperature of experimentation is 289 K. (1 The optimal temperature of interaction between alpha-amylase and its inhibitors was 280 K without crystal water that was close to the results of experimentation. The forming of enzyme-water and inhibitor-water was easy, but incorporating third monomer was impossible. (2 Having analyzed the potential energy data, the optimal temperature of interaction energy between alpha-amylase and its inhibitors covering 9 : 1, 5 : 5, 4 : 6, and 1 : 9 proportion crystal water was 290 K. (3 We compared the correlative QSAR properties. The proportion of crystal water was close to the data of polarizability (12.4% in the QSAR properties. The optimal temperature was 280 K. This result was close to 289 K. These findings have theoretical and practical implications.

  3. Helmholtz free energy and equation of state of an fcc crystal with the interaction of hard sphere Yukawa potential

    Directory of Open Access Journals (Sweden)

    M. Moradi

    2003-06-01

    Full Text Available  The Helmholtz free energy and equation of the state of an fcc crystal are calculated, where the interaction between the molecules is hard sphere-Yukawa potential. Here the perturbational density functional method is used. This method is introduced by Ebner and co-workers. In this method the density functional Taylor expansion is applied for the crystal configuration up to second order. And for the uniform parts an exact expression is used. The results are compared with those obtained by Monte Carlo computer simulation. The agreement is good.

  4. Voltage-induced defect mode interaction in a one-dimensional photonic crystal with a twisted-nematic defect layer

    CERN Document Server

    Timofeev, Ivan V; Gunyakov, Vladimir A; Myslivets, Sergey A; Arkhipkin, Vasily G; Vetrov, Stepan Ya; Lee, Wei; Zyryanov, Victor Ya

    2011-01-01

    Defect modes are investigated in a band gap of an electrically tunable one-dimensional photonic crystal infiltrated with a twisted-nematic liquid crystal (1D PC/TN). Their frequency shift and interference under applied voltage are studied both experimentally and theoretically. We deal with the case where the defect layer thickness is much larger than the wavelength (Mauguin condition). It is shown theoretically that the defect modes could have a complex structure with the elliptic polarization. Two series of polarized modes interact with each other and exhibit an avoided crossing phenomenon in the case of opposite parity.

  5. Cascaded interactions between Raman induced solitons and dispersive waves in photonic crystal fibers at the advanced stage of supercontinuum generation.

    Science.gov (United States)

    Driben, Rodislav; Mitschke, Fedor; Zhavoronkov, Nickolai

    2010-12-06

    The complex mechanism of multiple interactions between solitary and dispersive waves at the advanced stage of supercontinuum generation in photonic crystal fiber is studied in experiment and numerical simulations. Injection of high power negatively chirped pulses near zero dispersion frequency results in an effective soliton fission process with multiple interactions between red shifted Raman solitons and dispersive waves. These interactions may result in relative acceleration of solitons with further collisions between them of quasi-elastic or quasi-plastic kinds. In the spectral domain these processes result in enhancement of certain wavelength regions within the spectrum or development of a new significant band at the long wavelength side of the spectrum.

  6. Heuristics for Multidimensional Packing Problems

    DEFF Research Database (Denmark)

    Egeblad, Jens

    In this thesis we consider solution methods for packing problems. Packing problems occur in many different situations both directly in the industry and as sub-problems of other problems. High-quality solutions for problems in the industrial sector may be able to reduce transportation and production...... costs significantly. For packing problems in general are given a set of items and one of more containers. The items must be placed within the container such that some objective is optimized and the items do not overlap. Items and container may be rectangular or irregular (e.g. polygons and polyhedra...... methods. Two important problem variants are the knapsack packing problem and the strip-packing problem. In the knapsack packing problem, each item is given a profit value, and the problem asks for the subset with maximal profit that can be placed within one container. The strip-packing problem asks...

  7. Helix-packing motifs in membrane proteins.

    Science.gov (United States)

    Walters, R F S; DeGrado, W F

    2006-09-12

    The fold of a helical membrane protein is largely determined by interactions between membrane-imbedded helices. To elucidate recurring helix-helix interaction motifs, we dissected the crystallographic structures of membrane proteins into a library of interacting helical pairs. The pairs were clustered according to their three-dimensional similarity (rmsd universe of common transmembrane helix-pairing motifs is relatively simple. The largest cluster, which comprises 29% of the library members, consists of an antiparallel motif with left-handed packing angles, and it is frequently stabilized by packing of small side chains occurring every seven residues in the sequence. Right-handed parallel and antiparallel structures show a similar tendency to segregate small residues to the helix-helix interface but spaced at four-residue intervals. Position-specific sequence propensities were derived for the most populated motifs. These structural and sequential motifs should be quite useful for the design and structural prediction of membrane proteins.

  8. New bounds for multi-dimensional packing

    OpenAIRE

    Seiden, S.; Stee, van, Rob

    2001-01-01

    New upper and lower bounds are presented for a multi-dimensional generalization of bin packing called box packing. Several variants of this problem, including bounded space box packing, square packing, variable sized box packing and resource augmented box packing are also studied. The main results, stated for d=2, are as follows: A new upper bound of 2.66013 for online box packing, a new $14/9 + varepsilon$ polynomial time offline approximation algorithm for square packing, a new upper bound ...

  9. Liquid crystals and their interactions with colloidal particles and phospholipid membranes: Molecular simulation studies

    Science.gov (United States)

    Kim, Evelina B.

    Experimentally, liquid crystals (LC) can be used as the basis for optical biomolecular sensors that rely on LC ordering. Recently, the use of LC as a reporting medium has been extended to investigations of molecular scale processes at lipid laden aqueous-LC interfaces and at biological cell membranes. In this thesis, we present two related studies where liquid crystals are modelled at different length scales. We examine (a) the behavior of nanoscopic colloidal particles in LC systems, using Monte Carlo (MC) molecular simulations and a mesoscopic dynamic field theory (DyFT); and (b) specific interactions of two types of mesogens with a model phospholipid bilayer, using atomistic molecular dynamics (MD) at the A-nm scale. In (a), we consider colloidal particles suspended in a LC, confined between two walls. We calculate the colloid-substrate and colloid-colloid potentials of mean force (PMF). For the MC simulations, we developed a new technique (ExEDOS or Expanded Ensemble Density Of States) that ensures good sampling of phase space without prior knowledge of the energy landscape of the system. Both results, simulation and DyFT, indicate a repulsive force acting between a colloid and a wall. In contrast, both techniques indicate an overall colloid-colloid attraction and predict a new topology of the disclination lines that arises when the particles approach each other. In (b), we find that mesogens (pentylcyanobiphenyl [5CB] or difluorophenyl-pentylbicyclohexyl [5CF]) preferentially partition from the aqueous phase into a dipalmitoylphosphatidylcholine (DPPC) bilayer. We find highly favorable free energy differences for partitioning (-18kBT for 5CB, -26k BT for 5CF). We also simulated fully hydrated bilayers with embedded 5CB or 5CF at concentrations used in recent experiments (6 mol% and 20 mol%). The presence of mesogens in the bilayer enhances the order of lipid acyl tails and changes the spatial and orientational arrangement of lipid headgroup atoms. A stronger

  10. Packing anchored rectangles

    CERN Document Server

    Dumitrescu, Adrian

    2011-01-01

    Let $S$ be a set of $n$ points in the unit square $[0,1]^2$, one of which is the origin. We construct $n$ pairwise interior-disjoint axis-aligned empty rectangles such that the lower left corner of each rectangle is a point in $S$, and the rectangles jointly cover at least a positive constant area (about 0.09). This is a first step towards the solution of a longstanding conjecture that the rectangles in such a packing can jointly cover an area of at least 1/2.

  11. Packing ellipsoids with overlap

    CERN Document Server

    Uhler, Caroline

    2012-01-01

    The problem of packing ellipsoids of different sizes and shapes into an ellipsoidal container so as to minimize a measure of overlap between ellipsoids is considered. A bilevel optimization formulation is given, together with an algorithm for the general case and a simpler algorithm for the special case in which all ellipsoids are in fact spheres. Convergence results are proved and computational experience is described and illustrated. The motivating application - chromosome organization in the human cell nucleus - is discussed briefly, and some illustrative results are presented.

  12. New bounds for multi-dimensional packing

    NARCIS (Netherlands)

    S. Seiden; R. van Stee (Rob)

    2001-01-01

    textabstractNew upper and lower bounds are presented for a multi-dimensional generalization of bin packing called box packing. Several variants of this problem, including bounded space box packing, square packing, variable sized box packing and resource augmented box packing are also studied. The

  13. New bounds for multi-dimensional packing

    NARCIS (Netherlands)

    Seiden, S.; Stee, R. van

    2001-01-01

    New upper and lower bounds are presented for a multi-dimensional generalization of bin packing called box packing. Several variants of this problem, including bounded space box packing, square packing, variable sized box packing and resource augmented box packing are also studied. The main results,

  14. Two typical structure patterns in jammed monodisperse disk packings at high densities

    Science.gov (United States)

    Yuan, Ye; Jin, Weiwei; Liu, Lufeng; Li, Shuixiang

    2016-11-01

    We generate a large number of monodisperse disk packings in two dimensions via geometric-based packing algorithms including the relaxation algorithm and the Torquato-Jiao algorithm. Using the geometric-structure approach, a clear boundary of the geometrical feasible region in the order map is found which quite differs from that of the jammed region. For a certain packing density higher than 0.83, the crystalline degree varies in different packing samples. We find that the local hexatic order may increase in two fairly different ways as the system densifies. Therefore, two typical non-equilibrium jammed patterns, termed polycrystal and distorted crystal, are defined at high packing densities. Furthermore, their responses to isotropic compression are investigated using a compression-relaxation molecular dynamic protocol. The distorted crystal pattern is more stable than the polycrystal one with smaller displacements despite its low occurrence frequency. The results are helpful in understanding the structure and phase transition of disk packings.

  15. Static magnetic susceptibility, crystal field and exchange interactions in rare earth titanate pyrochlores

    NARCIS (Netherlands)

    Malkin, B. Z.; Lummen, T. T. A.; van Loosdrecht, P. H. M.; Dhalenne, G.; Zakirov, A. R.

    2010-01-01

    The experimental temperature dependence (T = 2-300 K) of single crystal bulk and site susceptibilities of rare earth titanate pyrochlores R2Ti2O7 (R = Sm, Eu, Gd, Tb, Dy, Ho, Er, Yb) is analyzed in the framework of crystal field theory and a mean field approximation. Analytical expressions for the s

  16. Crystal structure of dichloridobis(dimethyl N-cyanodithioiminocarbonatecobalt(II

    Directory of Open Access Journals (Sweden)

    Mouhamadou Birame Diop

    2016-01-01

    Full Text Available The structure of the mononuclear title complex, [{(H3CS2C=NC[triple-bond] N}2CoCl2], consists of a CoII atom coordinated in a distorted tetrahedral manner by two Cl− ligands and the terminal N atoms of two dimethyl N-cyanodithioiminocarbonate ligands. The two organic ligands are almost coplanar, with a dihedral angle of 5.99 (6° between their least-squares planes. The crystal packing features pairs of inversion-related complexes that are held together through C—H...Cl and C—H...S interactions and π–π stacking [centroid-to-centroid distance = 3.515 (su? Å]. Additional C—H...Cl and C—H...S interactions, as well as Cl...S contacts < 3.6 Å, consolidate the crystal packing.

  17. Grain neighbour effects on twin transmission in hexagonal close-packed materials

    Science.gov (United States)

    Arul Kumar, M.; Beyerlein, I. J.; McCabe, R. J.; Tomé, C. N.

    2016-12-01

    Materials with a hexagonal close-packed (hcp) crystal structure such as Mg, Ti and Zr are being used in the transportation, aerospace and nuclear industry, respectively. Material strength and formability are critical qualities for shaping these materials into parts and a pervasive deformation mechanism that significantly affects their formability is deformation twinning. The interaction between grain boundaries and twins has an important influence on the deformation behaviour and fracture of hcp metals. Here, statistical analysis of large data sets reveals that whether twins transmit across grain boundaries depends not only on crystallography but also strongly on the anisotropy in crystallographic slip. We show that increases in crystal plastic anisotropy enhance the probability of twin transmission by comparing the relative ease of twin transmission in hcp materials such as Mg, Zr and Ti.

  18. Cell packing structures

    KAUST Repository

    Pottmann, Helmut

    2015-03-03

    This paper is an overview of architectural structures which are either composed of polyhedral cells or closely related to them. We introduce the concept of a support structure of such a polyhedral cell packing. It is formed by planar quads and obtained by connecting corresponding vertices in two combinatorially equivalent meshes whose corresponding edges are coplanar and thus determine planar quads. Since corresponding triangle meshes only yield trivial structures, we focus on support structures associated with quad meshes or hex-dominant meshes. For the quadrilateral case, we provide a short survey of recent research which reveals beautiful relations to discrete differential geometry. Those are essential for successfully initializing numerical optimization schemes for the computation of quad-based support structures. Hex-dominant structures may be designed via Voronoi tessellations, power diagrams, sphere packings and various extensions of these concepts. Apart from the obvious application as load-bearing structures, we illustrate here a new application to shading and indirect lighting. On a higher level, our work emphasizes the interplay between geometry, optimization, statics, and manufacturing, with the overall aim of combining form, function and fabrication into novel integrated design tools.

  19. ExactPack Documentation

    Energy Technology Data Exchange (ETDEWEB)

    Singleton, Jr., Robert [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Israel, Daniel M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Doebling, Scott William [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Woods, Charles Nathan [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Kaul, Ann [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Walter, Jr., John William [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Rogers, Michael Lloyd [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-05-09

    For code verification, one compares the code output against known exact solutions. There are many standard test problems used in this capacity, such as the Noh and Sedov problems. ExactPack is a utility that integrates many of these exact solution codes into a common API (application program interface), and can be used as a stand-alone code or as a python package. ExactPack consists of python driver scripts that access a library of exact solutions written in Fortran or Python. The spatial profiles of the relevant physical quantities, such as the density, fluid velocity, sound speed, or internal energy, are returned at a time specified by the user. The solution profiles can be viewed and examined by a command line interface or a graphical user interface, and a number of analysis tools and unit tests are also provided. We have documented the physics of each problem in the solution library, and provided complete documentation on how to extend the library to include additional exact solutions. ExactPack’s code architecture makes it easy to extend the solution-code library to include additional exact solutions in a robust, reliable, and maintainable manner.

  20. Corrections for nuclear interaction in the case of light nuclei detection in NaI(Tl) crystal

    Energy Technology Data Exchange (ETDEWEB)

    Avdejchikov, V.V.; Bogdanov, A.I.; Zlomanchuk, Yu.; Majsyukov, V.D.; Abashidze, L.I.; Budilov, V. A.; Zhidkov, N.K.; Nikitin, V.A.; Nomokonov, P.V.; Povtorejko, A.A.

    1985-01-01

    Losses for nuclear interaction in a NaI(Tl) monocrystal forming together with a silicon semiconductor detector a ..delta..E-E telescope used for the light nucleus identification were measured experimentally. The measurements were performed with 3He nucleus beam extracted from the JINR synchrophasotron at five energy values: 428; 387; 295; 172 and 70 MeV. Nuclear losses for hydrogen and helium isotopes in NaI(Tl) crystals were calculated theoretically using the Glauber model. Comparing the estimated and experimental data obtained the conclusion is drawn on the serviceability of the model considered for determining corrections for the nuclear interaction during light nuclei recording by scintillation NaI(Tl) crystal detectors.

  1. Interactions of carbon nanotubes in a nematic liquid crystal. I. Theory

    Science.gov (United States)

    Galerne, Yves

    2016-04-01

    Elongated and rodlike objects such as carbon nanotubes (CNTs) are studied when immersed in a nematic liquid crystal. Their interaction energy in a uniform nematic field depends on their orientation relative to the director n , and its minimum determines if they stabilize parallel or perpendicular to n . Using free energy calculations, we deduce the orientation at equilibrium that they choose in a uniform director field n or when they are in contact with a splay-bend disclination line. Naturally, the CNT orientations also depend on the anchoring conditions at their surface. Essentially, three types of anchorings are considered, planar, homeotropic, and Janus anchorings in the cases of weak and strong anchoring strengths. In the presence of a splay-bend disclination line, they are attracted toward it and ultimately, they get out of the colloidal dispersion to stick on it. Their orientation relative to the line is found to be parallel or perpendicular to it, again depending on the anchoring conditions. When a sufficient number of particles are deposited on a disclination line, we finally obtain a micro- or nanonecklace in the shape of a thin thread or of a bottle brush, according to the CNTs being oriented parallel or perpendicular to the disclination line, respectively. The system exhibits a rich versatility even if up to now the weak anchorings appear to be difficult to control. As discussed in the associated experimental paper, these necklaces could be a step toward interesting applications for realizing nanowires self-connected in three dimensions to predesignated electrodes. This method could provide a way to increase the number of transistors that may be connected together on a small volume.

  2. Application of the short and long consecutive pairs model to the triplet-doublet interaction in molecular crystals

    Science.gov (United States)

    Barhoumi, T.; Monge, J. L.; Bouchriha, H.

    2010-10-01

    We have adapted the model of two consecutive pairs to the study of the triplet-doublet (T-D) interaction in molecular crystals. We have applied this model to the modulation of the photoconductivity in crystalline anthracene by a static magnetic field (MFE) and a microwave field (PDMR). We were able to reproduce, for the first time, quite perfectly two types of experiments with the same set of kinetic constants.

  3. Haphazard Packing of Unequal Spheres

    Institute of Scientific and Technical Information of China (English)

    叶大年; 张金民

    1991-01-01

    Haphazard packing of equal and unequal spheres can be performed for the spheres of molecular sieve material with a density of 1.80.The packing of such spheres in air is equivalent to that of nat-ural grains in water.Packing concentrations of equal spheres have been obtained for different pac-king intensities.Unequal spheres can be regarded as equal ones in a wide range of diameter ratios,so far as the packing concentration is concerned.A threshold of diameter ratio exists at 0.70,be-low which the packing concentration is expected to increase.The variation curves of concentration vs.diameter ratio were established in the experiment.The result will help us to understand the process of sedimentation and the concentration of voids in sedimentary rocks.

  4. Radiation of fast positrons interacting with periodic microstructure on the surface of a crystal

    Energy Technology Data Exchange (ETDEWEB)

    Epp, V., E-mail: epp@tspu.edu.ru [Tomsk State Pedagogical University, ul. Kievskaya 60, 634061 Tomsk (Russian Federation); Tomsk State University, pr. Lenina 36, 634050 Tomsk (Russian Federation); Janz, J.G., E-mail: Yanc@tpu.ru [Tomsk Polytechnic University, pr. Lenina 34, 634050 Tomsk (Russian Federation); Kaplin, V.V., E-mail: kaplin@tpu.ru [Tomsk Polytechnic University, pr. Lenina 34, 634050 Tomsk (Russian Federation)

    2016-12-01

    Highlights: • New tunable crystalline source of X-ray radiation is described. • Radiation is emitted by the channeling relativistic particles. • A set of crystal plates offers more effective monitoring of the photon energy. • Formulae describing the radiation properties are obtained. - Abstract: Radiation of positrons passing through a set of equidistant crystal plates is calculated. Each plate is of thickness of half of the particle trajectory period at planar channeling in a thick crystal. Positively charged particle entering the first plate at an angle smaller than the critical channeling angle is captured into channeling mode and changes the direction of its transversal velocity to reversed. Between the half-wave plates the particle moves along a straight line. The proposed setup can be realized as a set of equidistant ridges on the surface of a single crystal. Passing through such set of half-wave crystal plates the particle moves on quasi-undulator trajectories. Properties of the particle radiation emitted during their passage through such “multicrystal undulator” are calculated. The radiation spectrum in each particular direction is discrete, and the frequency of the first harmonic and the number of harmonics in the spectrum depend on the distance between the plates, on energy of the particles and on the averaged potential energy of atomic planes of the crystal. The radiation is bound to a narrow cone in the direction of the average particle velocity and polarized essentially in a plane orthogonal to the atomic planes in the crystal.

  5. Crystal Structure and Interaction with DNA of [Ni(phen)(mal)(H2O)2]·3H2O

    Institute of Scientific and Technical Information of China (English)

    GAO En-Jun; CHEN Mao-Sheng; YU Ying; SUN Ya-Guang

    2007-01-01

    A new complex [Ni(phen)(mal)(H2O)2]·3H2O (phen = 1,10-phenanthroline,mal2-= malonic acid) has been synthesized by the reaction of nickel nitrate,phen and malonic acid.EA,IR spectra and X-ray single-crystal diffraction were carried out to determine the composition and crystal structure of the title complex.Crystal data:monoclinic system,space group P2/c,a =8.937(3),b = 12.163(5),c = 9.725(3)(A),β = 119.36°,C15H19N2O9Ni,Mr= 430.03,Z = 2,F(000) =446,V = 921.3 (A)3,Dc = 1.550 g/cm3,μ = 1.104 mm-1,-10≤h≤ 10,-12≤k≤ 14,-11 ≤l≤7,R =0.0261 and wR = 0.0609 for 4376 (Rint = 0.0203) independent reflections and 1631 observed ones (I> 2σ(I)).Ni(Ⅱ) exhibits an octahedral coordination geometry,with hydrogen bonds and π-π interactions stabilizing the whole structure.UV spectrum of the complex interacting with protamine DNA indicates that the title compound interacts with DNA via insertion mode with bonding constant Kb of 1.11 × 104.

  6. Crack-impurity interactions and their role in the embrittlement of Fe alloy crystals charged with light elements

    Energy Technology Data Exchange (ETDEWEB)

    Narita, N. (Dept. of Metallurgy, Kyoto Univ. (Japan)); Shiga, T. (Dept. of Metallurgy, Kyoto Univ. (Japan)); Higashida, K. (Dept. of Metallurgy, Kyoto Univ. (Japan))

    1994-03-31

    The effect of mobile impurity doping on fracture behaviour has been investigated using plasma charging of light elements for Fe-2.5wt.%Si alloy crystals with particular attention to the role of crack-impurity elastic interactions. Fe-Si crystals are markedly embrittled by plasma charging of helium as well as hydrogen at around room temperature, this being accompanied by slow crack growth. Neon charging contributes little to the embrittlement, but argon charging does not contribute. The crystals are also embrittled by nitrogen charging in the tests at 450 K and exhibit slow crack growth during the tests. Elastic analyses indicate that crack-impurity interactions are induced not only by the applied K[sub I] field but also by the stress modification due to ambient impurities in the presence of a crack. The interactions serve effectively to concentrate mobile impurities ahead of a crack tip, leading to the increase in the local stress intensity k[sub I]. The effect of interstitial impurities on crack extension is discussed in connection with the modification of stress states due to impurities around a crack tip. (orig.)

  7. Different supramolecular architectures mediated by different weak interactions in the crystals of three N-aryl-2,5-dimethoxybenzenesulfonamides.

    Science.gov (United States)

    Shakuntala, K; Naveen, S; Lokanath, N K; Suchetan, P A; Abdoh, M

    2017-10-01

    The synthesis and evaluation of the pharmacological activities of molecules containing the sulfonamide moiety have attracted interest as these compounds are important pharmacophores. The crystal structures of three closely related N-aryl-2,5-dimethoxybenzenesulfonamides, namely N-(2,3-dichlorophenyl)-2,5-dimethoxybenzenesulfonamide, C14H13Cl2NO4S, (I), N-(2,4-dichlorophenyl)-2,5-dimethoxybenzenesulfonamide, C14H13Cl2NO4S, (II), and N-(2,4-dimethylphenyl)-2,5-dimethoxybenzenesulfonamide, C16H19NO4S, (III), are described. The asymmetric unit of (I) consists of two symmetry-independent molecules, while those of (II) and (III) contain one molecule each. The molecular conformations are stabilized by different intramolecular interactions, viz. C-H...O interactions in (I), N-H...Cl and C-H...O interactions in (II), and C-H...O interactions in (III). The crystals of the three compounds display different supramolecular architectures built by various weak intermolecular interactions of the types C-H...O, C-H...Cl, C-H...π(aryl), π(aryl)-π(aryl) and Cl...Cl. A detailed Hirshfeld surface analysis of these compounds has also been conducted in order to understand the relationship between the crystal structures. The dnorm and shape-index surfaces of (I)-(III) support the presence of various intermolecular interactions in the three structures. Analysis of the fingerprint plots reveals that the greatest contribution to the Hirshfeld surfaces is from H...H contacts, followed by H...O/O...H contacts. In addition, comparisons are made with the structures of some related compounds. Putative N-H...O hydrogen bonds are observed in 29 of the 30 reported structures, wherein the N-H...O hydrogen bonds form either C(4) chain motifs or R2(2)(8) rings. Further comparison reveals that the characteristics of the N-H...O hydrogen-bond motifs, the presence of other interactions and the resultant supramolecular architecture is largely decided by the position of the substituents on the

  8. Modelling the effective atomic number and the packing factor of polyatomic compounds: Applications to refractive index and dosimetry

    Science.gov (United States)

    Lima, H.; Couto dos Santos, M. A.

    2016-09-01

    In this work, based on fundamental physics and chemistry (charge distribution, electronegativity, induced dipole moment), we are introducing an analytical expression for Zeff and a general way of calculating the crystal packing factor, p, of any ionic material. By using the average separation between the atomic and crystal(ionic) radii of the interacting ions, we are postulating an effective distance(Rij) between the positive and the negative centre of charge. When compared to the available experimental data, predictions within 20% have been obtained to Zeff of materials applied to dosimetry. In photonics, the increasing behaviour of the refractive index with Zeff is confirmed. By combining crystal field and effective charge models, we have predicted Zeff of the Eu2O3 within the range of available experimental data.

  9. A preliminary study on the interaction of ferritin single crystals with chelating agents

    Science.gov (United States)

    Domininguez-Vera, Jose M.; Rondón, Deyanira; Moreno, Abel; García-Ruiz, Juan Ma.

    1996-10-01

    The crystallization of ferritin and the subsequent in situ study of the process of iron removal from the crystals by using chelating agents is reported. The chelating agents, oxalate and acetohydroxamate, were chosen because of their high iron(III) affinity. The formation of the corresponding soluble iron(III) complexes arising from the reaction with the iron cores was detected by UV-visible spectroscopy. Furthermore, we show that for a given concentration range of the chelating agents, the iron removal process takes place without crystal destruction. This ferritin-apoferritin (or iron-depleted ferritin) conversion was followed by video-microscopy and checked by X-ray diffraction.

  10. On the reduced interaction probability for fully stripped 33 TeV/c Pb ions channeled in a bent Si crystal

    Science.gov (United States)

    Biino, C.; Clément, M.; Doble, N.; Elsener, K.; Freund, A.; Gatignon, L.; Grafström, P.; Herr, W.; Taratin, A.; Uggerhøj, U. I.; Uzhinskii, V. V.; Velasco, M.

    2002-10-01

    We compare experimental results and computer simulations on the reduction of inelastic interactions for 33 TeV Pb 82+ ions channeled in a bent silicon crystal. The comparison shows that a very small fraction of the initially channeled ions suffer nuclear interactions while traversing the 60 mm long crystal under perfect alignment, even though its thickness would correspond to about 1.2 nuclear interaction lengths for an amorphous material. This result indicates that a bent crystal approach to extraction of high energy, fully stripped ions from e.g. RHIC or LHC might be feasible.

  11. On the reduced interaction probability for fully stripped 33 TeV/c Pb ions channeled in a bent Si crystal

    Energy Technology Data Exchange (ETDEWEB)

    Biino, C.; Clement, M.; Doble, N.; Elsener, K.; Freund, A.; Gatignon, L.; Grafstroem, P.; Herr, W.; Taratin, A.; Uggerhoej, U.I. E-mail: ulrik@ifa.au.dk; Uzhinskii, V.V.; Velasco, M

    2002-10-01

    We compare experimental results and computer simulations on the reduction of inelastic interactions for 33 TeV Pb{sup 82+} ions channeled in a bent silicon crystal. The comparison shows that a very small fraction of the initially channeled ions suffer nuclear interactions while traversing the 60 mm long crystal under perfect alignment, even though its thickness would correspond to about 1.2 nuclear interaction lengths for an amorphous material. This result indicates that a bent crystal approach to extraction of high energy, fully stripped ions from e.g. RHIC or LHC might be feasible.

  12. On the reduced interaction probability for fully stripped 33 TeV/c Pb ions channeled in a bent Si crystal

    CERN Document Server

    Uggerhøj, U; Clément, M; Doble, Niels T; Elsener, K; Freund, A; Gatignon, L; Grafström, P; Herr, Werner; Taratin, A; Uzhinskii, V V; Velasco, M

    2002-01-01

    We compare experimental results and computer simulations on the reduction of inelastic interactions for 33 TeV Pb**8**2**+ ions channeled in a bent silicon crystal. The comparison shows that a very small fraction of the initially channeled ions suffer nuclear interactions while traversing the 60 mm long crystal under perfect alignment, even though its thickness would correspond to about 1.2 nuclear interaction lengths for an amorphous material. This result indicates that a bent crystal approach to extraction of high energy, fully stripped ions from e.g. RHIC or LHC might be feasible.

  13. Method for dense packing discovery.

    Science.gov (United States)

    Kallus, Yoav; Elser, Veit; Gravel, Simon

    2010-11-01

    The problem of packing a system of particles as densely as possible is foundational in the field of discrete geometry and is a powerful model in the material and biological sciences. As packing problems retreat from the reach of solution by analytic constructions, the importance of an efficient numerical method for conducting de novo (from-scratch) searches for dense packings becomes crucial. In this paper, we use the divide and concur framework to develop a general search method for the solution of periodic constraint problems, and we apply it to the discovery of dense periodic packings. An important feature of the method is the integration of the unit-cell parameters with the other packing variables in the definition of the configuration space. The method we present led to previously reported improvements in the densest-known tetrahedron packing. Here, we use the method to reproduce the densest-known lattice sphere packings and the best-known lattice kissing arrangements in up to 14 and 11 dimensions, respectively, providing numerical evidence for their optimality. For nonspherical particles, we report a dense packing of regular four-dimensional simplices with density ϕ=128/219≈0.5845 and with a similar structure to the densest-known tetrahedron packing.

  14. Packing of crystalline structures of binary hard spheres: An analytical approach and application to amorphization

    NARCIS (Netherlands)

    Brouwers, H.J.H.

    2007-01-01

    The geometrical stability of the three lattices of the cubic crystal system, viz. face-centered cubic (fcc), body-centered cubic (bcc), and simple cubic (sc), consisting of bimodal discrete hard spheres, and the transition to amorphous packing is studied. First, the random close packing (rcp) fracti

  15. Packing of crystalline structures of binary hard spheres: an analytical approach and application to amorphisation

    NARCIS (Netherlands)

    Brouwers, Jos

    2007-01-01

    The geometrical stability of the three lattices of the cubic crystal system, viz. face-centered cubic (fcc), body-centered cubic (bcc), and simple cubic (sc), consisting of bimodal discrete hard spheres, and the transition to amorphous packing is studied. First, the random close packing (rcp)

  16. Polarizable protein packing.

    Science.gov (United States)

    Ng, Albert H; Snow, Christopher D

    2011-05-01

    To incorporate protein polarization effects within a protein combinatorial optimization framework, we decompose the polarizable force field AMOEBA into low order terms. Including terms up to the third-order provides a fair approximation to the full energy while maintaining tractability. We represent the polarizable packing problem for protein G as a hypergraph and solve for optimal rotamers with the FASTER combinatorial optimization algorithm. These approximate energy models can be improved to high accuracy [root mean square deviation (rmsd) < 1 kJ mol(-1)] via ridge regression. The resulting trained approximations are used to efficiently identify new, low-energy solutions. The approach is general and should allow combinatorial optimization of other many-body problems. Copyright © 2011 Wiley Periodicals, Inc.

  17. Polarizable protein packing

    KAUST Repository

    Ng, Albert H.

    2011-01-24

    To incorporate protein polarization effects within a protein combinatorial optimization framework, we decompose the polarizable force field AMOEBA into low order terms. Including terms up to the third-order provides a fair approximation to the full energy while maintaining tractability. We represent the polarizable packing problem for protein G as a hypergraph and solve for optimal rotamers with the FASTER combinatorial optimization algorithm. These approximate energy models can be improved to high accuracy [root mean square deviation (rmsd) < 1 kJ mol -1] via ridge regression. The resulting trained approximations are used to efficiently identify new, low-energy solutions. The approach is general and should allow combinatorial optimization of other many-body problems. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011 Copyright © 2011 Wiley Periodicals, Inc.

  18. Computational strain gradient crystal plasticity

    DEFF Research Database (Denmark)

    Niordson, Christian Frithiof; Kysar, Jeffrey W.

    2014-01-01

    of plane crystal plasticity are studied: pure shear of a single crystal between rigid platens as well as plastic deformation around cylindrical voids in hexagonal close packed and face centered cubic crystals. Effective in-plane constitutive slip parameters for plane strain deformation of specifically...

  19. NMR shows hydrophobic interactions replace glycine packing in the triple helix at a natural break in the (Gly-X-Y)n repeat.

    Science.gov (United States)

    Li, Yingjie; Brodsky, Barbara; Baum, Jean

    2007-08-03

    Little is known about the structural consequences of the more than 20 breaks in the (Gly-X-Y)(n) repeating sequence found in the long triple helix domain of basement membrane type IV collagen. NMR triple resonance studies of doubly labeled residues within a set of collagen model peptides provide distance and dihedral angle restraints that allow determination of model structures of both a standard triple helix and of a triple helix with a break in solution. Although the standard triple helix cannot continue when Gly is not every third residue, the NMR data support rod-like molecules that have standard triple-helical structures on both sides of a well defined and highly localized perturbation. The GAAVM break region may be described as a "pseudo triple helix," because it preserves the standard one-residue stagger of the triple helix but introduces hydrophobic interactions at the position normally occupied by the much smaller and hydrogen-bonded Gly residue of the repeating (Gly-X-Y)(n) sequence. This structure provides a rationale for the consensus presence of hydrophobic residues in breaks of similar length and defines a novel variant of a triple helix that could be involved in recognition.

  20. Form, symmetry and packing of biomacromolecules. II. Serotypes of human rhinovirus

    Science.gov (United States)

    Janner, A.

    2010-05-01

    The differentiation of the human rhinovirus into serotypes, all having very similar structures and the same architecture, is shown to be related to the packing of the viruses in the crystal and to its space-group symmetry.

  1. Radiation of fast positrons interacting with periodic microstructure on the surface of a crystal

    Science.gov (United States)

    Epp, V.; Janz, J. G.; Kaplin, V. V.

    2016-12-01

    Radiation of positrons passing through a set of equidistant crystal plates is calculated. Each plate is of thickness of half of the particle trajectory period at planar channeling in a thick crystal. Positively charged particle entering the first plate at an angle smaller than the critical channeling angle is captured into channeling mode and changes the direction of its transversal velocity to reversed. Between the half-wave plates the particle moves along a straight line. The proposed setup can be realized as a set of equidistant ridges on the surface of a single crystal. Passing through such set of half-wave crystal plates the particle moves on quasi-undulator trajectories. Properties of the particle radiation emitted during their passage through such "multicrystal undulator" are calculated. The radiation spectrum in each particular direction is discrete, and the frequency of the first harmonic and the number of harmonics in the spectrum depend on the distance between the plates, on energy of the particles and on the averaged potential energy of atomic planes of the crystal. The radiation is bound to a narrow cone in the direction of the average particle velocity and polarized essentially in a plane orthogonal to the atomic planes in the crystal.

  2. Impact of Molecular Orientation and Packing Density on Electronic Polarization in the Bulk and at Surfaces of Organic Semiconductors

    KAUST Repository

    Ryno, Sean M.

    2016-05-16

    The polarizable environment surrounding charge carriers in organic semiconductors impacts the efficiency of the charge transport process. Here, we consider two representative organic semiconductors, tetracene and rubrene, and evaluate their polarization energies in the bulk and at the organic-vacuum interface using a polarizable force field that accounts for induced-dipole and quadrupole interactions. Though both oligoacenes pack in a herringbone motif, the tetraphenyl substituents on the tetracene backbone of rubrene alter greatly the nature of the packing. The resulting change in relative orientations of neighboring molecules is found to reduce the bulk polarization energy of holes in rubrene by some 0.3 eV when compared to tetracene. The consideration of model organic-vacuum interfaces highlights the significant variation in the electrostatic environment for a charge carrier at a surface although the net change in polarization energy is small; interestingly, the environment of a charge even just one layer removed from the surface can be viewed already as representative of the bulk. Overall, it is found that in these herringbone-type layered crystals the polarization energy has a much stronger dependence on the intralayer packing density than interlayer packing density.

  3. Impact of Molecular Orientation and Packing Density on Electronic Polarization in the Bulk and at Surfaces of Organic Semiconductors.

    Science.gov (United States)

    Ryno, Sean M; Risko, Chad; Brédas, Jean-Luc

    2016-06-08

    The polarizable environment surrounding charge carriers in organic semiconductors impacts the efficiency of the charge transport process. Here, we consider two representative organic semiconductors, tetracene and rubrene, and evaluate their polarization energies in the bulk and at the organic-vacuum interface using a polarizable force field that accounts for induced-dipole and quadrupole interactions. Though both oligoacenes pack in a herringbone motif, the tetraphenyl substituents on the tetracene backbone of rubrene alter greatly the nature of the packing. The resulting change in relative orientations of neighboring molecules is found to reduce the bulk polarization energy of holes in rubrene by some 0.3 eV when compared to tetracene. The consideration of model organic-vacuum interfaces highlights the significant variation in the electrostatic environment for a charge carrier at a surface although the net change in polarization energy is small; interestingly, the environment of a charge even just one layer removed from the surface can be viewed already as representative of the bulk. Overall, it is found that in these herringbone-type layered crystals the polarization energy has a much stronger dependence on the intralayer packing density than interlayer packing density.

  4. A search for nEDM and new constraints on short-range "pseudo-magnetic" interaction using neutron optics of noncentrosymmetric crystal

    Science.gov (United States)

    Fedorov, V. V.; Kuznetsov, I. A.; Voronin, V. V.

    2013-08-01

    New approach to measure both neutron electric dipole moment (EDM) and short-range pseudomagnetic nucleon-nucleon interaction using neutron optics of a crystal without center of symmetry is presented. This approach allows getting best direct constraint on the parameters of short range pseudomagnetic interaction of a free neutron with matter for the range of interaction distances λ<10-7 m.

  5. Role of supramolecular synthons in the formation of the supramolecular architecture of molecular crystals revisited from an energetic viewpoint.

    Science.gov (United States)

    Shishkin, Oleg V; Zubatyuk, Roman I; Shishkina, Svitlana V; Dyakonenko, Viktoriya V; Medviediev, Volodymyr V

    2014-04-14

    Analysis of the strengths and directionality of intermolecular interactions in the crystals containing only one type of supramolecular synthon allows the suggestion of a general classification of molecular crystals depending on type of their basic structural motifs. All crystals may be divided on four classes namely (I) crystals with isotropic packing of the building units; (II) columnar crystals where the basic structural motif (BSM) is a chain/column; (III) layered crystals with layers as the BSM; (IV) columnar-layered crystals containing chains/columns as the primary basic structural motif and layers as the secondary BSM. Taking into account the participation of different supramolecular synthons in the formation of different levels of the organization of molecular crystals, they may be considered as basic (responsible for the formation of molecular complexes as building units of crystals), primary, secondary and auxiliary, which are involved in the agglomeration of molecules in primary or secondary basic structural motifs or in the packing of these motifs, respectively. The ranking of supramolecular synthons depends on values of energies of intermolecular interactions and it is individual for each crystal.

  6. Quantitative characterization of new supramolecular synthons involving fluorine atoms in the crystal structures of di- and tetrafluorinated benzamides.

    Science.gov (United States)

    Mondal, Pradip Kumar; Yadav, Hare Ram; Choudhury, Angshuman Roy; Chopra, Deepak

    2017-10-01

    Strong hydrogen bonds play a significant role in crystal packing. In particular, the involvement of interactions involving fluorine in controlling the crystal packing requires appropriate attention, especially in the presence of other strong hydrogen bonds. In the present study, a detailed quantitative assessment has been performed of the nature, energetics and topological properties derived from the electron density in model compounds based on fluorinated benzamides (a total of 46 fluorine-substituted benzamides containing multiple fluorine atoms) in the solid state. The primary motivation in the design of such molecules is to enhance the acidity of the interacting H atoms in the presence of an increasing number of F atoms on the molecular scaffold, resulting in increased propensity towards the formation of intermolecular interactions involving organic fluorine. This exercise has resulted in the identification of new and frequently occurring supramolecular synthons involving F atoms in the packing of molecules in the solid state. The energetics associated with short and directional intermolecular Csp(2)-H...F-Csp(2) interactions with significantly high electrostatic contributions is noteworthy, and the topological analysis reveals the bonding character of these ubiquitous interactions in crystal packing in addition to the presence of Csp(2)-F...F-Csp(2) contacts.

  7. Packing Products: Polystyrene vs. Cornstarch

    Science.gov (United States)

    Starr, Suzanne

    2009-01-01

    Packing materials such as polystyrene take thousands of years to decompose, whereas packing peanuts made from cornstarch, which some companies are now using, can serve the same purpose, but dissolve in water. The author illustrates this point to her class one rainy day using the sculptures students made from polystyrene and with the cornstarch…

  8. Crystal structure of bis(2-methyl-1H-imidazol-3-ium tetrachloridocobaltate(II

    Directory of Open Access Journals (Sweden)

    Mouhamadou Birame Diop

    2015-09-01

    Full Text Available The asymmetric unit of the title compound, (C4H7N22[CoCl4], consists of two 2-methylimidazolium cations and one tetrahedral [CoCl4]2− anion. The anions and cations interact through N—H...Cl hydrogen bonds to define layers with a stacking direction along [100]. Besides van der Waals forces, weak C—H...Cl interactions between these layers stabilize the crystal packing.

  9. Crystal structure of a heterodimer of editosome interaction proteins in complex with two copies of a cross-reacting nanobody.

    Science.gov (United States)

    Park, Young-Jun; Pardon, Els; Wu, Meiting; Steyaert, Jan; Hol, Wim G J

    2012-02-01

    The parasite Trypanosoma brucei, the causative agent of sleeping sickness across sub-Saharan Africa, depends on a remarkable U-insertion/deletion RNA editing process in its mitochondrion. A approximately 20 S multi-protein complex, called the editosome, is an essential machinery for editing pre-mRNA molecules encoding the majority of mitochondrial proteins. Editosomes contain a common core of twelve proteins where six OB-fold interaction proteins, called A1-A6, play a crucial role. Here, we report the structure of two single-strand nucleic acid-binding OB-folds from interaction proteins A3 and A6 that surprisingly, form a heterodimer. Crystal growth required the assistance of an anti-A3 nanobody as a crystallization chaperone. Unexpectedly, this anti-A3 nanobody binds to both A3(OB) and A6, despite only ~40% amino acid sequence identity between the OB-folds of A3 and A6. The A3(OB)-A6 heterodimer buries 35% more surface area than the A6 homodimer. This is attributed mainly to the presence of a conserved Pro-rich loop in A3(OB). The implications of the A3(OB)-A6 heterodimer, and of a dimer of heterodimers observed in the crystals, for the architecture of the editosome are profound, resulting in a proposal of a 'five OB-fold center' in the core of the editosome.

  10. Physicochemical analyses of a bioactive 4-aminoantipyrine analogue - synthesis, crystal structure, solid state interactions, antibacterial, conformational and docking studies.

    Science.gov (United States)

    Alam, Mohammad Sayed; Lee, Dong-Ung

    2016-01-01

    A novel Schiff base derivative of 4-aminoantipyrine, that is, (E)-4-(2-methoxybenzylideneamino)-1,5-dimethyl-2-phenyl-1H-pyrazol-3(2H)-one (MBA-dMPP), was synthesized and characterized by FT-IR, (1)H-NMR, and EI-MS. Single-crystal X-ray diffraction data revealed MBA-dMPP adopts a trans configuration around its central C=N double bond, and forms orthorhombic crystals. XRD revealed that MBA-dMPP possess two different planes, in which the pyrazolone and benzylidene groups attached to C9 of the pyrazolone ring are almost coplanar and the phenyl ring connected to the N1 atom of the pyrazolone moiety lies in another plane. The intermolecular, host-guest C-H…O, C-H…N, and C-H…C van der Waals interactions were found to form a 3D network and confer stability to the MBA-dMPP crystal structure. The quantitative and qualitative solid state behaviors of MBA-dMPP were subjected to 3D Hirshfeld surface analysis and 2D fingerprint plotting. Reciprocal H…H contacts contributed most (52.9 %) to the Hirshfeld surface, followed by C…H/H…C contacts (30.2 %), whereas, O…H/H…O and N…H/H…N interactions contributed 15.5 % to the Hirshfeld surface. Electrostatic potentials were mapped over the Hirshfeld surface to analyze electrostatic complementarities within the MBA-dMPP crystal. In addition, geometrical descriptors were also analyzed to the extent of surface interactions. MBA-dMPP was also investigated for in vitro antibacterial activity against Gram-positive and Gram-negative bacterial strains, and showed highest activity against Bacillus cereus (MIC = 12.5 μg mL(-1)) and Salmonellatythimurium (MIC = 50 μg mL(-1)). In silico screening was conducted by docking MBA-dMPP on the active site of S12 bacterial protein (an important therapeutic target of antibacterial agents) and its binding properties were compared with those of ciprofloxacin. Moreover, a field points map of MBA-dMPP ligand was studied to determine electrostatic and van der Waals forces, hydrophobic

  11. Physicochemical analyses of a bioactive 4-aminoantipyrine analogue - synthesis, crystal structure, solid state interactions, antibacterial, conformational and docking studies

    Science.gov (United States)

    Alam, Mohammad Sayed; Lee, Dong-Ung

    2016-01-01

    A novel Schiff base derivative of 4-aminoantipyrine, that is, (E)-4-(2-methoxybenzylideneamino)-1,5-dimethyl-2-phenyl-1H-pyrazol-3(2H)-one (MBA-dMPP), was synthesized and characterized by FT-IR, 1H-NMR, and EI-MS. Single-crystal X-ray diffraction data revealed MBA-dMPP adopts a trans configuration around its central C=N double bond, and forms orthorhombic crystals. XRD revealed that MBA-dMPP possess two different planes, in which the pyrazolone and benzylidene groups attached to C9 of the pyrazolone ring are almost coplanar and the phenyl ring connected to the N1 atom of the pyrazolone moiety lies in another plane. The intermolecular, host-guest C-H…O, C-H…N, and C-H…C van der Waals interactions were found to form a 3D network and confer stability to the MBA-dMPP crystal structure. The quantitative and qualitative solid state behaviors of MBA-dMPP were subjected to 3D Hirshfeld surface analysis and 2D fingerprint plotting. Reciprocal H…H contacts contributed most (52.9 %) to the Hirshfeld surface, followed by C…H/H…C contacts (30.2 %), whereas, O…H/H…O and N…H/H…N interactions contributed 15.5 % to the Hirshfeld surface. Electrostatic potentials were mapped over the Hirshfeld surface to analyze electrostatic complementarities within the MBA-dMPP crystal. In addition, geometrical descriptors were also analyzed to the extent of surface interactions. MBA-dMPP was also investigated for in vitro antibacterial activity against Gram-positive and Gram-negative bacterial strains, and showed highest activity against Bacillus cereus (MIC = 12.5 μg mL-1) and Salmonella tythimurium (MIC = 50 μg mL-1). In silico screening was conducted by docking MBA-dMPP on the active site of S12 bacterial protein (an important therapeutic target of antibacterial agents) and its binding properties were compared with those of ciprofloxacin. Moreover, a field points map of MBA-dMPP ligand was studied to determine electrostatic and van der Waals forces, hydrophobic potentials

  12. Heuristics for Multidimensional Packing Problems

    DEFF Research Database (Denmark)

    Egeblad, Jens

    for a minimum height container required for the items. The main contributions of the thesis are three new heuristics for strip-packing and knapsack packing problems where items are both rectangular and irregular. In the two first papers we describe a heuristic for the multidimensional strip-packing problem...... for a three-dimensional knapsack packing problem involving furniture is presented in the fourth paper. The heuristic is based on a variety of techniques including tree-search, wall-building, and sequential placement. The solution process includes considerations regarding stability and load bearing strength...... paper. Ensuring that a loaded consignment of items are balanced throughout a container can reduce fuel consumption and prolong the life-span of vehicles. The heuristic can be used as a post-processing tool to reorganize an existing solution to a packing problem. A method for optimizing the placement...

  13. Horizontally-aligned carbon nanotubes arrays and their interactions with liquid crystal molecules: Physical characteristics and display applications

    Directory of Open Access Journals (Sweden)

    Frédérick Roussel

    2012-03-01

    Full Text Available We report on the physical characteristics of horizonthally-grown Single-Walled Carbon Nanotubes (h-al-SWNT arrays and their potential use as transparent and conducting alignment layer for liquid crystals display devices. Microscopy (SEM and AFM, spectroscopic (Raman and electrical investigations demonstrate the strong anisotropy of h-al-SWNT arrays. Optical measurements show that h-al-SWNTs are efficient alignment layers for Liquid Crystal (LC molecules allowing the fabrication of optical wave plates. Interactions between h-al-SWNT arrays and LC molecules are also investigated evidencing the weak azimuthal anchoring energy at the interface, which, in turn, leads to LC devices with a high pretilt angle. The electro-optical reponses of h-al-SWNT/LC cells demonstrate that h-al-SWNT arrays are efficient nanostructured electrodes with potential use for the combined replacement of Indium Tin Oxyde and polymeric alignment layers in conventional displays.

  14. Toward crystal design in organic conductors and superconductors.

    Energy Technology Data Exchange (ETDEWEB)

    Geiser, U.

    1999-04-23

    We have seen that many different types of intermolecular interactions in organic conducting cation radical salts. Hydrogen bonding between the donor molecules and the anions is weak but not negligible. The ionic Madelung energy is insufficient to completely intersperse anions and cations, thus the layers favored by the van der Waals interactions remain intact. The search for new conducting and superconducting salts has been mainly by trial-and-error methods, even though simple substitutions have been employed in order to obtain isostructural analogs of successful (e.g., superconducting) salts. However, even seemingly minor substitutions sometimes destroy the packing type, and different crystal structures result. Simulations with the aim at predicting crystal structures have not succeeded, mainly because the different interaction types are of comparable energy, and the delocalized and partial charges render the calculations of the ionic terms extremely unreliable. Clearly, the development of suitable crystal modeling techniques with predictive capabilities is one of the great needs of the field.

  15. The generic geometry of helices and their close-packed structures

    DEFF Research Database (Denmark)

    Olsen, Kasper; Bohr, Jakob

    2010-01-01

    The formation of helices is an ubiquitous phenomenon for molecular structures whether they are biological, organic, or inorganic, in nature. Helical structures have geometrical constraints analogous to close packing of three-dimensional crystal structures. For helical packing the geometrical cons....... For double helices comparisons are made to the A,B, and Z forms of DNA. The helical geometry of the A form is nearly close-packed. The packing density for the B and Z form are found to be approximately equal to each other....

  16. Advanced Protein Crystallization Facility (APCF)

    Science.gov (United States)

    1998-01-01

    This section of the Life and Microgravity Spacelab (LMS) publication contains articles entitled: (1) Crystallization of EGFR-EGF; (2) Crystallization of Apocrustacyanin C1; (3) Crystallization and X-ray Analysis of 5S rRNA and the 5S rRNA Domain A; (4) Growth of Lysozyme Crystals at Low Nucleation Density; (5) Comparative Analysis of Aspartyl tRNA-synthetase and Thaumatin Crystals Grown on Earth and In Microgravity; (6) Lysosome Crystal Growth in the Advanced Protein Crystallization Facility Monitored via Mach-Zehnder Interferometry and CCD Video; (7) Analysis of Thaumatin Crystals Grown on Earth and in Microgravity; (8) Crystallization of the Nucleosome Core Particle; (9) Crystallization of Photosystem I; (10) Mechanism of Membrane Protein Crystal Growth: Bacteriorhodopsin-mixed Micelle Packing at the Consolution Boundary, Stabilized in Microgravity; (11) Crystallization in a Microgravity Environment of CcdB, a Protein Involved in the Control of Cell Death; and (12) Crystallization of Sulfolobus Solfataricus

  17. Interactions between crystal violet and AOT in aqueous solutions and in AOT/isooctane/water microemulsions

    Institute of Scientific and Technical Information of China (English)

    HAO Xiaojuan; AN Xueqin; CHEN Zhiyun; SHEN Weiguo

    2004-01-01

    The absorbance of crystal violet (CV) in a series of aqueous solutions and a series of sodium bis(2-ethyl- hexyl) sulfosuccinate (AOT)/isooctane/water microemulsions has been determined. Association models have been used to analyse the experimental data to obtain the association constants of CV and AOT in the above two media. It was found that about up to 57% CV was associated by AOT in AOT/ isooctane/water microemulsions, which reduced the reaction rate of alkaline fading of crystal violet in the microemulsions.

  18. FROM THE PACKED TOWERS

    Directory of Open Access Journals (Sweden)

    Valderi D. Leite

    2013-01-01

    Full Text Available About 245 thousand tones of municipal solid w aste are collected daily in Brazil. Nearly 32 thousand tones of the collected amount are treated in sanitary landfill, which generates biogas and leachate as byproduct. The leachate resulting from sanitary landfill contains high concentration of carbonaceous and nitrogenized material. The crucial question is that the biodegradation of the carbonaceous material is difficult as long as the nitrogenized material is presen t in the form of ammoniacal nitrogen (NH 4 + , which compromises performance of biological tr eatment process. Therefore, a physical and chemical treatment of the leachate should be done before its biological treatment, especially for reduction of ammoniacal nitr ogen concentration and for propitiating the realization of application of biological treatment. The treatment of leachate requires specific consideration, which is not needed fo r other types of waste. In the specific case in this study, where ammoniacal nitrogen concentration was about 2,200 mgN L -1 and the BOD 5 /COD ratio was 0.3, the study of ammonia stripping process was performed. Ammonia stripping process was studied in pack ed towers of 35 L capacity each and the parameters investigated were pH, ratio of contact area/leach volume and the aeration time. One of the parameters that influenced most in efficiency of ammonia stripping process was pH of the leachate since it contributes in conversion of ammoniacal nitrogen from NH 4 + to NH 3 .

  19. Enabling Microliquid Chromatography by Microbead Packing of Microchannels

    Science.gov (United States)

    Balvin, Manuel; Zheng, Yun

    2014-01-01

    The microbead packing is the critical element required in the success of on-chip microfabrication of critical microfluidic components for in-situ analysis and detection of chiral amino acids. In order for microliquid chromatography to occur, there must be a stationary phase medium within the microchannel that interacts with the analytes present within flowing fluid. The stationary phase media are the microbeads packed by the process discussed in this work. The purpose of the microliquid chromatography is to provide a lightweight, low-volume, and low-power element to separate amino acids and their chiral partners efficiently to understand better the origin of life. In order to densely pack microbeads into the microchannels, a liquid slurry of microbeads was created. Microbeads were extracted from a commercially available high-performance liquid chromatography column. The silica beads extracted were 5 microns in diameter, and had surface coating of phenyl-hexyl. These microbeads were mixed with a 200- proof ethanol solution to create a microbead slurry with the right viscosity for packing. A microfilter is placed at the outlet via of the microchannel and the slurry is injected, then withdrawn across a filter using modified syringes. After each injection, the channel is flushed with ethanol to enhance packing. This cycle is repeated numerous times to allow for a tightly packed channel of microbeads. Typical microbead packing occurs in the macroscale into tubes or channels by using highly pressurized systems. Moreover, these channels are typically long and straight without any turns or curves. On the other hand, this method of microbead packing is completed within a microchannel 75 micrometers in diameter. Moreover, the microbead packing is completed into a serpentine type microchannel, such that it maximizes microchannel length within a microchip. Doing so enhances the interactions of the analytes with the microbeads to separate efficiently amino acids and amino acid

  20. Statistical mechanics of the lattice sphere packing problem.

    Science.gov (United States)

    Kallus, Yoav

    2013-06-01

    We present an efficient Monte Carlo method for the lattice sphere packing problem in d dimensions. We use this method to numerically discover de novo the densest lattice sphere packing in dimensions 9 through 20. Our method goes beyond previous methods, not only in exploring higher dimensions but also in shedding light on the statistical mechanics underlying the problem in question. We observe evidence of a phase transition in the thermodynamic limit d→∞. In the dimensions explored in the present work, the results are consistent with a first-order crystallization transition but leave open the possibility that a glass transition is manifested in higher dimensions.

  1. Apparatus and method for determining microscale interactions based on compressive sensors such as crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    McAdams, Harley; AlQuraishi, Mohammed

    2015-04-21

    Techniques for determining values for a metric of microscale interactions include determining a mesoscale metric for a plurality of mesoscale interaction types, wherein a value of the mesoscale metric for each mesoscale interaction type is based on a corresponding function of values of the microscale metric for the plurality of the microscale interaction types. A plurality of observations that indicate the values of the mesoscale metric are determined for the plurality of mesoscale interaction types. Values of the microscale metric are determined for the plurality of microscale interaction types based on the plurality of observations and the corresponding functions and compressed sensing.

  2. Experimental and theoretical investigation of a pyridine containing Schiff base: Hirshfeld analysis of crystal structure, interaction with biomolecules and cytotoxicity

    Science.gov (United States)

    Chithiraikumar, S.; Neelakantan, M. A.

    2016-03-01

    A pyridine containing Schiff base (E)-2-methoxy-6-(((pyridin-2-ylmethyl)imino)methyl) phenol (L) was isolated in single crystals. The molecular structure of L was studied by FT-IR, NMR, UV-Vis techniques, single crystal XRD analysis and computationally by DFT method. L prefers enol form in the solid state. Electronic spectrum of L was recorded in different organic solvents to investigate the dependence of tautomerism on solvent types. The polar solvents facilitate the proton transfer by decreasing the activation energy needed for transition state. Potential energy curve for the intramolecular proton transfer in the ground state is generated in gas and solution phases. The 3D Hirshfeld surfaces and the associated 2D fingerprint plots were investigated. The percentages of various interactions were analyzed by fingerprint plots of Hirshfeld surface. The interaction of L with CT DNA was investigated under physiological conditions using UV-Vis spectroscopy, fluorescence quenching and molecular docking methods. Molecular docking studies reveal that binding of L to the groove of B-DNA is through hydrogen bonding and hydrophobic interactions. The in vitro cytotoxicity of L was carried out in two different human tumor cell lines, MCF 7 and MIA-Pa-Ca-2 exhibits moderate activity.

  3. Correlation of inhibitory effects of polymers on indomethacin precipitation in solution and amorphous solid crystallization based on molecular interaction.

    Science.gov (United States)

    Chauhan, Harsh; Kuldipkumar, Anuj; Barder, Timothy; Medek, Ales; Gu, Chong-Hui; Atef, Eman

    2014-02-01

    To correlate the polymer's degree of precipitation inhibition of indomethacin in solution to the amorphous stabilization in solid state. Precipitation of indomethacin (IMC) in presence of polymers was continuously monitored by a UV spectrophotometer. Precipitates were characterized by PXRD, IR and SEM. Solid dispersions with different polymer to drug ratios were prepared using solvent evaporation. Crystallization of the solid dispersion was monitored using PXRD. Modulated differential scanning calorimetry (MDSC), IR, Raman and solid state NMR were used to explore the possible interactions between IMC and polymers. PVP K90, HPMC and Eudragit E100 showed precipitation inhibitory effects in solution whereas Eudragit L100, Eudragit S100 and PEG 8000 showed no effect on IMC precipitation. The rank order of precipitation inhibitory effect on IMC was found to be PVP K90 > Eudragit E100 > HPMC. In the solid state, polymers showing precipitation inhibitory effect also exhibited amorphous stabilization of IMC with the same rank order of effectiveness. IR, Raman and solid state NMR studies showed that rank order of crystallization inhibition correlates with strength of molecular interaction between IMC and polymers. Correlation is observed in the polymers ability to inhibit precipitation in solution and amorphous stabilization in the solid state for IMC and can be explained by the strength of drug polymer interactions.

  4. Valve stem and packing assembly

    Energy Technology Data Exchange (ETDEWEB)

    Wordin, J.J.

    1990-12-31

    A valve stem and packing assembly is provided in which a rotatable valve stem includes a first tractrix surface for sliding contact with a stem packing and also includes a second tractrix surface for sliding contact with a bonnet. Force is applied by means of a spring, gland flange, and gland on the stem packing so the stem packing seals to the valve stem and bonnet. This configuration serves to create and maintain a reliable seal between the stem packing and the valve stem. The bonnet includes a second complementary tractrix surface for contacting the second sliding tractrix surface, the combination serving as a journal bearing for the entire valve stem and packing assembly. The journal bearing so configured is known as a Schiele`s pivot. The Schiele`s pivot also serves to maintain proper alignment of the valve stem with respect to the bonnet. Vertical wear between the surfaces of the Schiele`s pivot is uniform at all points of contact between the second sliding tractrix surface and the second complementary tractrix surface of a bonnet. The valve stem is connected to a valve plug by means of a slip joint. The valve is opened and closed by rotating the valve stem. The slip joint compensates for wear on the Schiele`s pivot and on the valve plug. A ledge is provided on the valve bonnet for the retaining nut to bear against. The ledge prevents overtightening of the retaining nut and the resulting excessive friction between stem and stem packing.

  5. The role of solvent interaction with crystalline surfaces in crystal growth

    NARCIS (Netherlands)

    Voort, E. van der

    1990-01-01

    The agreement between theoretical habits of crystals obtained from PBC-analyses and observed habits is often remarkably good, even though only the internal crystalline structure is taken into account. Sometimes discrepancies are observed. The purpose of the research described in this thesis is to ex

  6. Crystal structure of Pb3(IO4(OH22

    Directory of Open Access Journals (Sweden)

    Matthias Weil

    2014-07-01

    Full Text Available The structure of the title compound, trilead(II bis[dihydroxidotetraoxidoiodate(VII], was determined from a crystal twinned by non-merohedry with two twin domains present [twin fraction 0.73 (1:0.27 (1]. It contains three Pb2+ cations and two IO4(OH23− anions in the asymmetric unit. Each of the Pb2+ cations is surrounded by eight O atoms (cut-off value = 3.1 Å in the form of a distorted polyhedron. The octahedral IO4(OH23− anions are arranged in rows extending parallel to [021], forming a distorted hexagonal rod packing. The cations and anions are linked into a framework structure. Although H-atom positions could not be located, O...O distances suggest medium-strength hydrogen-bonding interactions between the IO4(OH2 octahedra, further consolidating the crystal packing.

  7. Evolution of the dense packings of spherotetrahedral particles: from ideal tetrahedra to spheres.

    Science.gov (United States)

    Jin, Weiwei; Lu, Peng; Li, Shuixiang

    2015-10-22

    Particle shape plays a crucial role in determining packing characteristics. Real particles in nature usually have rounded corners. In this work, we systematically investigate the rounded corner effect on the dense packings of spherotetrahedral particles. The evolution of dense packing structure as the particle shape continuously deforms from a regular tetrahedron to a sphere is investigated, starting both from the regular tetrahedron and the sphere packings. The dimer crystal and the quasicrystal approximant are used as initial configurations, as well as the two densest sphere packing structures. We characterize the evolution of spherotetrahedron packings from the ideal tetrahedron (s = 0) to the sphere (s = 1) via a single roundness parameter s. The evolution can be partitioned into seven regions according to the shape variation of the packing unit cell. Interestingly, a peak of the packing density Φ is first observed at s ≈ 0.16 in the Φ-s curves where the tetrahedra have small rounded corners. The maximum density of the deformed quasicrystal approximant family (Φ ≈ 0.8763) is slightly larger than that of the deformed dimer crystal family (Φ ≈ 0.8704), and both of them exceed the densest known packing of ideal tetrahedra (Φ ≈ 0.8563).

  8. Anthraphane: An Anthracene-Based, Propeller-Shaped D(3h)-Symmetric Hydrocarbon Cyclophane and Its Layered Single Crystal Structures.

    Science.gov (United States)

    Servalli, Marco; Trapp, Nils; Wörle, Michael; Klärner, Frank-Gerrit

    2016-03-18

    The novel hydrocarbon propeller-shaped D3h-symmetric cyclophane (3), "anthraphane", was prepared through a revisited and optimized gram-scale synthesis of the key building block anthracene-1,8-ditriflate 7. Anthraphane has a high tendency to crystallize and single crystals in size ranges of 100-200 μm are easily obtained from different solvents. The crystallization behavior of 3 was extensively studied to unravel packing motifs and determine whether the packing can be steered into a desired direction, so to allow topochemical photopolymerization. SC-XRD shows that anthraphane packs in layers irrespective of the solvent used for crystallization. However, within the layers, intermolecular arrangements and π-π interactions of the anthracene units vary strongly. Four interaction motifs for the anthracene moieties are observed and discussed in detail: two types of exclusively edge-to-face (etf), a mixture of edge-to-face and face-to-face (ftf), and no anthracene-anthracene interaction at all. To elucidate why an exclusive ftf stacking was not observed, electrostatic potential surface (EPS) calculations with the semiempirical PM3 method were performed. They show qualitatively that the anthracene faces bear a strong negative surface potential, which may be the cause for this cyclophane to avoid ftf interactions. This combined crystallographic and computational study provides valuable insights on how to create all-ftf packings.

  9. Compactness Theorems for Geometric Packings

    OpenAIRE

    Martin, Greg

    2000-01-01

    Moser asked whether the collection of rectangles of dimensions 1 x 1/2, 1/2 x 1/3, 1/3 x 1/4, ..., whose total area equals 1, can be packed into the unit square without overlap, and whether the collection of squares of side lengths 1/2, 1/3, 1/4, ... can be packed without overlap into a rectangle of area pi^2/6-1. Computational investigations have been made into packing these collections into squares of side length 1+epsilon and rectangles of area pi^2/6-1+epsilon, respectively, and one can c...

  10. Aspiration of Nasopore nasal packing.

    Science.gov (United States)

    Smith, Jonathan; Reddy, Ekambar

    2017-10-04

    We present a case of postoperative Nasopore aspiration in an otherwise fit and well 11-year-old. An endoscopic adenoidectomy had been performed without incident and Nasopore packing placed into each nasal cavity. Immediately after extubation, there was marked hypoxia, tachypnoea and high clinical suspicion of pack aspiration. The patient returned to theatre for emergency rigid bronchoscopy and retrieval of nasal packing. © BMJ Publishing Group Ltd (unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  11. Pseudo-molecular approach for the elastic constants of nematic liquid crystals interacting via anisotropic dispersion forces

    Energy Technology Data Exchange (ETDEWEB)

    Simonário, P.S., E-mail: simonario@gmail.com [Departamento de Física, Universidade Estadual de Maringá, Avenida Colombo, 5790, 87020-900 Maringá, Paraná (Brazil); Freire, F.C.M.; Evangelista, L.R. [Departamento de Física, Universidade Estadual de Maringá, Avenida Colombo, 5790, 87020-900 Maringá, Paraná (Brazil); Teixeira-Souza, R.T. [Universidade Tecnológica Federal do Paraná – Câmpus Apucarana, Rua Marcílio Dias, 635, 86812-460 Apucarana, Paraná (Brazil)

    2014-01-17

    The bulk and the surface-like elastic constants of a nematic liquid crystal are calculated for an ensemble of particles interacting via anisotropic dispersion forces using the pseudo-molecular method. The geometrical anisotropy of the molecules is also taken into account in the calculations by choosing a molecular volume of ellipsoidal shape. Analytical expressions for the elastic constants are obtained as a function of the eccentricity in the molecular volume shape. The method allows one to explore the dependence on the molecular orientation with respect to the intermolecular vector by analyzing the magnitude and the behaviour of macroscopic elastic parameters defining the nematic phase.

  12. Hard, soft, and sticky spheres for dynamical studies of disordered colloidal packings

    Science.gov (United States)

    Gratale, Matthew Daniel

    This thesis describes experiments which explore the role of interparticle interactions as a means to alter, and control, the properties of dense colloidal packings. The first set of experiments studied phonon modes in two-dimensional colloidal crystals composed of soft microgel particles with hard polystyrene particle dopants distributed randomly on the triangular lattice. By mixing hard and soft spheres we obtain close-packed lattices of spheres with random bond strength disorder, textit{i.e.,} the effective springs coupling nearest-neighbors are either very stiff, very soft, or of intermediate stiffness. Video microscopy, particle tracking, and covariance matrix techniques are employed to derive the phonon modes of the corresponding ``shadow'' crystals, thereby enabling us to study how bond strength disorder affects vibrational properties. Hard and soft particles participate equally in low frequency phonon modes, and the samples exhibit Debye-like density of states behavior characteristic of crystals at low frequency. For mid- and high-frequency phonons, the relative participation of hard versus soft particles in each mode is found to vary systematically with dopant concentration. The second set of experiments investigated depletion interaction potentials between micron-size colloidal particles induced by nanometer-scale micelles composed of the surfactant hexaethylene glycol monododecyl ether (C12E6). The strength and range of the depletion interaction is revealed to arise from variations in shape anisotropy of the rod-like surfactant micelles. This shape anisotropy increases with increasing sample temperature. By fitting the colloidal interaction potentials to theoretical models, we extract the rod-like micelle length and shape anisotropy as a function of temperature. This work introduces micelle shape anisotropy as a means to control interparticle interactions in colloidal suspensions, and shows how interparticle depletion potentials of micron-scale objects

  13. Solid-state 13C NMR study of banana liquid crystals - 3: Alkyl-tail-group packing environments of an acute-angle bent-core molecule in the hexagonal columnar and cubic phases

    Science.gov (United States)

    Kurosu, Hiromichi; Endo, Yumi; Kimura, Saori; Hashimoto, Tomoko; Harada, Motoi; Lee, Eun-Woo; Sone, Masato; Watanabe, Junji; Kang, Sungmin

    2016-02-01

    Solid-state 13C nuclear magnetic resonance (NMR) measurements were performed on the hexagonal columnar and cubic phases of an acute-angle banana-shaped molecule, N(1,7)-S30. In the hexagonal columnar phase, three peaks appear at the NMR chemical shifts assigned to the internal methylene carbons of alkyl tails, indicating that the two alkyl tails have different packing structures, and one of the tails has two different conformations within a single molecule. Combined cross-polarization/magic-angle spinning and pulse saturation transfer/magic-angle spinning measurements show that one of the alkyl chains is located inside and the other is located outside the columnar structure. In the cubic phase, pulse saturation transfer/magic-angle spinning measurement shows that only one peak appears at the NMR chemical shifts assigned to the internal methylene carbons of alkyl tails, indicating that both of the alkyl chains are located outside the cubic structure.

  14. Mapping the distribution of packing topologies within protein interiors shows predominant preference for specific packing motifs

    Directory of Open Access Journals (Sweden)

    Banerjee Rahul

    2011-05-01

    Full Text Available Abstract Background Mapping protein primary sequences to their three dimensional folds referred to as the 'second genetic code' remains an unsolved scientific problem. A crucial part of the problem concerns the geometrical specificity in side chain association leading to densely packed protein cores, a hallmark of correctly folded native structures. Thus, any model of packing within proteins should constitute an indispensable component of protein folding and design. Results In this study an attempt has been made to find, characterize and classify recurring patterns in the packing of side chain atoms within a protein which sustains its native fold. The interaction of side chain atoms within the protein core has been represented as a contact network based on the surface complementarity and overlap between associating side chain surfaces. Some network topologies definitely appear to be preferred and they have been termed 'packing motifs', analogous to super secondary structures in proteins. Study of the distribution of these motifs reveals the ubiquitous presence of typical smaller graphs, which appear to get linked or coalesce to give larger graphs, reminiscent of the nucleation-condensation model in protein folding. One such frequently occurring motif, also envisaged as the unit of clustering, the three residue clique was invariably found in regions of dense packing. Finally, topological measures based on surface contact networks appeared to be effective in discriminating sequences native to a specific fold amongst a set of decoys. Conclusions Out of innumerable topological possibilities, only a finite number of specific packing motifs are actually realized in proteins. This small number of motifs could serve as a basis set in the construction of larger networks. Of these, the triplet clique exhibits distinct preference both in terms of composition and geometry.

  15. Mapping the distribution of packing topologies within protein interiors shows predominant preference for specific packing motifs.

    Science.gov (United States)

    Basu, Sankar; Bhattacharyya, Dhananjay; Banerjee, Rahul

    2011-05-24

    Mapping protein primary sequences to their three dimensional folds referred to as the 'second genetic code' remains an unsolved scientific problem. A crucial part of the problem concerns the geometrical specificity in side chain association leading to densely packed protein cores, a hallmark of correctly folded native structures. Thus, any model of packing within proteins should constitute an indispensable component of protein folding and design. In this study an attempt has been made to find, characterize and classify recurring patterns in the packing of side chain atoms within a protein which sustains its native fold. The interaction of side chain atoms within the protein core has been represented as a contact network based on the surface complementarity and overlap between associating side chain surfaces. Some network topologies definitely appear to be preferred and they have been termed 'packing motifs', analogous to super secondary structures in proteins. Study of the distribution of these motifs reveals the ubiquitous presence of typical smaller graphs, which appear to get linked or coalesce to give larger graphs, reminiscent of the nucleation-condensation model in protein folding. One such frequently occurring motif, also envisaged as the unit of clustering, the three residue clique was invariably found in regions of dense packing. Finally, topological measures based on surface contact networks appeared to be effective in discriminating sequences native to a specific fold amongst a set of decoys. Out of innumerable topological possibilities, only a finite number of specific packing motifs are actually realized in proteins. This small number of motifs could serve as a basis set in the construction of larger networks. Of these, the triplet clique exhibits distinct preference both in terms of composition and geometry.

  16. Hard convex lens-shaped particles: Densest-known packings and phase behavior

    Energy Technology Data Exchange (ETDEWEB)

    Cinacchi, Giorgio, E-mail: giorgio.cinacchi@uam.es [Departamento de Física Teórica de la Materia Condensada, Instituto de Física de la Materia Condensada (IFIMAC), Instituto de Ciencias de Materiales “Nicolás Cabrera,” Universidad Autónoma de Madrid, Campus de Cantoblanco, E-28049 Madrid (Spain); Torquato, Salvatore, E-mail: torquato@princeton.edu [Department of Chemistry, Department of Physics, Institute for the Science and Technology of Materials, Program for Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544 (United States)

    2015-12-14

    By using theoretical methods and Monte Carlo simulations, this work investigates dense ordered packings and equilibrium phase behavior (from the low-density isotropic fluid regime to the high-density crystalline solid regime) of monodisperse systems of hard convex lens-shaped particles as defined by the volume common to two intersecting congruent spheres. We show that, while the overall similarity of their shape to that of hard oblate ellipsoids is reflected in a qualitatively similar phase diagram, differences are more pronounced in the high-density crystal phase up to the densest-known packings determined here. In contrast to those non-(Bravais)-lattice two-particle basis crystals that are the densest-known packings of hard (oblate) ellipsoids, hard convex lens-shaped particles pack more densely in two types of degenerate crystalline structures: (i) non-(Bravais)-lattice two-particle basis body-centered-orthorhombic-like crystals and (ii) (Bravais) lattice monoclinic crystals. By stacking at will, regularly or irregularly, laminae of these two crystals, infinitely degenerate, generally non-periodic in the stacking direction, dense packings can be constructed that are consistent with recent organizing principles. While deferring the assessment of which of these dense ordered structures is thermodynamically stable in the high-density crystalline solid regime, the degeneracy of their densest-known packings strongly suggests that colloidal convex lens-shaped particles could be better glass formers than colloidal spheres because of the additional rotational degrees of freedom.

  17. Domain Discretization and Circle Packings

    DEFF Research Database (Denmark)

    Dias, Kealey

    A circle packing is a configuration of circles which are tangent with one another in a prescribed pattern determined by a combinatorial triangulation, where the configuration fills a planar domain or a two-dimensional surface. The vertices in the triangulation correspond to centers of circles......, and edges correspond to two circles (having centers corresponding to the endpoints of the edge) being tangent to each other. This circle packing creates a rigid structure having an underlying geometric triangulation, where the centers of circles again correspond to vertices in the triangulation......, and the edges are geodesic segments (Euclidean, hyperbolic, or spherical) connecting centers of circles that are tangent to each other. Three circles that are mutually tangent form a face of the triangulation. Since circle packing is closely related to triangulation, circle packing methods can be applied...

  18. The pursuit of perfect packing

    CERN Document Server

    Weaire, Denis

    2008-01-01

    Coauthored by one of the creators of the most efficient space packing solution, the Weaire-Phelan structure, The Pursuit of Perfect Packing, Second Edition explores a problem of importance in physics, mathematics, chemistry, biology, and engineering: the packing of structures. Maintaining its mathematical core, this edition continues and revises some of the stories from its predecessor while adding several new examples and applications. The book focuses on both scientific and everyday problems ranging from atoms to honeycombs. It describes packing models, such as the Kepler conjecture, Voronoï decomposition, and Delaunay decomposition, as well as actual structure models, such as the Kelvin cell and the Weaire-Phelan structure. The authors discuss numerous historical aspects and provide biographical details on influential contributors to the field, including emails from Thomas Hales and Ken Brakke. With examples from physics, crystallography, engineering, and biology, this accessible and whimsical bo...

  19. Efficient parametric interactions in a low loss GaInP photonic crystal waveguide

    DEFF Research Database (Denmark)

    Cestier, I.; Willinger, A.; Colman, Pierre

    2011-01-01

    We describe time domain characterizations of dynamic four-wave mixing in a low loss modified W1 GaInP photonic crystal waveguide. Using 32 ps wide pump pulses with peak powers of up to 1:1W we achieved a very large conversion efficiency of ?6:8 dB as well as a 1:3 dB parametric gain experienced b...

  20. Efficient parametric interactions in a low loss GaInP photonic crystal waveguide.

    Science.gov (United States)

    Cestier, I; Willinger, A; Colman, P; Combrié, S; Lehoucq, G; De Rossi, A; Eisenstein, G

    2011-10-01

    We describe time domain characterizations of dynamic four-wave mixing in a low loss modified W1 GaInP photonic crystal waveguide. Using 32 ps wide pump pulses with peak powers of up to 1.1 W we achieved a very large conversion efficiency of -6.8 dB as well as a 1.3 dB parametric gain experienced by a weak CW probe signal. Time domain simulations confirm quantitatively all the measured results.

  1. Nanowire photonic crystal waveguides for single-atom trapping and strong light-matter interactions

    CERN Document Server

    Yu, S -P; Muniz, J A; Martin, M J; Norte, Richard; Hung, C -L; Meenehan, Seán M; Cohen, Justin D; Painter, Oskar; Kimble, H J

    2014-01-01

    We present a comprehensive study of dispersion-engineered nanowire photonic crystal waveguides suitable for experiments in quantum optics and atomic physics with optically trapped atoms. Detailed design methodology and specifications are provided, as are the processing steps used to create silicon nitride waveguides of low optical loss in the near-IR. Measurements of the waveguide optical properties and power-handling capability are also presented.

  2. Direct Visualization of Spruce Budworm Antifreeze Protein Interacting with Ice Crystals: Basal Plane Affinity Confers Hyperactivity

    OpenAIRE

    Pertaya, Natalya; Marshall, Christopher B.; Celik, Yeliz; Davies, Peter L.; Braslavsky, Ido

    2008-01-01

    Antifreeze proteins (AFPs) protect certain organisms from freezing by adhering to ice crystals, thereby preventing their growth. All AFPs depress the nonequilibrium freezing temperature below the melting point; however AFPs from overwintering insects, such as the spruce budworm (sbw) are 10–100 times more effective than most fish AFPs. It has been proposed that the exceptional activity of these AFPs depends on their ability to prevent ice growth at the basal plane. To test the hypothesis that...

  3. Applications of the Cambridge Structural Database in organic chemistry and crystal chemistry.

    Science.gov (United States)

    Allen, Frank H; Motherwell, W D Samuel

    2002-06-01

    The Cambridge Structural Database (CSD) and its associated software systems have formed the basis for more than 800 research applications in structural chemistry, crystallography and the life sciences. Relevant references, dating from the mid-1970s, and brief synopses of these papers are collected in a database, DBUse, which is freely available via the CCDC website. This database has been used to review research applications of the CSD in organic chemistry, including supramolecular applications, and in organic crystal chemistry. The review concentrates on applications that have been published since 1990 and covers a wide range of topics, including structure correlation, conformational analysis, hydrogen bonding and other intermolecular interactions, studies of crystal packing, extended structural motifs, crystal engineering and polymorphism, and crystal structure prediction. Applications of CSD information in studies of crystal structure precision, the determination of crystal structures from powder diffraction data, together with applications in chemical informatics, are also discussed.

  4. Are the Crystal Structures of Enantiopure and Racemic Mandelic Acids Determined by Kinetics or Thermodynamics?

    Science.gov (United States)

    Hylton, Rebecca K; Tizzard, Graham J; Threlfall, Terence L; Ellis, Amy L; Coles, Simon J; Seaton, Colin C; Schulze, Eric; Lorenz, Heike; Seidel-Morgenstern, Andreas; Stein, Matthias; Price, Sarah L

    2015-09-02

    Mandelic acids are prototypic chiral molecules where the sensitivity of crystallized forms (enantiopure/racemic compound/polymorphs) to both conditions and substituents provides a new insight into the factors that may allow chiral separation by crystallization. The determination of a significant number of single crystal structures allows the analysis of 13 enantiopure and 30 racemic crystal structures of 21 (F/Cl/Br/CH3/CH3O) substituted mandelic acid derivatives. There are some common phenyl packing motifs between some groups of racemic and enantiopure structures, although they show very different hydrogen-bonding motifs. The computed crystal energy landscape of 3-chloromandelic acid, which has at least two enantiopure and three racemic crystal polymorphs, reveals that there are many more possible structures, some of which are predicted to be thermodynamically more favorable as well as slightly denser than the known forms. Simulations of mandelic acid dimers in isolation, water, and toluene do not differentiate between racemic and enantiopure dimers and also suggest that the phenyl ring interactions play a major role in the crystallization mechanism. The observed crystallization behavior of mandelic acids does not correspond to any simple "crystal engineering rules" as there is a range of thermodynamically feasible structures with no distinction between the enantiopure and racemic forms. Nucleation and crystallization appear to be determined by the kinetics of crystal growth with a statistical bias, but the diversity of the mandelic acid crystallization behavior demonstrates that the factors that influence the kinetics of crystal nucleation and growth are not yet adequately understood.

  5. Salts of hexamethylenetetramine with organic acids: Enhanced anomeric interactions with a lowering of molecular symmetry revealed by crystal structures

    Science.gov (United States)

    Chandrasekhar, Sosale; Mukherjee, Somnath

    2015-02-01

    The hexamethylenetetramine (HMT) framework displays interesting stereoelectronic interactions of the anomeric type. In the highly symmetrical parent system, the nitrogen centres act as both donors and acceptors. Protonation lowers symmetry and also leads to an enhancement of the anomeric interaction around the protonated centre. X-ray diffraction crystal structures of four derivatives of HMT - with succinic, (DL)-malic, phthalic and 4-hydroxybenzoic acids - reveal significant trends. (The first three form well-defined salts, 4-hydroxybenzoic acid forming a co-crystalline compound.) Each molecular structure is essentially characterised by a major anomeric interaction involving the protonated centre as acceptor. In two cases (succinic and 4-hydroxybenzoic), secondary protonation leads to a weaker anomeric interaction site that apparently competes with the dominant one. Bond length changes indicate that the anomeric interaction decreases as malic > phthalic > succinic > 4-hydroxybenzoic, which correlates with the degree of proton transfer to the nitrogen centre. Along with other bond length and angle changes, the results offer insight into the applicability of the antiperiplanar lone pair hypothesis (ALPH) in a rigid system.

  6. Pattern formations and optimal packing.

    Science.gov (United States)

    Mityushev, Vladimir

    2016-04-01

    Patterns of different symmetries may arise after solution to reaction-diffusion equations. Hexagonal arrays, layers and their perturbations are observed in different models after numerical solution to the corresponding initial-boundary value problems. We demonstrate an intimate connection between pattern formations and optimal random packing on the plane. The main study is based on the following two points. First, the diffusive flux in reaction-diffusion systems is approximated by piecewise linear functions in the framework of structural approximations. This leads to a discrete network approximation of the considered continuous problem. Second, the discrete energy minimization yields optimal random packing of the domains (disks) in the representative cell. Therefore, the general problem of pattern formations based on the reaction-diffusion equations is reduced to the geometric problem of random packing. It is demonstrated that all random packings can be divided onto classes associated with classes of isomorphic graphs obtained from the Delaunay triangulation. The unique optimal solution is constructed in each class of the random packings. If the number of disks per representative cell is finite, the number of classes of isomorphic graphs, hence, the number of optimal packings is also finite.

  7. The short range anion-H interaction is the driving force for crystal formation of ions in water.

    Science.gov (United States)

    Alejandre, José; Chapela, Gustavo A; Bresme, Fernando; Hansen, Jean-Pierre

    2009-05-07

    The crystal formation of NaCl in water is studied by extensive molecular dynamics simulations. Ionic solutions at room temperature and various concentrations are studied using the SPC/E and TIP4P/2005 water models and seven force fields of NaCl. Most force fields of pure NaCl fail to reproduce the experimental density of the crystal, and in solution some favor dissociation at saturated conditions, while others favor crystal formation at low concentration. A new force field of NaCl is proposed, which reproduces the experimental phase diagram in the solid, liquid, and vapor regions. This force field overestimates the solubility of NaCl in water at saturation conditions when used with standard Lorentz-Berthelot combining rules for the ion-water pair potentials. It is shown that precipitation of ions is driven by the short range interaction between Cl-H pairs, a term which is generally missing in the simulation of ionic solutions. The effects of intramolecular flexibility of water on the solubility of NaCl ions are analyzed and is found to be small compared to rigid models. A flexible water model, extending the rigid SPC/E, is proposed, which incorporates Lennard-Jones interactions centered on the hydrogen atoms. This force field gives liquid-vapor coexisting densities and surface tensions in better agreement with experimental data than the rigid SPC/E model. The Cl-H, Na-O, and Cl-O pair distribution functions of the rigid and flexible models agree well with experiment. The predicted concentration dependence of the electric conductivity is in fair agreement with available experimental data.

  8. Primary and secondary interactions between CK2alpha and CK2beta lead to ring-like structures in the crystals of the CK2 holoenzyme

    DEFF Research Database (Denmark)

    Niefind, Karsten; Issinger, Olaf-Georg

    2005-01-01

    a distinct aggregation propensity of CK2. We demonstrate here that in the CK2 holoenzyme crystals contacts between different CK2 tetramers exists which provide structural details of the secondary CK2alpha/CK2beta interactions. These mainly ionic interactions lead to trimeric rings of CK2 holoenzymes...

  9. Analysis of the stabilization process of indomethacin crystals via π-π and CH-π interactions measured by Raman spectroscopy and X-ray diffraction

    Science.gov (United States)

    Hattori, Yusuke; Otsuka, Makoto

    2016-09-01

    In this study, formations of π-π and CH-π interactions in the crystallization of amorphous indomethacin (IMC) were investigated by simultaneous Raman spectroscopy and X-ray diffraction (XRD) measurements. The activation energy obtained from the change in the peak at 1616 cm-1 corresponded to the energy obtained from the XRD diffraction peak at 21.6°. We suggest that the stable IMC crystal forms by carboxyl-carboxyl interactions, which is followed by CH-π and π-π interactions supporting stabilization in the indole and chlorophenyl rings.

  10. Synthesis, crystal structure, Hirshfeld surface analysis, electronic structure through DFT study and fluorescence properties of a new anthracene based organic tecton

    Science.gov (United States)

    Pal, Nilasish; Singha, Debabrata; Jana, Atish Dipankar

    2017-10-01

    A new organic molecule 9,10-bis((2-(pyridin-2-yl)-1H-imidazol-1-yl)methyl)anthracene (APIM) has been synthesized. Crystal structure analysis of the molecular solid reveals that CH⋯π and π⋯π interactions are the molecular packing forces in the solid state. Thermal analysis of the molecular solid shows relatively higher decomposition temperature of the crystalline molecular solid that correlates well with the cooperative nature of CH⋯π and π⋯π interactions. Density Functional Theory (DFT) optimized structure of the molecule closely correlates with that found in the crystal. DFT optimizations also lead to the similar CH⋯π and π⋯π interaction motifs that are found within the crystal. Hirshfeld surface analysis provides detailed insight into the relative importance of various weak forces in the molecular packing. Study of the fluorescence behavior of the molecules shows quenching in the presence of metal ions.

  11. Random close packing revisited: ways to pack frictionless disks.

    Science.gov (United States)

    Xu, Ning; Blawzdziewicz, Jerzy; O'Hern, Corey S

    2005-06-01

    We create collectively jammed (CJ) packings of 50-50 bidisperse mixtures of smooth disks in two dimensions (2D) using an algorithm in which we successively compress or expand soft particles and minimize the total energy at each step until the particles are just at contact. We focus on small systems in 2D and thus are able to find nearly all of the collectively jammed states at each system size. We decompose the probability P(phi) for obtaining a collectively jammed state at a particular packing fraction phi into two composite functions: (1) the density of CJ packing fractions rho(phi), which only depends on geometry, and (2) the frequency distribution beta(phi), which depends on the particular algorithm used to create them. We find that the function rho(phi) is sharply peaked and that beta(phi) depends exponentially on phi. We predict that in the infinite-system-size limit the behavior of P(phi) in these systems is controlled by the density of CJ packing fractions--not the frequency distribution. These results suggest that the location of the peak in P(phi) when N --> infinity can be used as a protocol-independent definition of random close packing.

  12. cellPACK: A Virtual Mesoscope to Model and Visualize Structural Systems Biology

    Science.gov (United States)

    Johnson, Graham T.; Autin, Ludovic; Al-Alusi, Mostafa; Goodsell, David S.; Sanner, Michel F.; Olson, Arthur J.

    2014-01-01

    cellPACK assembles computational models of the biological mesoscale, an intermediate scale (10−7–10−8m) between molecular and cellular biology. cellPACK’s modular architecture unites existing and novel packing algorithms to generate, visualize and analyze comprehensive 3D models of complex biological environments that integrate data from multiple experimental systems biology and structural biology sources. cellPACK is currently available as open source code, with tools for validation of models and with recipes and models for five biological systems: blood plasma, cytoplasm, synaptic vesicles, HIV and a mycoplasma cell. We have applied cellPACK to model distributions of HIV envelope protein to test several hypotheses for consistency with experimental observations. Biologists, educators, and outreach specialists can interact with cellPACK models, develop new recipes and perform packing experiments through scripting and graphical user interfaces at http://cellPACK.org. PMID:25437435

  13. Protein-detergent interactions in single crystals of membrane proteins studied by neutron crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Timmins, P.A. [ILL, Grenoble (France); Pebay-Peyroula, E. [IBS-UJF Grenoble (France)

    1994-12-31

    The detergent micelles surrounding membrane protein molecules in single crystals can be investigated using neutron crystallography combined with H{sub 2}O/D{sub 2}O contrast variation. If the protein structure is known then the contrast variation method allows phases to be determined at a contrast where the detergent dominates the scattering. The application of various constraints allows the resulting scattering length density map to be realistically modeled. The method has been applied to two different forms of the membrane protein porin. In one case both hydrogenated and partially deuterated protein were used, allowing the head group and tail to be distinguished.

  14. Strong Raman-induced non-instantaneous soliton interactions in gas-filled photonic crystal fibers

    CERN Document Server

    Saleh, Mohammed F; Marini, Andrea; Biancalana, Fabio

    2015-01-01

    We have developed an analytical model based on the perturbation theory in order to study the optical propagation of two successive intense solitons in hollow-core photonic crystal fibers filled with Raman-active gases. Based on the time delay between the two solitons, we have found that the trailing soliton dynamics can experience unusual nonlinear phenomena such as spectral and temporal soliton oscillations and transport towards the leading soliton. The overall dynamics can lead to a spatiotemporal modulation of the refractive index with a uniform temporal period and a uniform or chirped spatial period.

  15. Interaction between Heparin and Fibronectin:Using Quartz Crystal Microbalance with Dissipation, Immunochemistry and Isothermal Titration Calorimetry

    Institute of Scientific and Technical Information of China (English)

    LI Guicai; WANG Caiping; YANG Ping; ZHOU Jie; ZHU Pingchuan

    2015-01-01

    The adsorption behavior of heparin and ifbronectin was studied by quartz crystal microbalance with dissipation (QCM-D), and the interaction between heparin and fibronectin was evaluated using immunochemistry and isothermal titration calorimetry (ITC) measurement. The results showed that there was competitive adsorption between heparin and fibronectin, and the preadsorption of fibronectin could prevent subsequent heparin adsorption to some extent, and the adsorbed Hep/Fn complex on the surface was in a rigid form. The bioactivity of heparin and ifbronectin could be affected by the bulk concentration of each, and both heparin and ifbronectin in Hep/Fn complex formed under pH 4 condition displayed larger bioactivity than that formed under pH 7 condition. Moreover, the ifbronectin showed more exposed cell-binding sites at the pH value lower than physiological condition. The results of ITC further suggested that the interaction between heparin and ifbronectin under pH 4 was stronger than under pH 7, and the complex was also more stable. The study brings forth the detailed interaction between heparin and ifbronectin, which will be helpful for better understanding the interaction mechanism of the two biomolecules. The results may be potentially useful for the development of new generation of cardiovascular biomaterials.

  16. Valve stem and packing assembly

    Energy Technology Data Exchange (ETDEWEB)

    Wordin, J.J.

    1991-09-03

    A valve stem and packing assembly is provided in which a rotatable valve stem includes a first tractrix surface for sliding contact with a stem packing and also includes a second tractrix surface for sliding contact with a bonnet. Force is applied by means of a spring, gland flange, and gland on the stem packing so the stem packing seals to the valve stem and bonnet. This configuration serves to create and maintain a reliable seal between the stem packing and the valve stem. The bonnet includes a second complementary tractrix surface for contacting the second sliding tractrix surface, the combination serving as a journal bearing for the entire valve stem and packing assembly. The journal bearing so configured is known as a Schiele's pivot. The Schiele's pivot also serves to maintain proper alignment of the valve stem with respect to the bonnet. Vertical wear between the surfaces of the Schiele's pivot is uniform at all points of contact between the second sliding tractrix surface and the second complementary tractrix surface of a bonnet. The valve stem is connected to a valve plug by means of a slip joint. The valve is opened and closed by rotating the valve stem. The slip joint compensates for wear on the Schiele's pivot and on the valve plug. A ledge is provided on the valve bonnet for the retaining nut to bear against. The ledge prevents over tightening of the retaining nut and the resulting excessive friction between stem and stem packing. 2 figures.

  17. Valve stem and packing assembly

    Energy Technology Data Exchange (ETDEWEB)

    Wordin, John J. (Bingham County, ID)

    1991-01-01

    A valve stem and packing assembly is provided in which a rotatable valve stem includes a first tractrix surface for sliding contact with a stem packing and also includes a second tractrix surface for sliding contact with a bonnet. Force is applied by means of a spring, gland flange, and gland on the stem packing so the stem packing seals to the valve stem and bonnet. This configuration serves to create and maintain a reliable seal between the stem packing and the valve stem. The bonnet includes a second complementary tractrix surface for contacting the second sliding tractrix surface, the combination serving as a journal bearing for the entire valve stem and packing assembly. The journal bearing so configured is known as a Schiele's pivot. The Schiele's pivot also serves to maintain proper alignment of the valve stem with respect to the bonnet. Vertical wear between the surfaces of the Schiele's pivot is uniform at all points of contact between the second sliding tractrix surface and the second complementary tractrix surface of a bonnet. The valve stem is connected to a valve plug by means of a slip joint. The valve is opened and closed by rotating the valve stem. The slip joint compensates for wear on the Schiele's pivot and on the valve plug. A ledge is provided on the valve bonnet for the retaining nut to bear against. The ledge prevents overtightening of the retaining nut and the resulting excessive friction between stem and stem packing.

  18. Valve stem and packing assembly

    Energy Technology Data Exchange (ETDEWEB)

    Wordin, J.J.

    1990-01-01

    A valve stem and packing assembly is provided in which a rotatable valve stem includes a first tractrix surface for sliding contact with a stem packing and also includes a second tractrix surface for sliding contact with a bonnet. Force is applied by means of a spring, gland flange, and gland on the stem packing so the stem packing seals to the valve stem and bonnet. This configuration serves to create and maintain a reliable seal between the stem packing and the valve stem. The bonnet includes a second complementary tractrix surface for contacting the second sliding tractrix surface, the combination serving as a journal bearing for the entire valve stem and packing assembly. The journal bearing so configured is known as a Schiele's pivot. The Schiele's pivot also serves to maintain proper alignment of the valve stem with respect to the bonnet. Vertical wear between the surfaces of the Schiele's pivot is uniform at all points of contact between the second sliding tractrix surface and the second complementary tractrix surface of a bonnet. The valve stem is connected to a valve plug by means of a slip joint. The valve is opened and closed by rotating the valve stem. The slip joint compensates for wear on the Schiele's pivot and on the valve plug. A ledge is provided on the valve bonnet for the retaining nut to bear against. The ledge prevents overtightening of the retaining nut and the resulting excessive friction between stem and stem packing.

  19. 7 CFR 51.310 - Packing requirements.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Packing requirements. 51.310 Section 51.310... STANDARDS) United States Standards for Grades of Apples Packing Requirements § 51.310 Packing requirements... the contents. (e) Tolerances: In order to allow for variations incident to proper packing, not...

  20. 7 CFR 51.1270 - Packing.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Packing. 51.1270 Section 51.1270 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Summer and Fall Pears 1 Standard Pack § 51.1270 Packing. (a) Each package shall be packed...

  1. 7 CFR 51.1311 - Packing.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Packing. 51.1311 Section 51.1311 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Winter Pears 1 Standard Pack § 51.1311 Packing. (a) Each package shall be packed so that...

  2. The Crystal Structure of Coxsackievirus A21 and Its Interaction with ICAM-1

    Energy Technology Data Exchange (ETDEWEB)

    Xiao, Chuan; Bator-Kelly, Carol M.; Rieder, Elizabeth; Chipman, Paul R.; Craig, Alister; Kuhn, Richard J.; Wimmer, Eckard; Rossmann, Michael G. (Liverpool); (SBU); (Purdue)

    2010-11-30

    CVA21 and polioviruses both belong to the Enterovirus genus in the family of Picornaviridae, whereas rhinoviruses form a distinct picornavirus genus. Nevertheless, CVA21 and the major group of human rhinoviruses recognize intercellular adhesion molecule-1 (ICAM-1) as their cellular receptor, whereas polioviruses use poliovirus receptor. The crystal structure of CVA21 has been determined to 3.2 {angstrom} resolution. Its structure has greater similarity to poliovirus structures than to other known picornavirus structures. Cryo-electron microscopy (cryo-EM) was used to determine an 8.0 {angstrom} resolution structure of CVA21 complexed with an ICAM-1 variant, ICAM-1{sup Kilifi}. The cryo-EM map was fitted with the crystal structures of ICAM-1 and CVA21. Significant differences in the structure of CVA21 with respect to the poliovirus structures account for the inability of ICAM-1 to bind polioviruses. The interface between CVA21 and ICAM-1 has shape and electrostatic complementarity with many residues being conserved among those CVAs that bind ICAM-1.

  3. Molecular packing in bone collagen fibrils prior to mineralization

    Science.gov (United States)

    Hsiao, Benjamin; Zhou, Hong-Wen; Burger, Christian; Chu, Benjamin; Glimcher, Melvin J.

    2012-02-01

    The three-dimensional packing of collagen molecules in bone collagen fibrils has been largely unknown because even in moderately mineralized bone tissues, the organic matrix structure is severely perturbed by the deposition of mineral crystals. During the past decades, the structure of tendon collagen (e.g. rat tail) --- a tissue that cannot mineralize in vivo, has been assumed to be representative for bone collagen fibrils. Small-angle X-ray diffraction analysis of the native, uncalcified intramuscular fish bone has revealed a new molecular packing scheme, significantly different from the quasi-hexagonal arrangement often found in tendons. The deduced structure in bone collagen fibrils indicates the presence of spatially discrete microfibrils, and an arrangement of intrafibrillar space to form ``channels'', which could accommodate crystals with dimensions typically found in bone apatite.

  4. Experimental and theoretical investigations of the gain dependence at two-wave interaction on the thickness and orientation angle of the Bi12GeO20 crystal

    Science.gov (United States)

    Shepelevich, V. V.; Makarevich, A. V.; Shandarov, S. M.

    2017-06-01

    Experimental studies of the dependence of object wave gain at two-wave interaction on the effective thickness of cubic photorefractive optically active crystal Bi12GeO20 were performed using only one (\\bar 1\\bar 10) -cut crystal sample. It is shown that the obtained experimental results can be satisfactorily theoretically interpreted taking into account the inverse piezoelectric and the photo-elastic effects in addition to the traditionally considered electro-optical one.

  5. Beyond packing of hard spheres: The effects of core softness, non-additivity, intermediate-range repulsion, and many-body interactions on the glass-forming ability of bulk metallic glasses

    Science.gov (United States)

    Zhang, Kai; Fan, Meng; Liu, Yanhui; Schroers, Jan; Shattuck, Mark D.; O'Hern, Corey S.

    2015-11-01

    When a liquid is cooled well below its melting temperature at a rate that exceeds the critical cooling rate Rc, the crystalline state is bypassed and a metastable, amorphous glassy state forms instead. Rc (or the corresponding critical casting thickness dc) characterizes the glass-forming ability (GFA) of each material. While silica is an excellent glass-former with small Rc alloys are typically poor glass-formers with large Rc > 1010 K/s. Only in the past thirty years have bulk metallic glasses (BMGs) been identified with Rc approaching that for silica. Recent simulations have shown that simple, hard-sphere models are able to identify the atomic size ratio and number fraction regime where BMGs exist with critical cooling rates more than 13 orders of magnitude smaller than those for pure metals. However, there are a number of other features of interatomic potentials beyond hard-core interactions. How do these other features affect the glass-forming ability of BMGs? In this manuscript, we perform molecular dynamics simulations to determine how variations in the softness and non-additivity of the repulsive core and form of the interatomic pair potential at intermediate distances affect the GFA of binary alloys. These variations in the interatomic pair potential allow us to introduce geometric frustration and change the crystal phases that compete with glass formation. We also investigate the effect of tuning the strength of the many-body interactions from zero to the full embedded atom model on the GFA for pure metals. We then employ the full embedded atom model for binary BMGs and show that hard-core interactions play the dominant role in setting the GFA of alloys, while other features of the interatomic potential only change the GFA by one to two orders of magnitude. Despite their perturbative effect, understanding the detailed form of the intermetallic potential is important for designing BMGs with cm or greater casting thickness.

  6. Packing of crystalline structures of binary hard spheres: an analytical approach and application to amorphization.

    Science.gov (United States)

    Brouwers, H J H

    2007-10-01

    The geometrical stability of the three lattices of the cubic crystal system, viz. face-centered cubic (fcc), body-centered cubic (bcc), and simple cubic (sc), consisting of bimodal discrete hard spheres, and the transition to amorphous packing is studied. First, the random close packing (rcp) fraction of binary mixtures of amorphously packed spheres is recapitulated. Next, the packing of a binary mixture of hard spheres in randomly disordered cubic structures is analyzed, resulting in original analytical expressions for the unit cell volume and the packing fraction, and which are also valid for the other five crystal systems. The bimodal fcc lattice parameter appears to be in close agreement with empirical hard sphere data from literature, and this parameter could be used to distinguish the size mismatch effect from all other effects in distorted binary lattices of materials. Here, as a first model application, bimodal amorphous and crystalline fcc/bcc packing fractions are combined, yielding the optimum packing configuration, which depends on mixture composition and diameter ratio only. Maps of the closest packing mode are established and applied to colloidal mixtures of polydisperse spheres and to binary alloys of bcc, fcc, and hcp metals. The extensive comparison between the analytical expressions derived here and the published numerical and empirical data yields good agreement. Hence, it is seen that basic space-filling theories on "simple" noninteracting hard spheres are a valuable tool for the study of crystalline materials.

  7. Packing of crystalline structures of binary hard spheres: An analytical approach and application to amorphization

    Science.gov (United States)

    Brouwers, H. J. H.

    2007-10-01

    The geometrical stability of the three lattices of the cubic crystal system, viz. face-centered cubic (fcc), body-centered cubic (bcc), and simple cubic (sc), consisting of bimodal discrete hard spheres, and the transition to amorphous packing is studied. First, the random close packing (rcp) fraction of binary mixtures of amorphously packed spheres is recapitulated. Next, the packing of a binary mixture of hard spheres in randomly disordered cubic structures is analyzed, resulting in original analytical expressions for the unit cell volume and the packing fraction, and which are also valid for the other five crystal systems. The bimodal fcc lattice parameter appears to be in close agreement with empirical hard sphere data from literature, and this parameter could be used to distinguish the size mismatch effect from all other effects in distorted binary lattices of materials. Here, as a first model application, bimodal amorphous and crystalline fcc/bcc packing fractions are combined, yielding the optimum packing configuration, which depends on mixture composition and diameter ratio only. Maps of the closest packing mode are established and applied to colloidal mixtures of polydisperse spheres and to binary alloys of bcc, fcc, and hcp metals. The extensive comparison between the analytical expressions derived here and the published numerical and empirical data yields good agreement. Hence, it is seen that basic space-filling theories on “simple” noninteracting hard spheres are a valuable tool for the study of crystalline materials.

  8. Many-particle interactions and rainbow effects in grazing scattering of Ar atoms on the Al(1 1 1), Ag(1 1 1) crystals

    Science.gov (United States)

    Babenko, P. Yu.; Meluzova, D. S.; Shergin, A. P.; Zinoviev, A. N.

    2017-09-01

    Computer simulation of rainbow and ;ion focusing; effects taking place in scattering of Ar atoms on Al(1 1 1) and Ag(1 1 1) crystal surfaces have been performed. The trajectory calculation and vector summation of forces of the projectile atom interaction with crystal atoms have been shown to provide good fitting of the available experimental data. The thermal vibration amplitude for atoms located on the surface of crystals under study has been determined. A functional form of the potential has been proposed that fits well the experimental data.

  9. Deterministic indexing for packed strings

    DEFF Research Database (Denmark)

    Bille, Philip; Gørtz, Inge Li; Skjoldjensen, Frederik Rye

    2017-01-01

    Given a string S of length n, the classic string indexing problem is to preprocess S into a compact data structure that supports efficient subsequent pattern queries. In the deterministic variant the goal is to solve the string indexing problem without any randomization (at preprocessing time...... or query time). In the packed variant the strings are stored with several character in a single word, giving us the opportunity to read multiple characters simultaneously. Our main result is a new string index in the deterministic and packed setting. Given a packed string S of length n over an alphabet σ......, we show how to preprocess S in O(n) (deterministic) time and space O(n) such that given a packed pattern string of length m we can support queries in (deterministic) time O (m/α + log m + log log σ), where α = w/log σ is the number of characters packed in a word of size w = θ(log n). Our query time...

  10. Hard sphere packings within cylinders.

    Science.gov (United States)

    Fu, Lin; Steinhardt, William; Zhao, Hao; Socolar, Joshua E S; Charbonneau, Patrick

    2016-03-07

    Arrangements of identical hard spheres confined to a cylinder with hard walls have been used to model experimental systems, such as fullerenes in nanotubes and colloidal wire assembly. Finding the densest configurations, called close packings, of hard spheres of diameter σ in a cylinder of diameter D is a purely geometric problem that grows increasingly complex as D/σ increases, and little is thus known about the regime for D > 2.873σ. In this work, we extend the identification of close packings up to D = 4.00σ by adapting Torquato-Jiao's adaptive-shrinking-cell formulation and sequential-linear-programming (SLP) technique. We identify 17 new structures, almost all of them chiral. Beyond D ≈ 2.85σ, most of the structures consist of an outer shell and an inner core that compete for being close packed. In some cases, the shell adopts its own maximum density configuration, and the stacking of core spheres within it is quasiperiodic. In other cases, an interplay between the two components is observed, which may result in simple periodic structures. In yet other cases, the very distinction between the core and shell vanishes, resulting in more exotic packing geometries, including some that are three-dimensional extensions of structures obtained from packing hard disks in a circle.

  11. Investigation of Crystal Surface Finish and Geometry on Single LYSO Scintillator Detector Performance for Depth-of-Interaction Measurement with Silicon Photomultipliers.

    Science.gov (United States)

    Bircher, Chad; Shao, Yiping

    2012-11-21

    Depth of Interaction (DOI) information can improve quality of reconstructed images acquired from Positron Emission Tomography (PET), especially in high resolution and compact scanners dedicated for breast, brain, or small animal imaging applications. Additionally, clinical scanners with time of flight capability can also benefit from DOI information. One of the most promising methods of determining DOI in a crystal involves reading the signal from two ends of a scintillation crystal, and calculating the signal ratio between the two detectors. This method is known to deliver a better DOI resolution with rough crystals compared to highly polished crystals. However, what is still not well studied is how much of a tradeoff is involved between spatial, energy, temporal, and DOI resolutions as a function of the crystal surface treatment and geometry with the use of Silicon Photomultipliers (SiPM) as the photo detectors. This study investigates the effects of different crystal surface finishes and geometries on energy, timing and DOI resolutions at different crystal depths. The results show that for LYSO scintillators of 1.5×1.5×20 mm(3) and 2×2×20 mm(3) with their surfaces finished from 0.5 to 30 micron roughness, almost the same energy and coincidence timing resolutions were maintained, around 15% and 2.4 ns respectively across different crystal depths, while the DOI resolutions were steadily improved from worse than 5 mm to better than 2 mm. They demonstrate that crystal roughness, with proper surface preparing, does not have a significant effect on the energy and coincidence timing resolutions in the crystals examined, and there does not appear to be a tradeoff between improving DOI resolution and degrading other detector performances. These results will be valuable to guide the selection of crystal surface conditions for developing a DOI measurable PET detector with a full array of LYSO scintillators coupled to SiPM arrays.

  12. A unified picture of the crystal structures of metals

    Science.gov (United States)

    Söderlind, Per; Eriksson, Olle; Johansson, Börje; Wills, J. M.; Boring, A. M.

    1995-04-01

    THE crystal structures of the light actinides have intrigued physicists and chemists for several decades1. Simple metals and transition metals have close-packed, high-symmetry structures, such as body-centred cubic, face-centred cubic and hexagonal close packing. In contrast, the structures of the light actinides are very loosely packed and of low symmetry-tetragonal, orthorhombic and monoclinic. To understand these differences, we have performed total-energy calculations, as a function of volume, for both high-and low-symmetry structures of a simple metal (aluminium), a non-magnetic transition metal (niobium), a ferromagnetic transition metal (iron) and a light actinide (uranium). We find that the crystal structure of all of these metals is determined by the balance between electrostatic (Madelung) interactions, which favour high symmetry, and a Peierls distortion of the crystal lattice, which favours low symmetry. We show that simple metals and transition metals can adopt low-symmetry structures on expansion of the lattice; and we predict that, conversely, the light actinides will undergo transitions to structures of higher symmetry on compression.

  13. Analytical approach to determining human biogenic amines and their metabolites using eVol microextraction in packed syringe coupled to liquid chromatography mass spectrometry method with hydrophilic interaction chromatography column.

    Science.gov (United States)

    Konieczna, Lucyna; Roszkowska, Anna; Synakiewicz, Anna; Stachowicz-Stencel, Teresa; Adamkiewicz-Drożyńska, Elżbieta; Bączek, Tomasz

    2016-04-01

    Analysis of biogenic amines (BAs) in different human samples provides insight into the mechanisms of various biological processes, including pathological conditions, and thus may be very important in diagnosing and monitoring several neurological disorders and cancerous tumors. In this work, we developed a simple and fast procedure using a digitally controlled microextraction in packed syringe (MEPS) coupled to liquid chromatography mass spectrometry (LC-MS) method for simultaneous determination of biogenic amines, their precursors and metabolites in human plasma and urine samples. The separation of 12 low molecular weight and hydrophilic molecules with a wide range of polarities was achieved with hydrophilic interaction chromatography (HILIC) column without derivatization step in 12 min. MEPS was implemented using the APS sorbent in semi-automated analytical syringe (eVol(®)) and small volume of urine and plasma samples, 5 0µL and 100 μL, respectively. We evaluated important parameters influencing MEPS efficiency, including stationary phase selection, sample pH and volume, number of extraction cycles, and washing and elution volumes. In optimized MEPS conditions, the analytes were eluted by 3 × 50 μL of methanol with 0.1% formic acid. The chromatographic separation of analytes was performed on XBridge Amide™ BEH analytical column (3.0mm × 100 mm, 3.5 µm) using gradient elution with mobile phase consisting of phase A: 10mM ammonium formate buffer in water pH 3.0 and phase B: 10mM ammonium formate buffer in acetonitrile pH 3.0. The LC-HILIC-MS method was validated and, in optimum conditions, presented good linearity in concentration range within 10-2000 ng/mL for all the analytes with a determination coefficient (r(2)) higher than 0.999 for plasma and urine samples. Method recovery ranged within 87.6-104.3% for plasma samples and 84.2-98.6% for urine samples. The developed method utilizing polar APS sorbent along with polar HILIC column was applied for

  14. Crystal lattice properties fully determine short-range interaction parameters for alkali and halide ions

    CERN Document Server

    Mao, Albert H; 10.1063/1.4742068

    2012-01-01

    Accurate models of alkali and halide ions in aqueous solution are necessary for computer simulations of a broad variety of systems. Previous efforts to develop ion force fields have generally focused on reproducing experimental measurements of aqueous solution properties such as hydration free energies and ion-water distribution functions. This dependency limits transferability of the resulting parameters because of the variety and known limitations of water models. We present a solvent-independent approach to calibrating ion parameters based exclusively on crystal lattice properties. Our procedure relies on minimization of lattice sums to calculate lattice energies and interionic distances instead of equilibrium ensemble simulations of dense fluids. The gain in computational efficiency enables simultaneous optimization of all parameters for Li+, Na+, K+, Rb+, Cs+, F-, Cl-, Br-, and I- subject to constraints that enforce consistency with periodic table trends. We demonstrate the method by presenting lattice-d...

  15. Quartz Crystal Microbalances for quantitative picosecond laser-material-interaction investigations - Part I: Technical considerations

    Science.gov (United States)

    Gierse, N.; Schildt, T.; Esser, H. G.; Sergienko, G.; Brezinsek, S.; Freisinger, M.; Zhao, D.; Ding, H.; Terra, A.; Samm, U.; Linsmeier, Ch.

    2016-12-01

    In this work the technical suitability of Quartz Crystal Microbalances (QMBs) for in situ, pulse resolved mass removal measurements is demonstrated for picosecond laser ablation of magnetron sputtered coatings. The QMBs show a linear characteristic of the sensitivity for layer thickness of different metals up to several microns. Laser pulse resolved measurements of the mass ablated from the metal layer were performed. About 400 ng of chromium was ablated during the first laser pulse while in subsequent pulses ablation of the QMBs is found to be larger than for deposition, which is explained by the radial sensitivity of the QMBs. Future refinements of the setup and the benefits of the pulse resolved mass loss measurements for laser based methods like LIBS and LIAS are discussed and will be presented in part II currently in preparation.

  16. Equilibrium crystal phases of triblock Janus colloids

    Science.gov (United States)

    Reinhart, Wesley F.; Panagiotopoulos, Athanassios Z.

    2016-09-01

    Triblock Janus colloids, which are colloidal spheres decorated with attractive patches at each pole, have recently generated significant interest as potential building blocks for functional materials. Their inherent anisotropy is known to induce self-assembly into open structures at moderate temperatures and pressures, where they are stabilized over close-packed crystals by entropic effects. We present a numerical investigation of the equilibrium phases of triblock Janus particles with many different patch geometries in three dimensions, using Monte Carlo simulations combined with free energy calculations. In all cases, we find that the free energy difference between crystal polymorphs is less than 0.2 kBT per particle. By varying the patch fraction and interaction range, we show that large patches stabilize the formation of structures with four bonds per patch over those with three. This transition occurs abruptly above a patch fraction of 0.30 and has a strong dependence on the interaction range. Furthermore, we find that a short interaction range favors four bonds per patch, with longer range increasingly stabilizing structures with only three bonds per patch. By quantifying the effect of patch geometry on the stability of the equilibrium crystal structures, we provide insights into the fundamental design rules for constructing complex colloidal crystals.

  17. Dealing with Nonregular Shapes Packing

    Directory of Open Access Journals (Sweden)

    Bonfim Amaro Júnior

    2014-01-01

    Full Text Available This paper addresses the irregular strip packing problem, a particular two-dimensional cutting and packing problem in which convex/nonconvex shapes (polygons have to be packed onto a single rectangular object. We propose an approach that prescribes the integration of a metaheuristic engine (i.e., genetic algorithm and a placement rule (i.e., greedy bottom-left. Moreover, a shrinking algorithm is encapsulated into the metaheuristic engine to improve good quality solutions. To accomplish this task, we propose a no-fit polygon based heuristic that shifts polygons closer to each other. Computational experiments performed on standard benchmark problems, as well as practical case studies developed in the ambit of a large textile industry, are also reported and discussed here in order to testify the potentialities of proposed approach.

  18. Planet Packing in Circumbinary Systems

    CERN Document Server

    Kratter, Kaitlin M

    2013-01-01

    The recent discovery of planets orbiting main sequence binaries will provide crucial constraints for theories of binary and planet formation. The formation pathway for these planets is complicated by uncertainties in the formation mechanism of the host stars. In this paper, we compare the dynamical states of single and binary star planetary systems. Specifically, we pose two questions: (1) What does it mean for a circumbinary system to be dynamically packed? (2) How many systems are required to differentiate between a population of packed or sparse planets? We determine when circumbinary systems become dynamically unstable as a function of the separation between the host-stars and the inner planet, and the first and second planets. We show that these represent unique stability constraints compared to single-star systems. We find that although the existing Kepler data is insufficient to distinguish between a population of packed or sparse circumbinary systems, a more thorough study of circumbinary TTVs combine...

  19. Heuristics for Multidimensional Packing Problems

    DEFF Research Database (Denmark)

    Egeblad, Jens

    In this thesis we consider solution methods for packing problems. Packing problems occur in many different situations both directly in the industry and as sub-problems of other problems. High-quality solutions for problems in the industrial sector may be able to reduce transportation and production...... costs significantly. For packing problems in general are given a set of items and one of more containers. The items must be placed within the container such that some objective is optimized and the items do not overlap. Items and container may be rectangular or irregular (e.g. polygons and polyhedra......) and may be defined in any number of dimensions. Solution methods are based on theory from both computational geometry and operations research. The scientific contributions of this thesis are presented in the form of six papers and a section which introduces the many problem types and recent solution...

  20. Interactions between X-ray induced transient defects and pre-existing damage precursors in DKDP crystals

    Energy Technology Data Exchange (ETDEWEB)

    Negres, R A; Saw, C K; Demos, S G

    2008-10-24

    Large-aperture laser systems, currently designed to achieve high energy densities at the target location (exceeding {approx} 10{sup 11} J/m{sup 3}), will enable studies of the physics of matter and radiation under extreme conditions. As a result, their optical components, such as the frequency conversion crystals (KDP/DKDP), may be exposed to X-rays and other ionizing radiation. This in turn may lead to a change in the damage performance of these materials as they may be affected by radiation-induced effects by either forming new damage initiation centers or interacting with the pre-existing damage initiating defects (so-called damage precursors). We present an experimental study on the laser-induced bulk damage performance at 355-nm of DKDP crystals following X-ray irradiation at room temperature. Results indicate that the damage performance of the material is affected by exposure to X-rays. We attribute this behavior to a change in the physical properties of the precursors which, in turn, affect their individual damage threshold.

  1. Metal-ion interactions with sugars. The crystal structure and FTIR study of an SrCl2-fructose complex.

    Science.gov (United States)

    Guo, Jianyu; Zhang, Xiangmin

    2004-06-01

    The single-crystal structure of SrCl2 x 2C6H12O6 x 3H2O was determined with Mr = 572.88, a = 16.252, b = 7.941(2), c = 10.751(3) angstroms, beta = 127.652(4) degrees, V = 1098.5(6) angstroms3, C2, Z = 2, mu = 0.71073 angstroms and R = 0.0296 for 1998 observed reflections. The fructose moiety of the complex exists as a beta-d-pyranose. The strontium atom is surrounded by eight oxygen atoms, which are arranged in symmetry-related pairs that are derived from four sugar and two water molecules. Three nonvicinal hydroxyl groups of fructose are involved in strontium binding. All the hydroxyl groups and water molecules are involved in forming an extensive hydrogen-bond network. The Sr-fructose complex is isostructural with the Ca-fructose complex, and the crystal structures and FTIR spectra of the two complexes are compared in this article. The O-H, C-O, and C-O-H vibrations are shifted, and the relative intensities changed in the complexes IR spectra, which indicate sugar metalation. By studying the metal-binding properties of fructose, it is hoped that such would aid in the understanding of the structural chemistry of metal ions interacting with saccharides, as an actual biological system, and thereby aid in the interpretation of some particular biological processes.

  2. Biomolecular interactions and tools for their recognition: focus on the quartz crystal microbalance and its diverse surface chemistries and applications.

    Science.gov (United States)

    Cheng, Cathy I; Chang, Yi-Pin; Chu, Yen-Ho

    2012-03-07

    Interactions between molecules are ubiquitous and occur in our bodies, the food we eat, the air we breathe, and myriad additional contexts. Although numerous tools are available for the recognition of biomolecular interactions, such tools are often limited in their sensitivity, expensive, and difficult to modify for various uses. In contrast, the quartz crystal microbalance (QCM) has sub-nanogram detection capabilities, is label-free, is inexpensive to create, and can be readily modified with a number of diverse surface chemistries to detect and characterize diverse interactions. To maximize the versatility of the QCM, scientists need to know available methods by which QCM surfaces can be modified. Therefore, in addition to summarizing the various tools currently used for biomolecular recognition, explicating the fundamental principles of the QCM as a tool for biomolecular recognition, and comparing the QCM with other acoustic sensors, we systematically review the numerous types of surface chemistries-including hydrophobic bonds, ionic bonds, hydrogen bonds, self-assembled monolayers, plasma-polymerized films, photochemistry, and sensing ionic liquids-used to functionalize QCMs for various purposes. We also review the QCM's diverse applications, which include the detection of gaseous species, detection of carbohydrates, detection of nucleic acids, detection of non-enzymatic proteins, characterization of enzymatic activity, detection of antigens and antibodies, detection of cells, and detection of drugs. Finally, we discuss the ultimate goals of and potential barriers to the development of future QCMs.

  3. Efficient Modeling of Coulomb Interaction Effect on Exciton in Crystal-Phase Nanowire Quantum Dot

    DEFF Research Database (Denmark)

    Taherkhani, Masoomeh; Gregersen, Niels; Mørk, Jesper

    2016-01-01

    The binding energy and oscillation strength of the ground-state exciton in type-II quantum dot (QD) is calculated by using a post Hartree-Fock method known as the configuration interaction (CI) method which is significantly more efficient than conventional methods like ab initio method. We show t...... that the Coulomb interaction between electron and holes in these structures considerably affects the transition dipole moment which is the key parameter of optical quantum gating in STIRAP (stimulated Raman adiabatic passage) process for implementing quantum gates [1], [2]....

  4. Use of the Primitive Unit Cell in Understanding Subtle Features of the Cubic Closest-Packed Structure

    Science.gov (United States)

    Hawkins, John A.; Rittenhouse, Jeffrey L.; Soper, Linda M.; Rittenhouse, Robert C.

    2008-01-01

    One of the most important crystal structures adopted by metals is characterized by the "abcabc"...stacking of close-packed layers. This structure is commonly referred to in textbooks as the cubic close-packed (ccp) or face-centered cubic (fcc) structure, since the entire lattice can be generated by replication of a face-centered cubic unit cell…

  5. Liquid-infiltrated photonic crystals - enhanced light-matter interactions for lab-on-a-chip applications

    CERN Document Server

    Mortensen, Niels Asger; Pedersen, Jesper

    2007-01-01

    Optical techniques are finding widespread use in analytical chemistry for chemical and bio-chemical analysis. During the past decade, there has been an increasing emphasis on miniaturization of chemical analysis systems and naturally this has stimulated a large effort in integrating microfluidics and optics in lab-on-a-chip microsystems. This development is partly defining the emerging field of optofluidics. Scaling analysis and experiments have demonstrated the advantage of micro-scale devices over their macroscopic counterparts for a number of chemical applications. However, from an optical point of view, miniaturized devices suffer dramatically from the reduced optical path compared to macroscale experiments, e.g. in a cuvette. Obviously, the reduced optical path complicates the application of optical techniques in lab-on-a-chip systems. In this paper we theoretically discuss how a strongly dispersive photonic crystal environment may be used to enhance the light-matter interactions, thus potentially compen...

  6. Van der Waals Interactions in Pyridine and Pyridine-like Molecular Crystals: An ab initio Molecular Dynamics Study

    Science.gov (United States)

    Ko, Hsin-Yu; Distasio, Robert A., Jr.; Santra, Biswajit; Car, Roberto

    2014-03-01

    Pyridine has recently been investigated as a potentially effective material for use in artificial light harvesting.In this work, we propose the use of ab initio molecular dynamics (AIMD) to gain valuable physical insight into the artificial photosynthetic processes occurring in condensed-phase pyridine, the study of which has been limited to semi-empirical force fields to date.For this purpose, we introduce an accurate and efficient AIMD method, based on density functional theory (DFT) and a self-consistent pairwise description of van der Waals (vdW) interactions, for use in finite temperature and pressure (NPT) simulations on pyridine and several pyridine-like molecular crystals (PLMCs). Utilizing this approach, we demonstrate that vdW forces play a crucial role in the theoretical prediction of the structure and density of pyridine and PLMCs, and therefore must be accounted for in studies of these potential alternative energy materials. DOE: DE-SC0008626, NSF: DMS-1065894.

  7. Cylinder valve packing nut studies

    Energy Technology Data Exchange (ETDEWEB)

    Blue, S.C. [Martin Marietta Energy Systems, Inc., Paducah, KY (United States)

    1991-12-31

    The design, manufacture, and use of cylinder valve packing nuts have been studied to improve their resistance to failure from stress corrosion cracking. Stress frozen photoelastic models have been analyzed to measure the stress concentrations at observed points of failure. The load effects induced by assembly torque and thermal expansion of stem packing were observed by strain gaging nuts. The effects of finishing operations and heat treatment were studied by the strain gage hole boring and X-ray methods. Modifications of manufacturing and operation practices are reducing the frequency of stress corrosion failures.

  8. Multi-scale modeling and experimental study of twin inception and propagation in hexagonal close-packed materials using a crystal plasticity finite element approach; part II: Local behavior

    Science.gov (United States)

    Abdolvand, Hamidreza; Daymond, Mark R.

    2013-03-01

    In-situ tensile tests are performed on Zircaloy-2 samples with various grain sizes to study twin inception and propagation. Orientation maps of some areas at the surface are measured before and after deformation, using the Electron BackScattered Diffraction (EBSD) technique. Strain fields of the same areas are determined using the digital image correlation technique and are compared with results from Crystal Plasticity Finite Element (CPFE) simulations. Different assumptions are made within the CPFE code to simulate twin propagation. It is observed that the predictions of different models does not really change from one model to another when statistical information on the twins is compared, yet local predictions for each grain, i.e. twin direction, twin variant selection, and twin inception site, do change. Also, it is shown that the twin Schmid factor can vary drastically within grains and that for those grains with a low tendency for twinning this variation may make them susceptible to twinning.

  9. Crystal structure of 1-(2,4-dinitrophenyl-3,5-diphenyl-1H-pyrazole

    Directory of Open Access Journals (Sweden)

    Shaaban K. Mohamed

    2015-12-01

    Full Text Available In the title molecule, C21H14N4O4, the phenyl rings make dihedral angles of 39.61 (8 and 9.4 (1°, respectively, with the central pyrazole ring. The dihedral angle between the pyrazole and dinitrophenyl rings is 46.95 (5°. In the crystal, molecules pack in helical stacks parallel to the a axis aided by weak C—H...O interactions.

  10. Crystal and molecular structure of N-(-nitrobenzylidene)-3-chloro-4-fluoroaniline

    Indian Academy of Sciences (India)

    K V Arjuna Gowda; M K Kokila; Puttaraja; M V Kulkarni; N C Shivaprakash

    2000-09-01

    The crystal structure of N-(-nitrobenzylidene)-3-chloro-4-fluoroaniline (II) has been determined by X-ray structure analysis. This belongs to a class of benzylidene anilines. The structure was solved by direct method. The molecular packing of the non-planar molecules are held by Van der Waals and F$\\cdots\\cdot$H7, O$\\cdots\\cdot$Cl, F$\\cdots\\cdot$F and N$\\cdots\\cdot$H interactions.

  11. Molecular Docking Study of Conformational Polymorph: Building Block of Crystal Chemistry

    Directory of Open Access Journals (Sweden)

    Rashmi Dubey

    2013-01-01

    Full Text Available Two conformational polymorphs of novel 2-[2-(3-cyano-4,6-dimethyl-2-oxo-2H-pyridin-1-yl-ethoxy]-4,6-dimethyl nicotinonitrile have been developed. The crystal structure of both polymorphs (1a and 1b seems to be stabilized by weak interactions. A difference was observed in the packing of both polymorphs. Polymorph 1b has a better binding affinity with the cyclooxygenase (COX-2 receptor than the standard (Nimesulide.

  12. Molecular Docking Study of Conformational Polymorph: Building Block of Crystal Chemistry

    Science.gov (United States)

    Dubey, Rashmi; Tewari, Ashish Kumar; Singh, Ved Prakash; Singh, Praveen; Dangi, Jawahar Singh; Puerta, Carmen; Valerga, Pedro; Kant, Rajni

    2013-01-01

    Two conformational polymorphs of novel 2-[2-(3-cyano-4,6-dimethyl-2-oxo-2H-pyridin-1-yl)-ethoxy]-4,6-dimethyl nicotinonitrile have been developed. The crystal structure of both polymorphs (1a and 1b) seems to be stabilized by weak interactions. A difference was observed in the packing of both polymorphs. Polymorph 1b has a better binding affinity with the cyclooxygenase (COX-2) receptor than the standard (Nimesulide). PMID:24250264

  13. Crystal structure of bis(N,N,N′,N′-tetramethylguanidinium tetrachloridocuprate(II

    Directory of Open Access Journals (Sweden)

    Mamadou Ndiaye

    2016-07-01

    Full Text Available In the structure of the title salt, (C5H14N32[CuCl4], the CuII atom in the anion lies on a twofold rotation axis. The tetrachloridocuprate(II anion adopts a flattened tetrahedral coordination environment and interacts electrostatically with the tetramethylguanidinium cation. The crystal packing is additionally consolidated through N—H...Cl and C—H...Cl hydrogen bonds, resulting in a three-dimensional network structure.

  14. Crystal structure and terahertz spectroscopy of α,α,α‧,α‧-tetrabromo-p-xylene modeled using solid-state density functional theory

    Science.gov (United States)

    Pellizzeri, Steven; Smith, Tiffany M.; Delaney, Sean P.; Korter, Timothy M.; Zubieta, Jon

    2014-01-01

    The previously unknown crystal structure of α,α,α‧,α‧-tetrabromo-p-xylene has been determined using single-crystal X-ray diffraction, and it was discovered that the molecular packing primarily involves electrostatic interactions between neighboring molecules. Due to the unusual nature of the packing in this system, the vibrational motions were investigated. The low energy lattice and molecular vibrations unique to molecular crystals were measured in the terahertz (THz) region (10-100 cm-1). These vibrational motions were then reproduced using solid-state density functional theory (DFT) as implemented in CRYSTAL09, and it was found that the majority of the motions in this region involve either whole molecular translation or molecular scissoring.

  15. Melt-rock interaction near the Moho: Evidence from crystal cargo in lavas from near-ridge seamounts

    Science.gov (United States)

    Coumans, Jason P.; Stix, John; Clague, David A.; Minarik, William G.; Layne, Graham D.

    2016-10-01

    The Taney Seamounts are a NW-SE trending linear, near mid-ocean ridge chain consisting of five volcanoes located on the Pacific plate 300 km west of San Francisco, California. Taney Seamount-A, the largest and oldest in the chain, is defined by four well-exposed calderas, which expose previously infilled lavas. The calderas can be differentiated in time by their cross-cutting relationships, creating a relative chronology. The caldera walls and intracaldera pillow mounds were sampled systematically by a remotely operated vehicle (ROV) to obtain stratigraphically-controlled samples, a unique aspect of this study. The geochemistry of the seamount varies from more differentiated to more primitive with time (6.2-8.6 wt.% MgO), suggesting that the sub-caldera reservoir is open and undergoes periodic collapse, replenishment, crystallization, and eruption. The youngest and least differentiated lavas entrained a crystal cargo of plagioclase (An80-90) with melt inclusion volatile saturation pressures indicating entrapment in the lower oceanic crust and upper mantle (6-12 km, with 45% between 8 and 10 km below the sea floor). Melt inclusions exhibit high Al2O3, low SiO2, positive Sr and Eu anomalies and negative Zr and Nb anomalies when normalized to typical Pacific mid-ocean ridge basalt (MORB). In comparison, the host lavas exhibit positive Sr anomalies, but no concurrent Zr, and Nb anomalies. Based on thermodynamic modeling using alphaMELTS, we develop a melt-rock interaction model defined by melting and assimilation of plagioclase-rich cumulates by hot, primitive mantle-derived melts. Significantly, the variability of the negative Zr and Nb anomalies cannot be explained by either cumulate melting or AFC alone. We propose that the melt inclusions record the interaction between cumulate partial melts and the assimilating melt, demonstrating the importance of cumulate melting during the assimilation process. Later percolating melts underwent diffusive interaction with, and

  16. Interaction of intense femtosecond laser pulses with KDP and DKDP crystals in the short wavelength regime

    Science.gov (United States)

    Duchateau, Guillaume; Geoffroy, Ghita; Belsky, Andrei; Fedorov, Nikita; Martin, Patrick; Guizard, Stéphane

    2013-10-01

    We investigate the electronic photo-excitation and relaxation mechanisms involved in the optical breakdown of potassium dihydrogen phosphate crystal (KH2PO4) and its deuterated form. The dynamics and spectroscopic properties of electron-hole pair formation are investigated using time-resolved measurement of the dielectric function, and luminescence spectroscopy. The non-common mechanical and electronic characteristics of these dielectric materials are revealed by the particular structure of ablation craters and also by the complex dynamics observed in the relaxation of excited carriers. This relaxation occurs in two steps, and varies with the initial carrier density and thus with the laser intensity. We show that the defect states play a key role in the excitation pathways, and also determine the relaxation stage. The latter also depends upon the initial amount of energy of the electron-hole pair after photo-excitation. A model based on kinetic equations describing the evolution of the different level populations allows us to successfully interpret and reproduce the experimental data.

  17. Zinc(II) complexes of carboxamide derivatives: Crystal structures and interaction with calf thymus DNA

    Indian Academy of Sciences (India)

    Biplab Mondal; Buddhadeb Sen; Ennio Zangrando; Pabitra Chattopadhyay

    2015-10-01

    Two mononuclear zinc(II) complexes of newly designed carboxamide derivatives, formulated as [Zn(L1)3](ClO4)2 (1) and [Zn(L2)3](ClO4)2 (2) [where L1 = -(furan-2-ylmethyl)-2-pyridinecarboxamide and L2 = -(thiophen-2-ylmethyl)-2-pyridine-carboxamide], have been isolated in pure form in the reaction of perchlorate salts of Zn(II) with ligands L1 and L2, respectively. The two complexes were characterized by physicochemical and spectroscopic tools, and by X-ray crystal structures of both ligands and the complex 1. In complex 1, zinc(II) is chelated by three ligands with a distorted octahedral geometry. The DNA-binding properties of zinc complexes 1 and 2 have been investigated by spectroscopic methods and viscosity measurements. The results suggest that both complexes 1 and 2 bind to DNA in an intercalation mode between the uncoordinated furan or thiophene chromophore and the base pairs of DNA.

  18. Parametric wave interaction in quadratic crystal with randomized distribution of ferroelectric domains

    CERN Document Server

    Kalinowski, Ksawery; Łukasiewicz, Tadeusz; Świrkowicz, Marek; Sheng, Yan; Krolikowski, Wieslaw

    2012-01-01

    We study the parametric wave interaction in qua- dratic nonlinear media with randomized distribution of the ferroelectric domains. In particular, we discuss properties of second and cascaded third harmonic generation. We derive analytical formulas describing emission properties of the second and third harmonics in the presence of domain disorder and show that the latter process is governed by the characteristics of the constituent processes, i.e. second harmonic generation and sum frequency mixing. We demonstrate the role of randomness on various second and third harmonic generation regimes such as Raman-Nath and \\v{C}erenkov nonlinear diffraction. We show that the randomness-induced incoherence in the wave interaction leads to deterioration of conversion efficiency and angular spreading of harmonic generated in the processes relying on transverse phase matching such as Raman-Nath. On the other hand forward and \\v{C}erenkov frequency generation are basically insensitive to the domain randomness.

  19. Singlet Fission in Rubrene Derivatives: Impact of Molecular Packing

    KAUST Repository

    Sutton, Christopher

    2017-03-13

    We examine the properties of six recently synthesized rubrene derivatives (with substitutions on the side phenyl rings) that show vastly different crystal structures. In order to understand how packing in the solid state affects the excited states and couplings relevant for singlet fission, the lowest excited singlet (S), triplet (T), multiexciton (TT), and charge-transfer (CT) states of the rubrene derivatives are compared to known singlet fission materials [tetracene, pentacene, 5,12-diphenyltetracene (DPT), and rubrene itself]. While a small difference of less than 0.2 eV is calculated for the S and TT energies, a range of 0.50 to 1.2 eV in the CT energies and nearly 3 orders of magnitude in the electronic couplings are computed for the rubrene derivatives in their crystalline packings, which strongly affects the role of the CT state in facilitating SF. To rationalize experimental observations of singlet fission occurring in amorphous phases of rubrene, DPT, and tetracene, we use molecular dynamics (MD) simulations to assess the impact of molecular packing and orientations and to gain a better understanding of the parameters that control singlet fission in amorphous films compared to crystalline packings. The MD simulations point to a crystalline-like packing for thin films of tetracene; on the other hand, DPT, rubrene, and the rubrene derivatives all show various degrees of disorder with a number of sites that have larger electronic couplings than in the crystal, which can facilitate singlet fission in such thin films. Our analysis underlines the potential of these materials as promising candidates for singlet fission and helps understand how various structural motifs affect the critical parameters that control the ability of a system to undergo singlet fission.

  20. Analysis of Cl…Cl and C-H…Cl intermolecular interactions involving chlorine in substituted 2-chloroquinoline derivatives

    Indian Academy of Sciences (India)

    Venkatesha R Hathwar; S Mohana Roopan; R Subashini; F Nawaz Khan; T N Guru Row

    2010-09-01

    Six crystal structures of substituted 2-chloroquinoline derivatives have been analysed to evaluate the role of Cl atom as a self recognizing unit resulting in the formation of Cl…Cl and C-H…Cl interactions to generate supramolecular assembly in the solid state. The features of Type I and Type II geometries associated with Cl…Cl interactions have been analysed to show directional preferences leading to differences in the packing motifs in these crystal structures. C-H…Cl interactions are generated exclusively in structures depicting Type II Cl…Cl interaction have been observed in these structures.

  1. Surface characterization and orientation interaction between diamond- like carbon layer structure and dimeric liquid crystals

    Science.gov (United States)

    Naradikian, H.; Petrov, M.; Katranchev, B.; Milenov, T.; Tinchev, S.

    2017-01-01

    Diamond-like carbon (DLC) and amorphous carbon films are very promising type of semiconductor materials. Depending on the hybridization sp2/sp3 ratio, the material’s band gap varies between 0.8 and 3 eV. Moreover carbon films possess different interesting for practice properties: comparable to the Silicon, Diamond like structure has 22-time better thermal conductivity etc. Here we present one type of implementation of such type nanostructure. That is one attempt for orientation of dimeric LC by using of pre-deposited DLC layer with different ratio of sp2/sp3 hybridized carbon content. It could be expected a pronounced π1-π2interaction between s and p orbital levels on the surface and the dimeric ring of LC. We present comparison of surface anchoring strengths of both orientation inter-surfaces DLC/dimeric LC and single wall carbon nanotubes (SWCNT)/dimeric LC. The mechanism of interaction of dimeric LC and activated surfaces with DLC or SWCNT will be discussed. In both cases we have π-π interaction, which in combination with hydrogen bonding, typical for the dimeric LCs, influence the LC alignment. The Raman spectroscopy data evidenced the presence of charge transfer between contacting hexagonal rings of DLC and the C = O groups of the LC molecules.

  2. Crystal structure of nicotinic acid mononucleotide adenylyltransferase from Staphyloccocus aureus: structural basis for NaAD interaction in functional dimer.

    Science.gov (United States)

    Han, Seungil; Forman, Michael D; Loulakis, Pat; Rosner, Michelle H; Xie, Zhi; Wang, Hong; Danley, Dennis E; Yuan, Wei; Schafer, John; Xu, Zuoyu

    2006-07-21

    Bacterial nicotinic acid mononucleotide adenylyltransferase (NaMNAT; EC 2.7.7.18) encoded by the nadD gene, is essential for cell survival and is thus an attractive target for developing new antibacterial agents. The NaMNAT catalyzes the transfer of an adenylyl group of ATP to nicotinic acid mononucleotide (NaMN) to form nicotinic acid dinucleotide (NaAD). Two independently derived, high-resolution structures of Staphylococcus aureus NaMNAT-NaAD complexes establish the conserved features of the core dinucleotide-binding fold with other adenylyltransferases from bacteria to human despite a limited sequence conservation. The crystal structures reveal that the nicotinate carboxylates of NaAD are recognized by interaction with the main-chain amides of Thr85 and Tyr117, a positive helix dipole and two bridged-water molecules. Unlike other bacterial adenylyltransferases, where a partially conserved histidine residue interacts with the nicotinate ring, the Leu44 side-chain interacts with the nicotinate ring by van der Waals contact. Importantly, the S. aureus NaMNAT represents a distinct adenylyltransferase subfamily identifiable in part by common features of dimerization and substrate recognition in the loop connecting beta5 to beta6 (residues 132-146) and the additional beta6 strand. The unique beta6 strand helps orient the residues in the loop connecting beta5 to beta6 for substrate/product recognition and allows the beta7 strand structural flexibility to make key dimer interface interactions. Taken together, these structural results provide a molecular basis for understanding the coupled activity and recognition specificity for S. aureus NaMNAT and for rational design of selective inhibitors.

  3. Pack cementation coatings for alloys

    Energy Technology Data Exchange (ETDEWEB)

    He, Yi-Rong; Zheng, Minhui; Rapp, R.A. [Ohio State Univ., Columbus, OH (United States)

    1996-08-01

    The halide-activated pack cementation process was modified to produce a Ge-doped silicide diffusion coating on a Cr-Cr{sub 2}Nb alloy in a single processing step. The morphology and composition of the coating depended both on the composition of the pack and on the composition and microstructure of the substrate. Higher Ge content in the pack suppressed the formation of CrSi{sub 2} and reduced the growth kinetics of the coating. Ge was not homogeneously distributed in the coatings. In cyclic and isothermal oxidation in air at 700 and 1050{degrees}C, the Ge-doped silicide coating protected the Cr-Nb alloys from significant oxidation by the formation of a Ge-doped silica film. The codeposition and diffusion of aluminum and chromium into low alloy steel have been achieved using elemental Al and Cr powders and a two-step pack cementation process. Sequential process treatments at 925{degrees}C and 1150{degrees}C yield dense and uniform ferrite coatings, whose compositions are close to either Fe{sub 3}Al or else FeAl plus a lower Cr content, when processed under different conditions. The higher content of Al in the coatings was predicted by thermodynamic calculations of equilibrium in the gas phase. The effect of the particle size of the metal powders on the surface composition of the coating has been studied for various combinations of Al and Cr powders.

  4. Wire and Packing Tape Sandwiches

    Science.gov (United States)

    Rabinowitz, Sandy

    2009-01-01

    In this article, the author describes how students can combine craft wire with clear packing tape to create a two-dimensional design that can be bent and twisted to create a three-dimensional form. Students sandwich wire designs between two layers of tape. (Contains 1 online resource.)

  5. Crystal structure and Raman spectra of rubidium hydrogen squarate

    Science.gov (United States)

    Georgopoulos, Stéfanos L.; Diniz, Renata; Rodrigues, Bernardo L.; de Oliveira, Luiz F. C.

    2005-05-01

    Rubidium hydrogen squarate (RbHC 4O 4, RbHSQ) crystallized in monoclinic space group P2 1/ c. This compound form a short asymmetric intermolecular hydrogen bond whose O-O distance is 2.482(4) Å. The hydrogen squarate anions are forming head-to-tail infinite chain hydrogen-bonding motifs. A long interplanar separation (4.15 Å) indicates that a weak π interaction occurs between hydrogen squarate anions in RbHSQ. The hydrogen bond and cation-anion interactions are the predominant driving forces in the crystal packing. The Raman spectrum of RbHSQ shows an average behaviour between squaric acid and squarate dianion, however, the vibrational modes at ca. 1800 cm -1 (CO stretching mode) and in the region 1500-1700 cm -1 (CO+CC stretching modes) are the most affected by the presence of strong hydrogen bonding interactions.

  6. The Crystal Structure and Behavior of Fenamic Acid-Acridine Complex Under High Pressure.

    Science.gov (United States)

    Jerzykiewicz, Lucjan; Sroka, Adam; Majerz, Irena

    2016-12-01

    The crystal structure of fenamic acid-acridine complex is determined by X-ray diffraction. The strong OHN hydrogen bond linking the complex components and other interactions responsible for packing of the molecules into a crystal are investigated within the Quantum Theory of Atom in Molecule theory. The crystal structure is compared with the structure optimized at B3LYP/6-311++G** level and with the theoretical structures optimized under systematically changed pressure. Analysis of the lattice constants, hydrogen bond lengths, and angles of the inter- and intramolecular hydrogen bond under compression is performed. The structural transformation observed at 5 GPa is connected with a change in the intermolecular OHN hydrogen bond. The proton shifts to acceptor and a new interaction in the crystal appears.

  7. Beyond packing of hard spheres: The effects of core softness, non-additivity, intermediate-range repulsion, and many-body interactions on the glass-forming ability of bulk metallic glasses

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Kai; Fan, Meng; Liu, Yanhui; Schroers, Jan [Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut 06520 (United States); Center for Research on Interface Structures and Phenomena, Yale University, New Haven, Connecticut 06520 (United States); Shattuck, Mark D. [Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut 06520 (United States); Department of Physics and Benjamin Levich Institute, The City College of the City University of New York, New York, New York 10031 (United States); O’Hern, Corey S. [Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut 06520 (United States); Center for Research on Interface Structures and Phenomena, Yale University, New Haven, Connecticut 06520 (United States); Department of Physics, Yale University, New Haven, Connecticut 06520 (United States); Department of Applied Physics, Yale University, New Haven, Connecticut 06520 (United States)

    2015-11-14

    When a liquid is cooled well below its melting temperature at a rate that exceeds the critical cooling rate R{sub c}, the crystalline state is bypassed and a metastable, amorphous glassy state forms instead. R{sub c} (or the corresponding critical casting thickness d{sub c}) characterizes the glass-forming ability (GFA) of each material. While silica is an excellent glass-former with small R{sub c} < 10{sup −2} K/s, pure metals and most alloys are typically poor glass-formers with large R{sub c} > 10{sup 10} K/s. Only in the past thirty years have bulk metallic glasses (BMGs) been identified with R{sub c} approaching that for silica. Recent simulations have shown that simple, hard-sphere models are able to identify the atomic size ratio and number fraction regime where BMGs exist with critical cooling rates more than 13 orders of magnitude smaller than those for pure metals. However, there are a number of other features of interatomic potentials beyond hard-core interactions. How do these other features affect the glass-forming ability of BMGs? In this manuscript, we perform molecular dynamics simulations to determine how variations in the softness and non-additivity of the repulsive core and form of the interatomic pair potential at intermediate distances affect the GFA of binary alloys. These variations in the interatomic pair potential allow us to introduce geometric frustration and change the crystal phases that compete with glass formation. We also investigate the effect of tuning the strength of the many-body interactions from zero to the full embedded atom model on the GFA for pure metals. We then employ the full embedded atom model for binary BMGs and show that hard-core interactions play the dominant role in setting the GFA of alloys, while other features of the interatomic potential only change the GFA by one to two orders of magnitude. Despite their perturbative effect, understanding the detailed form of the intermetallic potential is important for

  8. Coking technology using packed coal mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Kuznichenko, V.M.; Shteinberg, Eh.A.; Tolstoi, A.P. (Khar' kovskii Nauchno-Issledovatel' skii Uglekhimicheskii Institut, Kharkov (Ukrainian SSR))

    1991-08-01

    Discusses coking of packed coal charges in the FRG, USSR, France, India, Poland and Czechoslovakia. The following aspects are evaluated: types of weakly caking coals that are used as components of packed mixtures, energy consumption of packing, effects of coal mixture packing on coke oven design, number of coke ovens in a battery, heating temperature, coking time, coke properties, investment and operating cost. Statistical data that characterize the Saarberg packing process used in the FRG are analyzed. Packing coal mixtures for coking improves coke quality and reduces environmental pollution. 4 refs.

  9. The Maximum Resource Bin Packing Problem

    DEFF Research Database (Denmark)

    Boyar, J.; Epstein, L.; Favrholdt, L.M.

    2006-01-01

    Usually, for bin packing problems, we try to minimize the number of bins used or in the case of the dual bin packing problem, maximize the number or total size of accepted items. This paper presents results for the opposite problems, where we would like to maximize the number of bins used...... algorithms, First-Fit-Increasing and First-Fit-Decreasing for the maximum resource variant of classical bin packing. For the on-line variant, we define maximum resource variants of classical and dual bin packing. For dual bin packing, no on-line algorithm is competitive. For classical bin packing, we find...

  10. Packing hyperspheres in high-dimensional Euclidean spaces.

    Science.gov (United States)

    Skoge, Monica; Donev, Aleksandar; Stillinger, Frank H; Torquato, Salvatore

    2006-10-01

    We present a study of disordered jammed hard-sphere packings in four-, five-, and six-dimensional Euclidean spaces. Using a collision-driven packing generation algorithm, we obtain the first estimates for the packing fractions of the maximally random jammed (MRJ) states for space dimensions d=4, 5, and 6 to be phi(MRJ) approximately 0.46, 0.31, and 0.20, respectively. To a good approximation, the MRJ density obeys the scaling form phi(MRJ)=c1/2(d)+(c2d)/2d, where c1=-2.72 and c2=2.56, which appears to be consistent with the high-dimensional asymptotic limit, albeit with different coefficients. Calculations of the pair correlation function g2(r) and structure factor S(k) for these states show that short-range ordering appreciably decreases with increasing dimension, consistent with a recently proposed "decorrelation principle," which, among other things, states that unconstrained correlations diminish as the dimension increases and vanish entirely in the limit d-->infinity. As in three dimensions (where phi(MRJ) approximately 0.64), the packings show no signs of crystallization, are isostatic, and have a power-law divergence in g2(r) at contact with power-law exponent approximately 0.4. Across dimensions, the cumulative number of neighbors equals the kissing number of the conjectured densest packing close to where g2(r) has its first minimum. Additionally, we obtain estimates for the freezing and melting packing fractions for the equilibrium hard-sphere fluid-solid transition, phi(F) approximately 0.32 and phi(M) approximately 0.39, respectively, for d=4, and phi(F) approximately 0.20 and phi(M) approximately 0.25, respectively, for d=5. Although our results indicate the stable phase at high density is a crystalline solid, nucleation appears to be strongly suppressed with increasing dimension.

  11. Mixed crystal organic scintillators

    Science.gov (United States)

    Zaitseva, Natalia P; Carman, M Leslie; Glenn, Andrew M; Hamel, Sebastien; Hatarik, Robert; Payne, Stephen A; Stoeffl, Wolfgang

    2014-09-16

    A mixed organic crystal according to one embodiment includes a single mixed crystal having two compounds with different bandgap energies, the organic crystal having a physical property of exhibiting a signal response signature for neutrons from a radioactive source, wherein the signal response signature does not include a significantly-delayed luminescence characteristic of neutrons interacting with the organic crystal relative to a luminescence characteristic of gamma rays interacting with the organic crystal. According to one embodiment, an organic crystal includes bibenzyl and stilbene or a stilbene derivative, the organic crystal having a physical property of exhibiting a signal response signature for neutrons from a radioactive source.

  12. Enhanced optoelastic interaction range in liquid crystals with negative dielectric anisotropy

    Energy Technology Data Exchange (ETDEWEB)

    Simoni, F.; Lalli, S.; Lucchetti, L. [Dipartimento di Scienze e Ingegneria della Materia, dell' Ambiente ed Urbanistica and CNISM, Università Politecnica delle Marche, Ancona (Italy); Criante, L. [Center for Nano Science and Technology-PoliMi, Istituto Italiano di Tecnologia, Via Giovanni Pascoli, 70/3, 20133 Milano (Italy); Brasselet, E. [Univ. Bordeaux and CNRS, Laboratoire Ondes et Matière d' Aquitaine, UMR 5798, F-33400 Talence (France)

    2014-01-06

    We demonstrate that the long-range interaction between surface-functionalized microparticles immersed a nematic liquid crystal—a “nematic colloid”—and a laser-induced “ghost colloid” can be enhanced by a low-voltage quasistatic electric field when the nematic mesophase has a negative dielectric anisotropy. The optoelastic trapping distance is shown to be enhanced by a factor up to 2.5 in presence of an electric field. Experimental data are quantitatively described with a theoretical model accounting for the spatial overlap between the orientational distortions around the microparticle and those induced by the trapping light beam itself.

  13. Peptide-membrane interactions of arginine-tryptophan peptides probed using quartz crystal microbalance with dissipation monitoring.

    Science.gov (United States)

    Rydberg, Hanna A; Kunze, Angelika; Carlsson, Nils; Altgärde, Noomi; Svedhem, Sofia; Nordén, Bengt

    2014-07-01

    Membrane-active peptides include peptides that can cross cellular membranes and deliver macromolecular cargo as well as peptides that inhibit bacterial growth. Some of these peptides can act as both transporters and antibacterial agents. It is desirable to combine the knowledge from these two different fields of membrane-active peptides into design of new peptides with tailored actions, as transporters of cargo or as antibacterial substances, targeting specific membranes. We have previously shown that the position of the amino acid tryptophan in the peptide sequence of three arginine-tryptophan peptides affects their uptake and intracellular localization in live mammalian cells, as well as their ability to inhibit bacterial growth. Here, we use quartz crystal microbalance with dissipation monitoring to assess the induced changes caused by binding of the three peptides to supported model membranes composed of POPC, POPC/POPG, POPC/POPG/cholesterol or POPC/lactosyl PE. Our results indicate that the tryptophan position in the peptide sequence affects the way these peptides interact with the different model membranes and that the presence of cholesterol in particular seems to affect the membrane interaction of the peptide with an even distribution of tryptophans in the peptide sequence. These results give mechanistic insight into the function of these peptides and may aid in the design of membrane-active peptides with specified cellular targets and actions.

  14. The Crystal Structure of Cdc42 in Complex with Collybisin II, a Gephyrin-Interacting Guanine Nucleotide Exchange Factor

    Energy Technology Data Exchange (ETDEWEB)

    Xiang,S.; Kim, E.; Connelly, J.; Nassar, N.; Kirsch, J.; WinkingSchwartz, G.; Schindelin, H.

    2006-01-01

    The synaptic localization of ion channel receptors is essential for efficient synaptic transmission and the precise regulation of diverse neuronal functions. In the central nervous system, ion channel receptors reside in the postsynaptic membrane where they are juxtaposed to presynaptic terminals. For proper function, these ion channels have to be anchored to the cytoskeleton, and in the case of the inhibitory glycine and {gamma}-amino-butyric acid type A (GABA{sub A}) receptors this interaction is mediated by a gephyrin centered scaffold. Highlighting its central role in this receptor anchoring scaffold, gephyrin interacts with a number of proteins, including the neurospecific guanine nucleotide exchange factor collybistin. Collybistin belongs to the Dbl family of guanine nucleotide exchange factors, occurs in multiple splice variants, and is specific for Cdc42, a small GTPase belonging to the Rho family. The 2.3 Angstroms resolution crystal structure of the Cdc42--collybistin II complex reveals a novel conformation of the switch I region of Cdc42. It also provides the first direct observation of structural changes in the relative orientation of the Dbl-homology domain and the pleckstrin-homology domain in the same Dbl family protein. Biochemical data indicate that gephyrin negatively regulates collybistin activity.

  15. Peptide-membrane interactions of arginine-tryptophan peptides probed using quartz crystal microbalance with dissipation monitoring.

    KAUST Repository

    Rydberg, Hanna A

    2014-04-18

    Membrane-active peptides include peptides that can cross cellular membranes and deliver macromolecular cargo as well as peptides that inhibit bacterial growth. Some of these peptides can act as both transporters and antibacterial agents. It is desirable to combine the knowledge from these two different fields of membrane-active peptides into design of new peptides with tailored actions, as transporters of cargo or as antibacterial substances, targeting specific membranes. We have previously shown that the position of the amino acid tryptophan in the peptide sequence of three arginine-tryptophan peptides affects their uptake and intracellular localization in live mammalian cells, as well as their ability to inhibit bacterial growth. Here, we use quartz crystal microbalance with dissipation monitoring to assess the induced changes caused by binding of the three peptides to supported model membranes composed of POPC, POPC/POPG, POPC/POPG/cholesterol or POPC/lactosyl PE. Our results indicate that the tryptophan position in the peptide sequence affects the way these peptides interact with the different model membranes and that the presence of cholesterol in particular seems to affect the membrane interaction of the peptide with an even distribution of tryptophans in the peptide sequence. These results give mechanistic insight into the function of these peptides and may aid in the design of membrane-active peptides with specified cellular targets and actions.

  16. Synthesis, Crystal Structure and Luminescent Property of a Novel Pt(II) Complex with Weak Metal-metal Interaction

    Institute of Scientific and Technical Information of China (English)

    YUE Cheng-Yang; JIANG Fei-Long; FENG Rui; HONG Mao-Chun

    2008-01-01

    The title complex cis-bis(tetrahydrothiophene)-bis(nitrate) platinum(II), (tht)2Pt(NO3)2, was the reducing product from potassium hexachloroplatinate(IV) K2PtCl6 where the platinum is tetra-valenced. Crystal data for C8H16N2O6PtS2: monoclinic, space group P21/c, a = 9.8833(5), b = 8.6744(4), c = 18.6407(9) (A), β = 114.401(3)°, V = 1455.35(12) (A)3, Z = 4, Mr = 495.44, Dc = 2.261 g/cm3, F(000) = 944, μ = 9.950 mm-1, λ(MoKα) = 0.71073 (A), T = 293(2) K, 2θmax = 54.96o, GOOF = 1.033, R = 0.0350 and wR = 0.0785 for 2572 observed reflections with I > 2σ(I). X-ray diffraction studies reveal that the title complex has interesting weak metal-metal interactions and two molecules linked by metal-metal interaction exist as a group. Luminescent spectrum illuminates red emission of the complex at room temperature.

  17. Interaction between helium and intrinsic point defects in 3C-SiC single crystal

    Science.gov (United States)

    Sun, Dan; Li, Ruihuan; Ding, Jianhua; Zhang, Pengbo; Wang, Yuanyuan; Zhao, Jijun

    2017-06-01

    Silicon carbide (SiC) is a candidate structural material for fission and fusion reactors as well as an important wide band-gap semiconductor for electronic devices. Using first-principles calculations, we systemically investigate the energetics and stability of helium (He) atoms and intrinsic point defects inside single-crystalline 3C-SiC. We find that the formation energy of interstitial He is lower than those of point defects. Inside 3C-SiC, the He-C interaction is stronger than He-Si. Hence, the interstitial He atom in the Si tetrahedral site has a stronger interaction with the six C atoms in the second nearest neighbor than the four nearest neighboring Si atoms. For interstitial He atoms, the equilibrium He-He distance is about 1.81 Å with a weak attraction of 0.09 eV. According to the binding energies of Hen (n = 2-4) clusters, He interstitials can form He bubbles without involving other types of structural defects. Moreover, a Si (C) monovacancy can accommodate up to 11 (9) He atoms. The Hen clusters trapped in the Si or C monovacancy induce large internal pressure in the order of magnitude of GPa and thus facilitate the creation of a new vacancy at the nearby lattice site.

  18. Interactions of carbon nanotubes in a nematic liquid crystal. II. Experiment

    Science.gov (United States)

    Agha, Hakam; Galerne, Yves

    2016-04-01

    Multiwall carbon nanotube (CNT) colloids with different anchoring conditions are dispersed in pentyl-cyanobiphenyl (5CB), a thermotropic liquid crystal (LC) that exhibits a room-temperature nematic phase. The experiments make use of CNTs treated for strong planar, homeotropic, or Janus anchorings. Observations with a polarizing microscope show that the CNTs placed in a uniform nematic field stabilize parallel or perpendicular to n depending on their anchoring conditions. In the presence of a splay-bend disclination line, they are first attracted toward it and ultimately, they get trapped on it. Their orientation relative to the line is then found to be parallel or perpendicular to it, again depending on the anchoring conditions. When a sufficient number of particles are deposited on a disclination line, they form a micro- or nanonecklace in the shape of a thin thread or of a bottle brush, with the CNTs being oriented parallel or perpendicular to the disclination line according to the anchoring treatment. The system exhibits a rich versatility, even if until now the weak anchorings appear to be difficult to control. In a next step, the necklaces may be glued by means of pyrrole electropolymerization. In this manner, we realize a true materialization of the disclination lines, and we obtain nanowires capable of conducting the electricity in the place of the initial disclinations that just worked as templates. The advantage of the method is that it finally provides nanowires that are automatically connected to predesignated three-dimensional (3D) electrodes. Such a 3D nanowiring could have important applications, as it could allow one to develop electronic circuits in the third dimension. They could thus help with increasing the transistor density per surface unit, although downsizing of integrated circuits will soon be limited to atomic sizes or so. In other words, the predicted limitation to Moore's law could be avoided. For the moment, the nanowires that we obtain

  19. Cavity optomechanics in photonic and phononic crystals: engineering the interaction of light and sound at the nanoscale

    Science.gov (United States)

    Eichenfield, Matthew

    . Because the optical and mechanical modes occupy a volume more than 100,000 times smaller than the volume of a single human cell, the optomechanical interaction in this system is again at the fundamental limit set by optical diffraction. The miniscule effective volume of the mechanical mode corresponds to effective motional masses in the femtogram regime, which, coupled with the enormous optomechanical interaction and high optical and mechanical quality factors, allows transduction of microwave-frequency mechanical motion nearly at the standard quantum limit, with the standard quantum limit easily within reach with simple modifications of the experimental apparatus. The combination of the small motional mass and strong optomechanical coupling allows each trapped photon to drive motion of an acoustic mode with a force more than 15 times the weight of the structure. This provides a powerful method for optically actuating microwave-frequency mechanical oscillators on a chip, and we demonstrate an on-chip phonon laser that emits over 1012 microwave-frequency phonons per second with a ratio of frequency to linewidth of 2 million—characteristics similar to those of the first optical lasers. With the ability to readily interconvert photons and microwave-frequency phonons on the surface of a microchip, new chip-scale technologies can be created. We discuss the future of optomechanical crystals and provide new methods of calculating all the otptomechanical properties of the structures.

  20. Neutron spectroscopic study of the crystal field interaction in Pr{sub 1-x}La{sub x}NiO{sub 3} (0{<=}x{<=}0.7)

    Energy Technology Data Exchange (ETDEWEB)

    Rosenkranz, S.; Medarde, M.; Mesot, J.; Zolliker, M.; Furrer, A. [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Lacorre, P. [LeMans, Univ. (France)

    1997-09-01

    The crystal field interaction at the rare earth site in Pr{sub 1-x}La{sub x}NiO{sub 3} has been studied using inelastic neutron scattering. A parametrization consistent over the whole series is obtained and discussed within the point-charge model. (author) 2 figs., 3 refs.

  1. Neutron spectroscopic study of the crystal field interaction in Pr{sub 1-x}La{sub x}NiO{sub 3} (0{<=}x{<=}0.7)

    Energy Technology Data Exchange (ETDEWEB)

    Rosenkranz, S.; Medarde, M.; Mesot, J.; Zolliker, M.; Furrer, A. [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Lacorre, P. [LeMans, Univ. (France)

    1997-09-01

    The crystal field interaction at the rare earth site in Pr{sub 1-x}La{sub x}NiO{sub 3} has been studied using inelastic neutron scattering. A parametrization consistent over the whole series is obtained and discussed within the point-charge model. (author) 2 figs., 3 refs.

  2. Synthesis,Crystal Structure of Cis—dioxo—catecholatotungsten(VI) Complex and Its NMR Studies on the Interaction with ATP

    Institute of Scientific and Technical Information of China (English)

    鲁晓明; 刘顺成; 姜凌; 毛希安; 叶朝晖

    2003-01-01

    Cis-dioxo-catecholatotungsten(VI) complex anion[W(VI)O2-(OC6H4O)2]2- was obtained with discrete protonated ethylenediamine (NH2CH2CH2NH3)+ cations by the reaction of tetrabutyl ammonium decatungstate with catechol in the mixed solvent of CH3OH,CH3CN and ethylenediamine,and compared with its molybdenum anaogue [Mo(V) O2(OC6H4O)2]3- by crystal structure,UV,EPR,The results of the UV and EPR spectra show that tungsten is less redox active than molybdenum since the molybdenum is reduced from Mo(VI) to Mo(V) but tungsten stays in the original highest oxidized state Mo(VI) when they are crystallized from the solution above.It is worthy to note that [W(VI)O2(OC6H4O)]2- shows the same coordination structure as its molybdenum analogue in which the metal center exhibits distorted octahedral coordination geometry with two cis-dioxocatecholate ligands and might have the related coordination structure feature with the cofactor of flavoenzyme because [Mo(V)O2(OC6H4O)2]3- presented essentially the same EPR spectra as flavoenzyme.The NMR studies on the interaction of the title complex with ATP reveal that the reduction of W(VI) to W(V) occurs when the title complex is dissolved in D2O and the W(V) is oxidized again when ATP solution is mixed with original solution and the hydrolysis of the catecholato ligand take places at mean time being monitored by 1H NMR and 13C NMR spectra.

  3. Role of Dispersion Interactions in the Polymorphism and Entropic Stabilization of the Aspirin Crystal

    Science.gov (United States)

    Reilly, Anthony M.; Tkatchenko, Alexandre

    2014-08-01

    Aspirin has been used and studied for over a century but has only recently been shown to have an additional polymorphic form, known as form II. Since the two observed solid forms of aspirin are degenerate in terms of lattice energy, kinetic effects have been suggested to determine the metastability of the less abundant form II. Here, first-principles calculations provide an alternative explanation based on free-energy differences at room temperature. The explicit consideration of many-body van der Waals interactions in the free energy demonstrates that the stability of the most abundant form of aspirin is due to a subtle coupling between collective electronic fluctuations and quantized lattice vibrations. In addition, a systematic analysis of the elastic properties of the two forms of aspirin rules out mechanical instability of form II as making it metastable.

  4. Crystal Structure of UBA2[superscript ufd]-Ubc9: Insights into E1-E2 Interactions in Sumo Pathways

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jing; Taherbhoy, Asad M.; Hunt, Harold W.; Seyedin, Steven N.; Miller, David W.; Miller, Darcie J.; Huang, Danny T.; Schulman, Brenda A. (SJCH)

    2012-04-30

    Canonical ubiquitin-like proteins (UBLs) such as ubiquitin, Sumo, NEDD8, and ISG15 are ligated to targets by E1-E2-E3 multienzyme cascades. The Sumo cascade, conserved among all eukaryotes, regulates numerous biological processes including protein localization, transcription, DNA replication, and mitosis. Sumo conjugation is initiated by the heterodimeric Aos1-Uba2 E1 enzyme (in humans called Sae1-Uba2), which activates Sumo's C-terminus, binds the dedicated E2 enzyme Ubc9, and promotes Sumo C-terminal transfer between the Uba2 and Ubc9 catalytic cysteines. To gain insights into details of E1-E2 interactions in the Sumo pathway, we determined crystal structures of the C-terminal ubiquitin fold domain (ufd) from yeast Uba2 (Uba2{sup ufd}), alone and in complex with Ubc9. The overall structures of both yeast Uba2{sup ufd} and Ubc9 superimpose well on their individual human counterparts, suggesting conservation of fundamental features of Sumo conjugation. Docking the Uba2{sup ufd}-Ubc9 and prior full-length human Uba2 structures allows generation of models for steps in Sumo transfer from Uba2 to Ubc9, and supports the notion that Uba2 undergoes remarkable conformational changes during the reaction. Comparisons to previous structures from the NEDD8 cascade demonstrate that UBL cascades generally utilize some parallel E1-E2 interaction surfaces. In addition, the structure of the Uba2{sup ufd}-Ubc9 complex reveals interactions unique to Sumo E1 and E2. Comparison with a previous Ubc9-E3 complex structure demonstrates overlap between Uba2 and E3 binding sites on Ubc9, indicating that loading with Sumo and E3-catalyzed transfer to substrates are strictly separate steps. The results suggest mechanisms establishing specificity and order in Sumo conjugation cascades.

  5. Protein packing defects "heat up" interfacial water.

    Science.gov (United States)

    Sierra, María Belén; Accordino, Sebastián R; Rodriguez-Fris, J Ariel; Morini, Marcela A; Appignanesi, Gustavo A; Fernández Stigliano, Ariel

    2013-06-01

    Ligands must displace water molecules from their corresponding protein surface binding site during association. Thus, protein binding sites are expected to be surrounded by non-tightly-bound, easily removable water molecules. In turn, the existence of packing defects at protein binding sites has been also established. At such structural motifs, named dehydrons, the protein backbone is exposed to the solvent since the intramolecular interactions are incompletely wrapped by non-polar groups. Hence, dehydrons are sticky since they depend on additional intermolecular wrapping in order to properly protect the structure from water attack. Thus, a picture of protein binding is emerging wherein binding sites should be both dehydrons rich and surrounded by easily removable water. In this work we shall indeed confirm such a link between structure and dynamics by showing the existence of a firm correlation between the degree of underwrapping of the protein chain and the mobility of the corresponding hydration water molecules. In other words, we shall show that protein packing defects promote their local dehydration, thus producing a region of "hot" interfacial water which might be easily removed by a ligand upon association.

  6. Fast Searching in Packed Strings

    DEFF Research Database (Denmark)

    Bille, Philip

    2009-01-01

    Given strings P and Q the (exact) string matching problem is to find all positions of substrings in Q matching P. The classical Knuth-Morris-Pratt algorithm [SIAM J. Comput., 1977] solves the string matching problem in linear time which is optimal if we can only read one character at the time....... However, most strings are stored in a computer in a packed representation with several characters in a single word, giving us the opportunity to read multiple characters simultaneously. In this paper we study the worst-case complexity of string matching on strings given in packed representation. Let m...... algorithm using time O(n/log(sigma) n + m + occ) Here occ is the number of occurrences of P in Q. For m = o(n) this improves the O(n) bound...

  7. Characteristics of fluidized-packed beds

    Science.gov (United States)

    Gabor, J. D.; Mecham, W. J.

    1968-01-01

    Study of fluidized-packed bed includes investigation of heat transfer, solids-gas mixing, and elutriation characteristics. A fluidized-packed bed is a system involving the fluidization of small particles in the voids of a packed bed of larger nonfluidized particles.

  8. Packing Superballs from Codes and Algebraic Curves

    Institute of Scientific and Technical Information of China (English)

    Li LIU; Chao Ping XING

    2008-01-01

    In the present paper, we make use of codes with good parameters and algebraic curves over finite fields with many rational points to construct dense packings of superballs. It turns out that our packing density is quite reasonable. In particular, we improve some values for the best-known lower bounds on packing density.

  9. Complications of balloon packing in epistaxis

    NARCIS (Netherlands)

    Vermeeren, Lenka; Derks, Wynia; Fokkens, Wytske; Menger, Dirk Jan

    2015-01-01

    Although balloon packing appears to be efficient to control epistaxis, severe local complications can occur. We describe four patients with local lesions after balloon packing. Prolonged balloon packing can cause damage to nasal mucosa, septum and alar skin (nasal mucosa, the cartilaginous skeleton

  10. 7 CFR 51.1527 - Standard pack.

    Science.gov (United States)

    2010-01-01

    ... package. The number of plums or prunes in California peach boxes or lug boxes shall not vary more than 4... Standards for Grades of Fresh Plums and Prunes Standard Pack § 51.1527 Standard pack. (a) Packing. (1) All... plums or prunes in the top layer of any package shall be reasonably representative in quality and...

  11. Random packing of colloids and granular matter

    NARCIS (Netherlands)

    Wouterse, A.

    2008-01-01

    This thesis deals with the random packing of colloids and granular matter. A random packing is a stable disordered collection of touching particles, without long-range positional and orientational order. Experimental random packings of particles with the same shape but made of different materials sh

  12. Odd-even chain packing, molecular and thermal models for some long chain sodium(I) n-alkanoates

    Science.gov (United States)

    Nelson, Peter N.; Ellis, Henry A.

    2014-10-01

    A homologous series of sodium(I) n-alkanoates, NaCnH2n-1O2, with chain lengths n = 8-18, inclusive, have been synthesized and their structural and thermal properties investigated via Fourier Transform Infrared and Solid State 13C NMR spectroscopies, X-ray powder diffraction, Thermogravimetry, Differential Scanning Calorimetry, Polarizing light microscopy and variable temperature Infrared spectroscopy. The measurements show that metal-carboxylate coordination is via asymmetric chelating bidentate bonding with extensive carboxyl group inter-molecular interactions in which four oxygen atoms are bonded tetrahedrally to a sodium atom. Furthermore, the compounds crystallize in a monoclinic crystal system with the hydrocarbon chains in the fully extended all-trans conformation, advancing along the c-axis. Moreover, the chains are packed as tilted (θ ∼ 63°), non-overlapping, tail-to-tail lamellar bilayers that are not in the same plane, within a lamellar. Though these compounds are nearly isostructural, there are subtle differences in the packing of the hydrocarbon chains in the crystal lattice, resulting in odd-even alternation in the terminal methyl group asymmetric stretching vibration and chemical shift. These differences arise from the relative vertical distances between hydrocarbon planes within the lamellar; such that, for odd-chain compounds, larger inter-planar distances result in less efficient packing in the crystal lattice and hence, lower inter-planar van der Waals interactions between hydrocarbon chains. Thermal traces, for all compounds, show several partially reversible solid-solid pre-melting transitions associated with different degrees of gauche conformers in the alkyl chains. The reversible gauche-trans isomerism, of the methylene groups, is kinetically controlled; hence, super-cooling of the melt and other transitions, are observed for all compounds. The kinetics of chain reversion follow the exponential law of nucleation, though complicated by

  13. Packing defects into ordered structures

    DEFF Research Database (Denmark)

    Bechstein, R.; Kristoffersen, Henrik Høgh; Vilhelmsen, L.B.

    2012-01-01

    We have studied vicinal TiO2(110) surfaces by high-resolution scanning tunneling microscopy and density functional theory calculations. On TiO2 surfaces characterized by a high density of ⟨11̅ 1⟩ steps, scanning tunneling microscopy reveals a high density of oxygen-deficient strandlike adstructur...... because building material is available at step sites. The strands on TiO2(110) represent point defects that are densely packed into ordered adstructures....

  14. Understanding the role of vibrations, exact exchange, and many-body van der Waals interactions in the cohesive properties of molecular crystals

    Science.gov (United States)

    Reilly, Anthony M.; Tkatchenko, Alexandre

    2013-07-01

    The development and application of computational methods for studying molecular crystals, particularly density-functional theory (DFT), is a large and ever-growing field, driven by their numerous applications. Here we expand on our recent study of the importance of many-body van der Waals interactions in molecular crystals [A. M. Reilly and A. Tkatchenko, J. Phys. Chem. Lett. 4, 1028 (2013), 10.1021/jz400226x], with a larger database of 23 molecular crystals. Particular attention has been paid to the role of the vibrational contributions that are required to compare experiment sublimation enthalpies with calculated lattice energies, employing both phonon calculations and experimental heat-capacity data to provide harmonic and anharmonic estimates of the vibrational contributions. Exact exchange, which is rarely considered in DFT studies of molecular crystals, is shown to have a significant contribution to lattice energies, systematically improving agreement between theory and experiment. When the vibrational and exact-exchange contributions are coupled with a many-body approach to dispersion, DFT yields a mean absolute error (3.92 kJ/mol) within the coveted "chemical accuracy" target (4.2 kJ/mol). The role of many-body dispersion for structures has also been investigated for a subset of the database, showing good performance compared to X-ray and neutron diffraction crystal structures. The results show that the approach employed here can reach the demanding accuracy of crystal-structure prediction and organic material design with minimal empiricism.

  15. Structure of crystals of hard colloidal spheres

    Energy Technology Data Exchange (ETDEWEB)

    Pusey, P.N.; van Megen, W.; Bartlett, P.; Ackerson, B.J.; Rarity, J.G.; Underwood, S.M. (Royal Signals and Radar Establishment, Malvern, WR14 3PS, United Kingsom (GB) Department of Applied Physics, Royal Melbourne Institute of Technology, Melbourne, Victoria, Australia School of Chemistry, Bristol University, Bristol, BS8 1TS, United Kingdom Department of Physics, Oklahoma State University, Stillwater, Oklahoma 74078)

    1989-12-18

    We report light-scattering measurements of powder diffraction patterns of crystals of essentially hard colloidal spheres. These are consistent with structures formed by stacking close-packed planes of particles in a sequence of permitted lateral positions, {ital A},{ital B},{ital C}, which shows a high degree of randomness. Crystals grown slowly, while still containing many stacking faults, show a tendency towards face-centered-cubic packing: possible explanations for this observation are discussed.

  16. Efficiency of various lattices from hard ball to soft ball: theoretical study of thermodynamic properties of dendrimer liquid crystal from atomistic simulation.

    Science.gov (United States)

    Li, Youyong; Lin, Shiang-Tai; Goddard, William A

    2004-02-18

    Self-assembled supramolecular organic liquid crystal structures at nanoscale have potential applications in molecular electronics, photonics, and porous nanomaterials. Most of these structures are formed by aggregation of soft spherical supramolecules, which have soft coronas and overlap each other in the packing process. Our main focus here is to study the possible packing mechanisms via molecular dynamics simulations at the atomistic level. We consider the relative stability of various lattices packed by the soft dendrimer balls, first synthesized and characterized by Percec et al. (J. Am. Chem. Soc. 1997, 119, 1539) with different packing methods. The dendrons, which form the soft dendrimer balls, have the character of a hard aromatic region from the point of the cone to the edge with C(12) alkane "hair". After the dendrons pack into a sphere, the core of the sphere has the hard aromatic groups, while the surface is covered with the C(12) alkane "hair". In our studies, we propose three ways to organize the hair on the balls, Smooth/Valentino balls, Sticky/Einstein balls, and Asymmetric/Punk balls, which lead to three different packing mechanisms, Slippery, Sticky, and Anisotropic, respectively. We carry out a series of molecular dynamics (MD) studies on three plausible crystal structures (A15, FCC, and BCC) as a function of density and analyze the MD based on the vibrational density of state (DoS) method to extract the enthalpy, entropy, and free energies of these systems. We find that anisotropic packed A15 is favored over FCC, BCC lattices. Our predicted X-ray intensities of the best structures are in excellent agreement with experiment. "Anisotropic ball packing" proposed here plays an intermediate role between the enthalpy-favored "disk packing" and entropy-favored "isotropic ball packing", which explains the phase transitions at different temperatures. Free energies of various lattices at different densities are essentially the same, indicating that the

  17. Vibrational Collapse of Hexapod Packings

    Science.gov (United States)

    Zhao, Yuchen; Ding, Jingqiu; Barés, Jonathan; Dierichs, Karola; Behringer, Robert

    2016-11-01

    Columns made of convex noncohesive grains like sand collapse after being released from a confining container. However, structures built from concave grains can be stable without external support. Previous research show that the stability of the columns depends on column diameter and height, by observing column stability after carefully lifting their confinement tubes. Thinner and taller columns collapse with higher probability. While the column stability weakly depends on packing density, it strongly depends on inter-particle friction. Experiments that cause the column to collapse also reveal similar trends, as more effort (such as heavier loading or shearing) is required to destabilize columns that are intrinsically more stable. In the current experiments, we invesitage the effect of vibration on destructing a column. Short columns collapse following the relaxation dynamics of disorder systems, which coincides with similar experiments on staple packings. However, tall columns collapse faster at the beginning, in addition to the relaxation process coming after. Using high-speed imaging, we analyze column collapse data from different column geometries. Ongoing work is focusing on characterizing the stability of hexapod packings to vibration. We thanks NSF-DMR-1206351 and the William M. Keck Foundation.

  18. Towards optimal packed string matching

    DEFF Research Database (Denmark)

    Ben-Kiki, Oren; Bille, Philip; Breslauer, Dany

    2014-01-01

    In the packed string matching problem, it is assumed that each machine word can accommodate up to α characters, thus an n-character string occupies n/α memory words.(a) We extend the Crochemore–Perrin constant-space O(n)-time string-matching algorithm to run in optimal O(n/α) time and even in real......-time, achieving a factor α speedup over traditional algorithms that examine each character individually. Our macro-level algorithm only uses the standard AC0 instructions of the word-RAM model (i.e. no integer multiplication) plus two specialized micro-level AC0 word-size packed-string instructions. The main word...... matching work.(b) We also consider the complexity of the packed string matching problem in the classical word-RAM model in the absence of the specialized micro-level instructions wssm and wslm. We propose micro-level algorithms for the theoretically efficient emulation using parallel algorithms techniques...

  19. Diffusion in Jammed Particle Packs.

    Science.gov (United States)

    Bolintineanu, Dan S; Grest, Gary S; Lechman, Jeremy B; Silbert, Leonardo E

    2015-08-21

    Using random walk simulations we explore diffusive transport through monodisperse sphere packings over a range of packing fractions ϕ in the vicinity of the jamming transition at ϕ(c). Various diffusion properties are computed over several orders of magnitude in both time and packing pressure. Two well-separated regimes of normal "Fickian" diffusion, where the mean squared displacement is linear in time, are observed. The first corresponds to diffusion inside individual spheres, while the latter is the long-time bulk diffusion. The intermediate anomalous diffusion regime and the long-time value of the diffusion coefficient are both shown to be controlled by particle contacts, which in turn depend on proximity to ϕ(c). The time required to recover normal diffusion t* scales as (ϕ-ϕ(c))(-0.5) and the long-time diffusivity D(∞)∼(ϕ-ϕ(c))0.5, or D(∞)∼1/t*. It is shown that the distribution of mean first passage times associated with the escape of random walkers between neighboring particles controls both t* and D(∞) in the limit ϕ→ϕ(c).

  20. Weak interactions involving organic fluorine: analysis of structural motifs in Flunazirine and Haloperidol

    Science.gov (United States)

    Prasanna, M. D.; Row, T. N. Guru

    2001-05-01

    The crystal structure of Flunazirine, an anticonvulsant drug, is analyzed in terms of intermolecular interactions involving fluorine. The structure displays motifs formed by only weak interactions C-H⋯F and C-H⋯π. The motifs thus generated show cavities, which could serve as hosts for complexation. The structure of Flunazirine displays cavities formed by C-H⋯F and C-H⋯π interactions. Haloperidol, an antipsychotic drug, shows F⋯F interactions in the crystalline lattice in lieu of Cl⋯Cl interactions. However, strong O-H⋯N interactions dominate packing. The salient features of the two structures in terms of intermolecular interactions reveal, even though organic fluorine has lower tendency to engage in hydrogen bonding and F⋯F interactions, these interactions could play a significant role in the design of molecular assemblies via crystal engineering.

  1. Strong suppression of nuclear-charge changing interactions for 18 TeV/c In ions channeled through a bent Si crystal

    Energy Technology Data Exchange (ETDEWEB)

    Uggerhoj, U.I. [Department of Physics and Astronomy, University of Aarhus (Denmark)]. E-mail: ulrik@phys.au.dk; Hansen, H.D. [Department of Physics and Astronomy, University of Aarhus (Denmark); Jessen, K. [Department of Physics and Astronomy, University of Aarhus (Denmark); Knudsen, H. [Department of Physics and Astronomy, University of Aarhus (Denmark); Uggerhoj, E. [Department of Physics and Astronomy, University of Aarhus (Denmark); Scheidenberger, C. [GSI, Darmstadt (Germany); Biino, C. [CERN, Geneva (Switzerland); Clement, M. [CERN, Geneva (Switzerland); Doble, N. [CERN, Geneva (Switzerland); Elsener, K. [CERN, Geneva (Switzerland); Gatignon, L. [CERN, Geneva (Switzerland); Grafstroem, P. [CERN, Geneva (Switzerland); Sona, P. [University of Florence, Florence (Italy); Mangiarotti, A. [University of Florence, Florence (Italy); Ballestrero, S. [University of Florence, Florence (Italy)

    2005-07-21

    We present experimental results giving evidence for the strong reduction-a factor of more than 20-of nuclear-charge changing interactions for 18 TeV In{sup 49+} ions channeled through a silicon crystal bent to 7.5, 11.9 and 19.8 mrad. A very small fraction of the deflected ions suffer electromagnetic or nuclear interactions leading to proton loss while traversing the 60 mm long crystal, even though its thickness corresponds to about 0.13 nuclear interaction lengths for an amorphous material. By considering the deflected ions only, we show experimentally that the nuclear-charge pickup reaction believed to be induced by virtual photons is a short-range phenomenon.

  2. Strong suppression of nuclear-charge changing interactions for 18 TeV/ c In ions channeled through a bent Si crystal

    Science.gov (United States)

    Uggerhøj, U. I.; Hansen, H. D.; Jessen, K.; Knudsen, H.; Uggerhøj, E.; Scheidenberger, C.; Biino, C.; Clément, M.; Doble, N.; Elsener, K.; Gatignon, L.; Grafström, P.; Sona, P.; Mangiarotti, A.; Ballestrero, S.

    2005-07-01

    We present experimental results giving evidence for the strong reduction-a factor of more than 20-of nuclear-charge changing interactions for 18 TeV In49+ ions channeled through a silicon crystal bent to 7.5, 11.9 and 19.8 mrad. A very small fraction of the deflected ions suffer electromagnetic or nuclear interactions leading to proton loss while traversing the 60 mm long crystal, even though its thickness corresponds to about 0.13 nuclear interaction lengths for an amorphous material. By considering the deflected ions only, we show experimentally that the nuclear-charge pickup reaction believed to be induced by virtual photons is a short-range phenomenon.

  3. The Effect of Filler-Polymer Interactions on Cold-Crystallization Kinetics in Crosslinked, Silica Filled PDMS/PDPS Copolymer Melts.

    Energy Technology Data Exchange (ETDEWEB)

    Chien, A; DeTeresa, S; Thompson, L; Cohenour, R; Balazs, B; Maxwell, R S

    2006-04-21

    Crystallization in a series of variable crosslink density poly(dimethyl-diphenyl) siloxanes random block copolymers reinforced through a mixture of precipitated and fumed silica fillers has been studied by Differential Scanning Calorimetry (DSC), Dynamic Mechanical Analysis (DMA), and X-ray Diffraction (XRD). The silicone composite studied was composed of 94.6 mol% Dimethoylsiloxane, 5.1 mol% diphenylsiloxane, and 0.3 mol% methyl-vinyl siloxane (which formed crosslinking after a peroxide cure). The polymer was filled with a mixture of 21.6 wt. % fumed silica and 4.0 wt. % precipitated silica previously treated with 6.8 wt. % ethoxy-endblocked siloxane processing aid. The base composite was characterized by a molecular weight between crosslinks in the polymer network of {approx}24 kDa and an overall molecular weight (including the influence of the silica fillers) between crosslinks of {approx}11 kDa. Molecular weight between crosslinks and filler-polymer interaction strength were then modified by exposure to {gamma}-irradiation in either air or vacuum. The unirradiated material exhibited crystallization at -80 C as measured by DSC with a 16% crystallization as measured by XRD. Isothermal DMA experiments illustrated that crystallization at -85 C occurred over a 1.8 hour period in silica-filled systems and 2.2-2.6 hours in unfilled systems. The onset of crystallization typically occurred after a 30-minute incubation/nucleation period. The crystallization kinetics were dependent on crosslink density. Changes in molecular weight of a factor of two did not, however, change the amount of crystallization. Irradiation in vacuum resulted in faster overall crystallization rates compared to air irradiation for the same crosslink density, likely due to a reduction in the interaction between the polymer chains and the silica filler surface. Modulated differential scanning calorimetry contrasted the crystallization and melting behavior of pure PDMS versus the PDMS/PDPS base

  4. Breaking of the selection rules for optical transitions in the dielectric PrFe3(BO3)4 crystal by a praseodymium-iron exchange interaction.

    Science.gov (United States)

    Popova, M N; Stanislavchuk, T N; Malkin, B Z; Bezmaternykh, L N

    2009-05-01

    We report on the emergence of new lines in the optical spectrum of the PrFe3(BO3)4 single crystal at the magnetic ordering temperature. The transitions between singlet crystal-field sublevels of Pr3+ ion with the same transformational properties, strictly forbidden for the trigonal D3 point symmetry of this ion in PrFe3(BO3)4, appear below the Néel temperature and grow in intensity as a square of the order parameter. We show that the phenomenon originates from the mixing of wave functions of different Pr3+ sublevels by the Pr-Fe exchange interaction.

  5. Ionic Strength, Surface Charge, and Packing Density Effects on the Properties of Peptide Self-Assembled Monolayers.

    Science.gov (United States)

    Leo, Norman; Liu, Juan; Archbold, Ian; Tang, Yongan; Zeng, Xiangqun

    2017-02-28

    The various environmental parameters of packing density, ionic strength, and solution charge were examined for their effects on the properties of the immobilized peptide mimotope CH19 (CGSGSGSQLGPYELWELSH) that binds with the therapeutic antibody Trastuzumab (Herceptin) on a gold substrate. The immobilization of CH19 onto gold was examined with a quartz crystal microbalance (QCM). The QCM data showed the presence of intermolecular interactions resulting in the increase of viscoelastic properties of the peptide self-assembled monolayer (SAM). The CH19 SAM was diluted with CS7 (CGSGSGS) to decrease the packing density as CH19/CS7. The packing density and ionic strength parameters were evaluated by atomic force microscopy (AFM), ellipsometry, and QCM. AFM and ellipsometry showed a distinct conformational difference between CH19 and CH19/CS7, indicating a relationship between packing density and conformational state of the immobilized peptide. The CH19 SAM thickness was 40 Å with a rough topology, while the CH19/CS7 SAM thickness was 20 Å with a smooth topology. The affinity studies showed that the affinity of CH19 and CH19/CS7 to Trastuzumab were both on the order of 10(7) M(-1) in undiluted PBS buffer, while the dilution of the buffer by 1000× increased both SAMs affinities to Trastuzumab to the order of 10(15) M(-2) and changed the binding behavior from noncooperative to cooperative binding. This indicated that ionic strength had a more pronounced effect on binding properties of the CH19 SAM than packing density. Electrochemical impedance spectroscopy (EIS) was conducted on the CH19/CS7 SAM, which showed an increase in impedance after each EIS measurement cycle. Cyclic voltammetry on the CH19/CS7 SAM decreased impedance to near initial values. The impact of the packing density, buffer ionic strength, and local charge perturbation of the peptide SAM properties was interpreted based on the titratable sites in CH19 that could participate in the proton transfer and

  6. Ternary mixed crystal effects on electron-interface optical phonon interactions in In{sub x}Ga{sub 1-x}N/GaN quantum wells

    Energy Technology Data Exchange (ETDEWEB)

    Huang Wendeng, E-mail: wdhuang2005@163.com [MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Science, Xi' an Jiaotong University, Xi' an, 710049 (China) and School of Physics and Telecommunication Engineering, Shaanxi University of Technology, Hanzhong 723001 (China); Chen Guangde; Ye Honggang [MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Science, Xi' an Jiaotong University, Xi' an, 710049 (China); Ren Yajie [School of Physics and Telecommunication Engineering, Shaanxi University of Technology, Hanzhong 723001 (China)

    2013-02-01

    Based on the modified random-element isodisplacement model and dielectric continuum model, the dispersions of interface optical phonons, electron-interface phonon interaction and ternary mixed crystal effect on interface optical phonons in In{sub x}Ga{sub 1-x}N/GaN quantum wells are studied in a fully numerical manner. The results indicate that there are two indium concentration intervals that interface optical phonons exist. The indium concentration has important effects on the dispersions and electron-phonon interactions of interface optical phonons. The electron-IO phonon interactions in higher indium concentration are more important than that in lower indium concentration.

  7. The crucial role of chelate-chelate stacking interactions in the crystal structure of a square planar copper(II) complex

    Science.gov (United States)

    Jana, Subrata; Khan, Samim; Bauzá, Antonio; Frontera, Antonio; Chattopadhyay, Shouvik

    2017-01-01

    A square planar copper(II) complex has been synthesized and characterized by elemental analysis, IR spectroscopy and single-crystal X-ray diffraction study. The X-ray structure of the complex is used to analyze the crucial role of the π-interactions in the solid state. The complex also shows significant hydrogen-bonding interactions. Moreover, we have evaluated energetically both interactions by means of high level DFT calculations (BP86-D3/def2-TZVP) and characterized them using the Bader's theory of "atoms-in-molecules".

  8. Improved Online Square-into-Square Packing

    OpenAIRE

    Brubach, Brian

    2014-01-01

    In this paper, we show an improved bound and new algorithm for the online square-into-square packing problem. This two-dimensional packing problem involves packing an online sequence of squares into a unit square container without any two squares overlapping. The goal is to find the largest area $\\alpha$ such that any set of squares with total area $\\alpha$ can be packed. We show an algorithm that can pack any set of squares with total area $\\alpha \\leq 3/8$ into a unit square in an online se...

  9. Study of the Interaction of Trastuzumab and SKOV3 Epithelial Cancer Cells Using a Quartz Crystal Microbalance Sensor

    Directory of Open Access Journals (Sweden)

    Louise Elmlund

    2015-03-01

    Full Text Available Analytical methods founded upon whole cell-based assays are of importance in early stage drug development and in fundamental studies of biomolecular recognition. Here we have studied the binding of the monoclonal antibody trastuzumab to human epidermal growth factor receptor 2 (HER2 on human ovary adenocarcinoma epithelial cancer cells (SKOV3 using quartz crystal microbalance (QCM technology. An optimized procedure for immobilizing the cells on the chip surface was established with respect to fixation procedure and seeding density. Trastuzumab binding to the cell decorated sensor surface was studied, revealing a mean dissociation constant, KD, value of 7 ± 1 nM (standard error of the mean. This study provides a new perspective on the affinity of the antibody-receptor complex presented a more natural context compared to purified receptors. These results demonstrate the potential for using whole cell-based QCM assay in drug development, the screening of HER2 selective antibody-based drug candidates, and for the study of biomolecular recognition. This real time, label free approach for studying interactions with target receptors present in their natural environment afforded sensitive and detailed kinetic information about the binding of the analyte to the target.

  10. NOXclass: prediction of protein-protein interaction types

    Directory of Open Access Journals (Sweden)

    Sommer Ingolf

    2006-01-01

    Full Text Available Abstract Background Structural models determined by X-ray crystallography play a central role in understanding protein-protein interactions at the molecular level. Interpretation of these models requires the distinction between non-specific crystal packing contacts and biologically relevant interactions. This has been investigated previously and classification approaches have been proposed. However, less attention has been devoted to distinguishing different types of biological interactions. These interactions are classified as obligate and non-obligate according to the effect of the complex formation on the stability of the protomers. So far no automatic classification methods for distinguishing obligate, non-obligate and crystal packing interactions have been made available. Results Six interface properties have been investigated on a dataset of 243 protein interactions. The six properties have been combined using a support vector machine algorithm, resulting in NOXclass, a classifier for distinguishing obligate, non-obligate and crystal packing interactions. We achieve an accuracy of 91.8% for the classification of these three types of interactions using a leave-one-out cross-validation procedure. Conclusion NOXclass allows the interpretation and analysis of protein quaternary structures. In particular, it generates testable hypotheses regarding the nature of protein-protein interactions, when experimental results are not available. We expect this server will benefit the users of protein structural models, as well as protein crystallographers and NMR spectroscopists. A web server based on the method and the datasets used in this study are available at http://noxclass.bioinf.mpi-inf.mpg.de/.

  11. Structural, crystal structure, Hirshfeld surface analysis and physicochemical studies of a new chlorocadmate template by 1-(2-hydroxyethyl)piperazine

    Science.gov (United States)

    Soudani, S.; Jeanneau, E.; Jelsch, C.; Lefebvre, F.; Ben Nasr, C.

    2016-11-01

    The synthesis, crystal structure and spectroscopic characterization of a new chlorocadmate template by the 1-(2-hydroxyethyl)piperazine ligand are reported. In the atomic arrangement, the CdCl5O entities are deployed in corrugated rows along the a-axis at y = 1/4 and y = 3/4 to form layers parallel to the (a,b) plane. In these crystals, piperazinediium cations are in a chair conformation and are inserted between these layers through Nsbnd H⋯Cl, Csbnd H⋯Cl, Osbnd H⋯Cl and Nsbnd H⋯O hydrogen bonds to form infinite three-dimensional network. Investigation of intermolecular interactions and crystal packing via Hirshfeld surface analysis reveals that H⋯Cl and Csbnd H⋯Hsbnd C intermolecular interactions are the most abundant contacts of the organic cation in the crystal packing. The crystal contacts enrichments reveals that, the Cd++ … Cl- salt bridges, the Cd⋯O complexation and Osbnd H⋯Cl- and Nsbnd H⋯Cl-strong H-bonds are the driving forces in the packing formation. The presence of twelve independent chloride anions and four organic cation in the asymmetric unit allowed comparing their contact propensities. The 13C and 15N CP-MAS NMR spectra are in agreement with the X-ray structure. Additional characterization of this compound has also been performed by IR spectroscopy.

  12. School meal sociality or lunch pack individualism?

    DEFF Research Database (Denmark)

    Andersen, Sidse Schoubye; Holm, Lotte; Baarts, Charlotte

    2015-01-01

    The present article specifies and broadens our understanding of the concept of commensality by investigating what it means to ‘share a meal’. The study utilizes a school meal intervention carried out in Denmark in 2011/2012. It shows how different types of school meal arrangement influence...... to school. The study discusses commensality by examining and comparing lunchtime interactions within the same group of children in the two contrasting meal situations. The results fail to confirm the conventional view that shared meals have greater social impacts and benefits than eating individualized...... foods. The article argues that the social entrepreneurship involved in sharing individual lunch packs might even outweigh some of the benefits of shared meals where everyone is served the same food....

  13. Compaction dynamics of wet granular packings

    Science.gov (United States)

    Vandewalle, Nicolas; Ludewig, Francois; Fiscina, Jorge E.; Lumay, Geoffroy

    2013-03-01

    The extremely slow compaction dynamics of wet granular assemblies has been studied experimentally. The cohesion, due to capillary bridges between neighboring grains, has been tuned using different liquids having specific surface tension values. The characteristic relaxation time for compaction τ grows strongly with cohesion. A kinetic model, based on a free volume kinetic equations and the presence of a capillary energy barrier (due to liquid bridges), is able to reproduce quantitatively the experimental curves. This model allows one to describe the cohesion in wet granular packing. The influence of relative humidity (RH) on the extremely slow compaction dynamics of a granular assembly has also been investigated in the range 20 % - 80 % . Triboelectric and capillary condensation effects have been introduced in the kinetic model. Results confirm the existence of an optimal condition at RH ~ 45 % for minimizing cohesive interactions between glass beads.

  14. Packing of charged chains on toroidal geometries

    Science.gov (United States)

    Yao, Zhenwei; de la Cruz, Monica Olvera

    2013-01-01

    We study a strongly adsorbed flexible polyelectrolyte chain on tori. In this generalized Thomson problem, the patterns of the adsorbed chain are analyzed in the space of the toroidal coordinates and in terms of the orientation of each chain segment. Various patterns are found, including double spirals, disclination-like structures, Janus tori, and uniform wrappings, arising from the long-range electrostatic interaction and the toroidal geometry. Their broken mirror symmetry is quantitatively characterized by introducing an order parameter, an integral of the torsion. The uniform packing, which breaks the mirror symmetry the least, has the lowest value of the order parameter. In addition, it is found that the electrostatic energy of confined chains on tori conforms to a power law regardless of the screening effect in some typical cases studied. Furthermore, we study random walks on tori that generate chain configurations in the large screening limit or at large thermal fluctuation; some features associated with the toroidal geometry are discussed.

  15. Adhesive loose packings of small dry particles

    Science.gov (United States)

    Liu, Wenwei; Li, Shuiqing; Baule, Adrian; Makse, Hernán A.

    We explore adhesive loose packings of dry small spherical particles of micrometer size using 3D discrete-element simulations with adhesive contact mechanics. A dimensionless adhesion parameter ($Ad$) successfully combines the effects of particle velocities, sizes and the work of adhesion, identifying a universal regime of adhesive packings for $Ad>1$. The structural properties of the packings in this regime are well described by an ensemble approach based on a coarse-grained volume function that includes correlations between bulk and contact spheres. Our theoretical and numerical results predict: (i) An equation of state for adhesive loose packings that appears as a continuation from the frictionless random close packing (RCP) point in the jamming phase diagram; (ii) The existence of a maximal loose packing point at the coordination number $Z=2$ and packing fraction $\\phi=1/2^{3}$. Our results highlight that adhesion leads to a universal packing regime at packing fractions much smaller than the random loose packing, which can be described within a statistical mechanical framework. We present a general phase diagram of jammed matter comprising frictionless, frictional, adhesive as well as non-spherical particles, providing a classification of packings in terms of their continuation from the spherical frictionless RCP.

  16. Synthesis,Characterization and Crystal Structure of (PhCH2)2Sn(S2CENt2) and (PhCH2)2Sn(S2CNC4H8)2

    Institute of Scientific and Technical Information of China (English)

    尹汉东; 王传华; 等

    2003-01-01

    Two new dibenzyltin bisditiocarbamates(PhCH2)2 Sn(S2CNEt2)2(1) and (PhCH2)2 Sn(S2CNC4H8)2(2) were synthesized by the reaction of dibenzyltin dichloride with dithiocarbamates and characterized by elemental analysis ,IR,1H NMR and MS spectra.The crystal structures were determined by X-ray single crystal diffraction analysis.In both complexes,the tin atom is six-coordinated in a distorted octahedral configuration.In the crystals of 1,the molecular packing in unit cell reveals that the two adjacent molecules are symmetrically linked to each other in dimers by two Sn S interactions of 0.3816nm.In the crystals of 2,the molecules are packed in the unit cell in one-dimensional chain structure linked by weaker intermolecular S S conmtacts.

  17. Crystal structure of 3-bromo-2-hydroxybenzoic acid

    Directory of Open Access Journals (Sweden)

    Gerhard Laus

    2015-05-01

    Full Text Available Mutual carboxyl–carboxyl O—H...O hydrogen bonds link the molecules of the title compound, C7H5BrO3, into centrosymmetric dimers which display a central R22(8 ring motif. In addition, there is an intramolecular hydroxyl–carboxyl O—H...O interaction present. A comparison with the crystal structures of 59 other substituted derivatives of salicylic acid shows that both the centrosymmetric carboxyl–carboxyl O—H...O dimer and the stacking mode of molecules along the short a axis observed in the title structure are frequent packing motifs in this set.

  18. Thermodynamics of sublimation, crystal lattice energies, and crystal structures of racemates and enantiomers: (+)- and (+/-)-ibuprofen.

    Science.gov (United States)

    Perlovich, German L; Kurkov, Sergey V; Hansen, Lars Kr; Bauer-Brandl, Annette

    2004-03-01

    Thermodynamic differences between ibuprofen (IBP) racemate and the (+)-enantiomer were studied by X-ray diffraction, thermoanalysis, and crystal energy calculations. The thermodynamic functions of sublimation (as a measure of crystal lattice energy) were obtained by the transpiration method. The sublimation enthalpies (DeltaH(sub)) of (+/-)-IBP and (+)-IBP are 115.8 +/- 0.6 and 107.4 +/- 0.5 kJ. mol(-1), respectively. Using the temperature dependency of the saturated vapor pressure, the relative fractions of enthalpy and entropy of the sublimation process were calculated, and the sublimation process for both the racemate and the enantiomer was found to be enthalpy driven (62%). Two different force fields, Mayo et al. (M) and Gavezzotti (G), were used for comparative analysis of crystal lattice energies. Both force fields revealed that the van der Waals term contributes more to the packing energy in (+)-IBP than in (+/-)-IBP. The hydrogen bonding energy, however, contributes at 29.7 and 32.3% to the total crystal lattice energy in (+)-IBP and (+/-)-IBP (M), respectively. Furthermore, different structure fragments of the IBP molecule were analyzed with respect to their contribution to nonbonded van der Waals interactions. The effect of the C-H distance on the van der Waals term of the crystal lattice energy was also studied.

  19. Crystal structures of bis(phenoxysilicon phthalocyanines: increasing π–π interactions, solubility and disorder and no halogen bonding observed

    Directory of Open Access Journals (Sweden)

    Benoît H. Lessard

    2016-07-01

    Full Text Available We report the syntheses and characterization of three solution-processable phenoxy silicon phthalocyanines (SiPcs, namely bis(3-methylphenoxy(phthalocyaninesilicon [(3MP2-SiPc], C46H30N8O2Si, bis(2-sec-butylphenoxy(phthalocyaninesilicon [(2secBP2-SiPc], C44H24I2N8O2Si, and bis(3-iodophenoxy(phthalocyaninesilicon [(3IP2-SiPc], C52H42N8O2Si. Crystals grown of these compounds were characterized by single-crystal X-ray diffraction and the π–π interactions between the aromatic SiPc cores were studied. It was determined that (3MP2-SiPc has similar interactions to previously reported bis(3,4,5-trifluorophenoxysilicon phthalocyanines [(345 F2-SiPc] with significant π–π interactions between the SiPc groups. (3IP2-SiPc and (2secBP2-SiPc both experienced a parallel stacking of two of the peripheral aromatic groups. In all three cases, the solubility of these molecules was increased by the addition of phenoxy groups while maintaining π–π interactions between the aromatic SiPc groups. The solubility of (2secBP2-SiPc was significantly higher than other bis-phenoxy-SiPcs and this was exemplified by the higher observed disorder within the crystal structure.

  20. Melt extraction from crystal mushes: Numerical model of texture evolution and calibration of crystallinity-ordering relationships

    Science.gov (United States)

    Špillar, Václav; Dolejš, David

    2015-12-01

    Mechanical crystal-melt interactions in magmatic systems by separation or accumulation of crystals or by extraction of interstitial melt are expected to modify the spatial distribution of crystals observed as phenocrysts in igneous rocks. Textural analysis of porphyritic products can thus provide a quantitative means of interpreting the magnitude of crystal accumulation or melt loss and reconstructing the initial crystal percentage, at which the process occurred. We present a new three-dimensional numerical model that evaluates the effects of crystal accumulation (or interstitial melt removal) on the spatial distribution of crystals. Both processes lead to increasing apparent crystallinity but also to increasing spatial ordering expressed by the clustering index (R). The trend of progressive crystal packing deviates from a random texture trend, produced by static crystal nucleation and growth, and it is universal for any texture with straight log-linear crystal size distribution. For sparse crystal suspensions (5 vol. % crystals, R = 1.03), up to 97% melt can be extracted, corresponding to a new crystallinity of 65 vol.% and R = 1.32, when the rheological threshold of crystal interlocking is reached. For initially crystal-rich suspensions, the compaction path is shorter, this is because the initial crystal population is more aggregated and it reaches the limit of interlocking sooner. Crystal suspensions with ~ 35 vol.% crystals cannot be compacted without mechanical failure. These results illustrate that the onset of the rheological threshold of magma immobility strongly depends on the spatial configuration of crystals in the mush: the primary rigid percolation threshold (~ 35 vol.% crystals) corresponds to touching or interlocking crystal framework produced by in situ closed-system crystallization, whereas the secondary rigid percolation threshold (~ 35 to ~ 75 vol.% crystals) can be reached by compaction, which is particularly spatially efficient when acting on

  1. Quantitative Crystal Structure Analysis of (E-1-[(2-Chloro-1,3-thiazol-5-ylmethyl]-3-methyl-2-nitroguanidine

    Directory of Open Access Journals (Sweden)

    Dhananjay Dey

    2014-01-01

    Full Text Available The crystal structure of a biologically active (E-1-[(2-chloro-1,3-thiazol-5-ylmethyl]-3-methyl-2-nitroguanidine with molecular formula C6H8N5O2ClS has been investigated based on the molecular conformation and the supramolecular packing in terms of intermolecular interactions involving N–H⋯O, N–H⋯N, and C–H⋯O–N (nitro group, C–H⋯N (thiazol hydrogen bonds, offset π–π stacking, C–H⋯π and N(–NO2⋯C=N intermolecular interactions. Furthermore, a short C–Cl⋯O–N contact is also present which contributes towards the crystal packing. The lattice energy of the title compound has been calculated using the PIXEL approach (the Coulomb-London-Pauli (CLP model and compared with periodic calculations performed using CRYSTAL09. In addition, Hirshfeld surface analysis and fingerprint plots provide a platform for the evaluation of the contribution of different intermolecular interactions towards the packing behaviour.

  2. Manufacturing and characterization of bent silicon crystals for studies of coherent interactions with negatively charged particles beams

    Energy Technology Data Exchange (ETDEWEB)

    Germogli, G.; Mazzolari, A.; Bandiera, L.; Bagli, E.; Guidi, V.

    2015-07-15

    Efficient steering of GeV-energy negatively charged particle beams was demonstrated to be possible with a new generation of thin bent silicon crystals. Suitable crystals were produced at the Sensor Semiconductor Laboratory of Ferrara starting from Silicon On Insulator wafers, adopting proper revisitation of silicon micromachining techniques such as Low Pressure Chemical Vapor Deposition, photolithography and anisotropic chemical etching. Mechanical holders, which allow to properly bend the crystal and to reduce unwanted torsions, were employed. Crystallographic directions and crystal holder design were optimized in order to excite quasi-mosaic effect along (1 1 1) planes. Prior to exposing the crystal to particle beams, a full set of characterizations were performed. Infrared interferometry was used to measure crystal thickness with high accuracy. White-light interferometry was employed to characterize surface deformational state and its torsion. High-resolution X-rays diffraction was used to precisely measure crystal bending angle along the beam. Manufactured crystals were installed and tested at the MAMI MAinz MIcrotron to steer sub-GeV electrons, and at SLAC to deflect an electron beam in the 1 to 10 GeV energy range.

  3. Relative stability of the FCC and HCP polymorphs with interacting polymers.

    Science.gov (United States)

    Mahynski, Nathan A; Kumar, Sanat K; Panagiotopoulos, Athanassios Z

    2015-01-14

    Recent work [Mahynski et al., Nat. Commun., 2014, 5, 4472] has demonstrated that the addition of long linear homopolymers thermodynamically biases crystallizing hard-sphere colloids to produce the hexagonal close-packed (HCP) polymorph over the closely related face-centered cubic (FCC) structure when the polymers and colloids are purely repulsive. In this report, we investigate the effects of thermal interactions on each crystal polymorph to explore the possibility of stabilizing the FCC crystal structure over the HCP. We find that the HCP polymorph remains at least as stable as its FCC counterpart across the entire range of interactions we explored, where interactions were quantified by the reduced second virial coefficient, -1.50 0, its tetrahedral voids produce a similar effect when B FCC crystals are elusive in these binary mixtures.

  4. Synthesis and Crystal Structure of 1-(4-Nitrobenzyl-3-allyl-1H-benzo[d]imidazol-2(3H-one

    Directory of Open Access Journals (Sweden)

    Dounia Belaziz

    2013-01-01

    Full Text Available A functionalized benzimidazole, 1-(4-nitrobenzyl-3-allyl-1H-benzo[d]imidazol-2(3H-one, has been synthesized, and the crystal structure was determined and analyzed. This compound crystallizes in the monoclinic, space group P21/n (number 14 c with cell parameters, a=7.12148(8 Å, b=16.12035(17 Å, c=13.04169(17 Å, β=93.3043(11, V=1494.71(3 Å3, and Dcalc = 1.375 g/mm3. The solid state geometry is stabilized by intermolecular π–π interactions along with the van der Waals interactions which contribute to the stability of the crystal packing. Computational calculations have been used to properly understand the main intermolecular interactions present in the crystal.

  5. The relationship between efficient packing and glass-forming ability in hard-sphere systems

    Science.gov (United States)

    Zhang, Kai

    2014-03-01

    When supercooled liquids are rapidly quenched at rates R exceeding a critical value Rc, they avoid crystallization and form amorphous solids, such as bulk metallic glasses (BMGs). However, engineering applications of BMGs are often limited by the high cost of the constituent elements and their small casting thickness. Thus, we seek to design particular alloys with controllable stoichiometry and maximal critical cooling rate Rc. We perform numerical simulations to compress binary hard-sphere mixtures into glasses as a function of the particle size ratio and stoichiometry. We measure the packing fraction and local structural order for each glass to determine the critical compression rate. We find that large packing fraction differences between the crystalline and amorphous states implies poor glass forming ability, whereas small packing fraction differences yield better glass-formers. In addition, we show that an abundance of icosahedral order in amorphous packings enhances the glass forming ability of the mixtures. NSF MRSEC DMR-1119826, DMR-1006537, CBET-0968013.

  6. The “Theoreticals” Pack

    CERN Document Server

    CERN Bulletin

    2011-01-01

    The Particle Zoo is a colourful set of hand-made soft toys representing the particles in the Standard Model and beyond. It includes a “theoreticals” pack where you can find yet undiscovered particles: the best-selling Higgs boson, the graviton, the tachyon, and dark matter. Supersymmetric particle soft toys are also available on demand. But what would happen to the zoo if Nature had prepared some unexpected surprises? Julie Peasley, the zookeeper, is ready to sew new smiling faces…   The "Theoreticals" pack in the Particle Zoo. There is only one place in the world where you can buy a smiling Higgs boson and it’s not at CERN, although this is where scientists hope to observe it. The blue star-shaped particle is the best seller of Julie Peasley’s Particle Zoo – a collection of tens of soft toys representing all sorts of particles, including composite and decaying particles.  Over the years Julie’s zoo ...

  7. Fast searching in packed strings

    DEFF Research Database (Denmark)

    Bille, Philip

    2011-01-01

    Given strings P and Q the (exact) string matching problem is to find all positions of substrings in Q matching P. The classical Knuth–Morris–Pratt algorithm [SIAM J. Comput. 6 (2) (1977) 323–350] solves the string matching problem in linear time which is optimal if we can only read one character...... at the time. However, most strings are stored in a computer in a packed representation with several characters in a single word, giving us the opportunity to read multiple characters simultaneously. In this paper we study the worst-case complexity of string matching on strings given in packed representation....... Let m⩽n be the lengths P and Q, respectively, and let σ denote the size of the alphabet. On a standard unit-cost word-RAM with logarithmic word size we present an algorithm using timeO(nlogσn+m+occ). Here occ is the number of occurrences of P in Q. For m=o(n) this improves the O(n) bound of the Knuth...

  8. Polyoxometalate/Polyethylene Glycol Interactions in Water: From Nanoassemblies in Water to Crystal Formation by Electrostatic Screening.

    Science.gov (United States)

    Buchecker, Thomas; Le Goff, Xavier; Naskar, Bappaditya; Pfitzner, Arno; Diat, Olivier; Bauduin, Pierre

    2017-06-22

    In the last decade organic-inorganic hybrid materials have become essential in materials science as they combine properties of both building blocks. Nowadays the main routes for their synthesis involve electrostatic coupling, covalent grafting, and/or solvent effects. In this field, polyoxometalates (POMs) have emerged as interesting inorganic functional building blocks due to their outstanding properties. In the present work the well-known α-Keggin polyoxometalate, α-PW12 O40(3-) (PW), is shown to form hybrid crystalline materials with industrial (neutral) polyethylene glycol oligomers (PEG) under mild conditions, that is, in aqueous medium and at room temperature. The formation of these materials originates from the spontaneous self-assembly of PW with EOx , (EO=ethylene oxide) with at least four EO units (x>4). The PW-PEG nanoassemblies, made of a POM surrounded by about two PEG oligomers, are stabilized by electrostatic repulsions between the negatively charged PW anions. Addition of NaCl, aimed at screening the inter-nanoassembly repulsions, induces aggregation and formation of hybrid crystalline materials. Single-crystal analysis showed a high selectivity of PW towards EO5 -EO6 oligomers from PEG200, which is made of a mixture of EO3-8 . Therefore, a general "soft" route to produce POM-organic composites is proposed here through the control of electrostatic repulsions between spontaneously formed nanoassemblies in water. However, this rational design of new POM hybrid (crystalline) materials with hydrophilic blocks, using such a simple mixing procedure of the components, requires a deep understanding of the molecular interactions. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. DNA hosted and aligned in aqueous interstitia of a lamellar liquid crystal – a membrane–biomacromolecule interaction model system

    KAUST Repository

    Carlsson, Nils

    2013-01-01

    We report that DNA molecules can be intercalated and macroscopically oriented in the aqueous interstitia of a lyotropic lamellar liquid crystal. Using UV-vis linear dichroism and fluorescence spectroscopy we show that double-stranded oligonucleotides (25 base pairs) in the water-octanoate-decanol system remain base-paired in the B conformation and are confined in two dimensions, with the helix axis preferentially parallel to the lipid bilayer surfaces but free to rotate within this plane. The degree of helix confinement and the corresponding 2-D orientation can be improved by decreasing the thickness of the water interstitia via the fraction of water in the ternary mixture. Not surprisingly, the corresponding single-stranded oligonucleotides are not aligned, with their persistence length being short in comparison to the lamellar interstitium thickness. We propose this as a model system for studying interactions of DNA-ligand complexes near a lipid bilayer membrane which we demonstrate by using dye probes that are either covalently attached to one end of the oligonucleotide or reversibly bound by intercalation between the base pairs. Three cationic dyes, all strongly bound by intercalation to DNA when free in solution, are found to not bind to DNA but to prefer the membrane surface. The covalently attached Cy5 also binds to the bilayer while Cy3 tends to end-stack to the oligonucleotide duplex. The orientation of Cy5 parallel to the membrane indicates that electrostatic surface binding predominates over insertion into the hydrophobic interior of the membrane. Anionic and zwitterionic dyes (FAM and ROX) are found to remain randomly oriented in the water between the lipid bilayer surfaces. © The Royal Society of Chemistry.

  10. Crystal structure and self-interaction of the type VI secretion tail-tube protein from enteroaggregative Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Badreddine Douzi

    Full Text Available The type VI secretion system (T6SS is a widespread machine used by bacteria to control their environment and kill or disable bacterial species or eukaryotes through toxin injection. The T6SS comprises a central tube formed of stacked hexamers of hemolysin co-regulated proteins (Hcp and terminated by a trimeric valine-glycine repeat protein G (VgrG component, the cell puncturing device. A contractile tail sheath, formed by the TssB and TssC proteins, surrounds this tube. This syringe-like machine has been compared to an inverted phage, as both Hcp and VgrG share structural homology with tail components of Caudovirales. Here we solved the crystal structure of a tryptophan-substituted double mutant of Hcp1 from enteroaggregative Escherichia coli and compared it to the structures of other Hcps. Interestingly, we observed that the purified Hcp native protein is unable to form tubes in vitro. To better understand the rationale for observation, we measured the affinity of Hcp1 hexamers with themselves by surface plasmon resonance. The intra-hexamer interaction is weak, with a KD value of 7.2 µM. However, by engineering double cysteine mutants at defined positions, tubes of Hcp1 gathering up to 15 stacked hexamers formed in oxidative conditions. These results, together with those available in the literature regarding TssB and TssC, suggest that assembly of the T6SS tube differs significantly from that of Sipho- or Myoviridae.

  11. Insight to the thermodynamic stability of molecular crystals through crystallographic studies of a multipolymorph system.

    Science.gov (United States)

    Ng, Alicia T; Lai, Chiajen; Dabros, Marta; Gao, Qi

    2014-11-01

    Five solvent-free polymorphs of a pharmaceutical compound were discovered during polymorph screening. Out of the five polymorphs, only one has strong intermolecular N-H···N hydrogen bonding, whereas the others exhibit only weak C-H···N and π-π stacking interactions in addition to all the other weak C-H···X and van der Waals interactions. The relative thermodynamic stability relationships among the polymorphs are not intuitive and quite complex due to enantiotropic phase behavior. For instance, the polymorph with the most efficient packing (i.e., highest density) is not always the most thermodynamically stable form, and the polymorph with strong intermolecular interactions is not thermodynamically more stable than the polymorph with weak intermolecular interactions at all temperatures. Nevertheless, systematic examination and comparison of the molecular packing and intermolecular interactions of these polymorphs provide insight into the importance of H-bonding and packing efficiency to the thermodynamic stability of a crystalline form, and how these effects are dependent on temperature. This study seeks to correlate single-crystal structure features with experimentally established thermodynamic stability, and provides an example where a polymorph with only van der Waals forces and weak intermolecular interactions can be more stable than a polymorph that displays strong H-bonding in its structural make-up.

  12. The Role of Coulomb Interactions for Spin Crossover Behaviors and Crystal Structural Transformation in Novel Anionic Fe(III Complexes from a π-Extended ONO Ligand

    Directory of Open Access Journals (Sweden)

    Suguru Murata

    2016-05-01

    Full Text Available To investigate the π-extension effect on an unusual negative-charged spin crossover (SCO FeIII complex with a weak N2O4 first coordination sphere, we designed and synthesized a series of anionic FeIII complexes from a π-extended naphthalene derivative ligand. Acetonitrile-solvate tetramethylammonium (TMA salt 1 exhibited an SCO conversion, while acetone-solvate TMA salt 2 was in a high-spin state. The crystal structural analysis for 2 revealed that two-leg ladder-like cation-anion arrays derived from π-stacking interactions between π-ligands of the FeIII complex anion and Coulomb interactions were found and the solvated acetone molecules were in one-dimensional channels between the cation-anion arrays. A desolvation-induced single-crystal-to-single-crystal transformation to desolvate compound 2’ may be driven by Coulomb energy gain. Furthermore, the structural comparison between quasi-polymorphic compounds 1 and 2 revealed that the synergy between Coulomb and π-stacking interactions induces a significant distortion of coordination structure of 2.

  13. The Maximum Resource Bin Packing Problem

    DEFF Research Database (Denmark)

    Boyar, J.; Epstein, L.; Favrholdt, L.M.

    2006-01-01

    algorithms, First-Fit-Increasing and First-Fit-Decreasing for the maximum resource variant of classical bin packing. For the on-line variant, we define maximum resource variants of classical and dual bin packing. For dual bin packing, no on-line algorithm is competitive. For classical bin packing, we find......Usually, for bin packing problems, we try to minimize the number of bins used or in the case of the dual bin packing problem, maximize the number or total size of accepted items. This paper presents results for the opposite problems, where we would like to maximize the number of bins used...... the competitive ratio of various natural algorithms. We study the general versions of the problems as well as the parameterized versions where there is an upper bound of on the item sizes, for some integer k....

  14. Thioarsenides: A case for long-range Lewis acid-base-directed van der Waals interactions

    Energy Technology Data Exchange (ETDEWEB)

    Gibbs, Gerald V.; Wallace, Adam F.; Downs, R. T.; Ross, Nancy L.; Cox, David F.; Rosso, Kevin M.

    2011-04-01

    Electron density distributions, bond paths, Laplacian and local energy density properties have been calculated for a number of As4Sn (n = 3,4,5) thioarsenide molecular crystals. On the basis of the distributions, the intramolecular As-S and As-As interactions classify as shared bonded interactions and the intermolecular As-S, As-As and S-S interactions classify as closed-shell van der Waals bonded interactions. The bulk of the intermolecular As-S bond paths link regions of locally concentrated electron density (Lewis base regions) with aligned regions of locally depleted electron density (Lewis acid regions) on adjacent molecules. The paths are comparable with intermolecular paths reported for several other molecular crystals that link aligned Lewis base and acid regions in a key-lock fashion, interactions that classified as long range Lewis acid-base directed van der Waals interactions. As the bulk of the intermolecular As-S bond paths (~70%) link Lewis acid-base regions on adjacent molecules, it appears that molecules adopt an arrangement that maximizes the number of As-S Lewis acid-base intermolecular bonded interactions. The maximization of the number of Lewis acid-base interactions appears to be connected with the close-packed array adopted by molecules: distorted cubic close-packed arrays are adopted for alacránite, pararealgar, uzonite, realgar and β-AsS and the distorted hexagonal close-packed arrays adopted by α- and β-dimorphite. A growth mechanism is proposed for thioarsenide molecular crystals from aqueous species that maximizes the number of long range Lewis acid-base vdW As-S bonded interactions with the resulting directed bond paths structuralizing the molecules as a molecular crystal.

  15. An amino acid code to define a protein's tertiary packing surface.

    Science.gov (United States)

    Fraga, Keith J; Joo, Hyun; Tsai, Jerry

    2016-02-01

    One difficult aspect of the protein-folding problem is characterizing the nonspecific interactions that define packing in protein tertiary structure. To better understand tertiary structure, this work extends the knob-socket model by classifying the interactions of a single knob residue packed into a set of contiguous sockets, or a pocket made up of 4 or more residues. The knob-socket construct allows for a symbolic two-dimensional mapping of pockets. The two-dimensional mapping of pockets provides a simple method to investigate the variety of pocket shapes to understand the geometry of protein tertiary surfaces. The diversity of pocket geometries can be organized into groups of pockets that share a common core, which suggests that some interactions in pockets are ancillary to packing. Further analysis of pocket geometries displays a preferred configuration that is right-handed in α-helices and left-handed in β-sheets. The amino acid composition of pockets illustrates the importance of nonpolar amino acids in packing as well as position specificity. As expected, all pocket shapes prefer to pack with hydrophobic knobs; however, knobs are not selective for the pockets they pack. Investigating side-chain rotamer preferences for certain pocket shapes uncovers no strong correlations. These findings allow a simple vocabulary based on knobs and sockets to describe protein tertiary packing that supports improved analysis, design, and prediction of protein structure.

  16. Terahertz Vibrations and Hydrogen-Bonded Networks in Crystals

    Directory of Open Access Journals (Sweden)

    Masae Takahashi

    2014-03-01

    Full Text Available The development of terahertz technology in the last few decades has made it possible to obtain a clear terahertz (THz spectrum. THz vibrations clearly show the formation of weak bonds in crystals. The simultaneous progress in the code of first-principles calculations treating noncovalent interactions has established the position of THz spectroscopy as a powerful tool for detecting the weak bonding in crystals. In this review, we are going to introduce, briefly, the contribution of weak bonds in the construction of molecular crystals first, and then, we will review THz spectroscopy as a powerful tool for detecting the formation of weak bonds and will show the significant contribution of advanced computational codes in treating noncovalent interactions. From the second section, following the Introduction, to the seventh section, before the conclusions, we describe: (1 the crystal packing forces, the hydrogen-bonded networks and their contribution to the construction of organic crystals; (2 the THz vibrations observed in hydrogen-bonded molecules; (3 the computational methods for analyzing the THz vibrations of hydrogen-bonded molecules; (4 the dispersion correction and anharmonicity incorporated into the first-principles calculations and their effect on the peak assignment of the THz spectrum (5 the temperature dependence; and (6 the polarization dependence of the THz spectrum.

  17. L1-norm packings from function fields

    Institute of Scientific and Technical Information of China (English)

    LI Hongli

    2005-01-01

    In this paper, we study some packings in a cube, namely, how to pack n points in a cube so as to maximize the minimal distance. The distance is induced by the L1-norm which is analogous to the Hamming distance in coding theory. Two constructions with reasonable parameters are obtained, by using some results from a function field including divisor class group, narrow ray class group, and so on. We also present some asymptotic results of the two packings.

  18. Circle Packing for Origami Design Is Hard

    CERN Document Server

    Demaine, Erik D; Lang, Robert J

    2010-01-01

    We show that deciding whether a given set of circles can be packed into a rectangle, an equilateral triangle, or a unit square are NP-hard problems, settling the complexity of these natural packing problems. On the positive side, we show that any set of circles of total area 1 can be packed into a square of size 8/pi=2.546... These results are motivated by problems arising in the context of origami design.

  19. Numerical Simulation on Dense Packing of Granular Materials by Container Oscillation

    Directory of Open Access Journals (Sweden)

    Jun Liu

    2013-01-01

    Full Text Available The packing of granular materials is a basic and important problem in geomechanics. An approach, which generates dense packing of spheres confined in cylindrical and cuboidal containers in three steps, is introduced in this work. A loose packing structure is first generated by means of a reference lattice method. Then a dense packing structure is obtained in a container by simulating dropping of particles under gravitational forces. Furthermore, a scheme that makes the bottom boundary fluctuate up and down was applied to obtain more denser packing. The discrete element method (DEM was employed to simulate the interactions between particle-particle and particle-boundary during the particles' motions. Finally, two cases were presented to indicate the validity of the method proposed in this work.

  20. Imaging phospholipid conformational disorder and packing in giant multilamellar liposome by confocal Raman microspectroscopy.

    Science.gov (United States)

    Noothalapati, Hemanth; Iwasaki, Keita; Yoshimoto, Chikako; Yoshikiyo, Keisuke; Nishikawa, Tomoe; Ando, Masahiro; Hamaguchi, Hiro-O; Yamamoto, Tatsuyuki

    2017-12-05

    Liposomes are closed phospholipid bilayer systems that have profound applications in fundamental cell biology, pharmaceutics and medicine. Depending on the composition (pure or mixture of phospholipids, presence of cholesterol) and preparation protocol, intra- and inter-chain molecular interactions vary leading to changes in the quality (order and packing) of liposomes. So far it is not possible to image conformational disorders and packing densities within a liposome in a straightforward manner. In this study, we utilized confocal Raman microspectroscopy to visualize structural disorders and packing efficiency within a giant multilamellar liposome model by focusing mainly on three regions in the vibrational spectrum (CC stretching, CH deformation and CH stretching). We estimated properties such as trans/gauche isomers and lateral packing probability. Interestingly, our Raman imaging studies revealed gel phase rich domains and heterogeneous lateral packing within the giant multilamellar liposome. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Crystal structure of (E-N1-[(anthracen-9-ylmethylidene]-N4-phenylbenzene-1,4-diamine

    Directory of Open Access Journals (Sweden)

    Md. Serajul Haque Faizi

    2017-02-01

    Full Text Available The title compound, C27H20N2, a Schiff base synthesized via a condensation reaction between anthracene-9-carbaldehyde and N-phenyl-p-phenylenediamine, crystallizes with three independent molecules in the asymmetric unit. The three molecules have slightly varying overall conformations, all having trans conformations with respect to the C=N bond. In the crystal, the packing features N—H...N hydrogen bonds, which connect molecules into chains extending along the c-axis direction, interlinked by C—H...π interactions (minimum H...Cg = 2.65 Å into sheets lying parallel to (001.

  2. Random close packing of polydisperse jammed emulsions

    Science.gov (United States)

    Brujic, Jasna

    2010-03-01

    Packing problems are everywhere, ranging from oil extraction through porous rocks to grain storage in silos and the compaction of pharmaceutical powders into tablets. At a given density, particulate systems pack into a mechanically stable and amorphous jammed state. Theoretical frameworks have proposed a connection between this jammed state and the glass transition, a thermodynamics of jamming, as well as geometric modeling of random packings. Nevertheless, a simple underlying mechanism for the random assembly of athermal particles, analogous to crystalline ordering, remains unknown. Here we use 3D measurements of polydisperse packings of emulsion droplets to build a simple statistical model in which the complexity of the global packing is distilled into a local stochastic process. From the perspective of a single particle the packing problem is reduced to the random formation of nearest neighbors, followed by a choice of contacts among them. The two key parameters in the model, the available space around a particle and the ratio of contacts to neighbors, are directly obtained from experiments. Remarkably, we demonstrate that this ``granocentric'' view captures the properties of the polydisperse emulsion packing, ranging from the microscopic distributions of nearest neighbors and contacts to local density fluctuations and all the way to the global packing density. Further applications to monodisperse and bidisperse systems quantitatively agree with previously measured trends in global density. This model therefore reveals a general principle of organization for random packing and lays the foundations for a theory of jammed matter.

  3. Random packing of spheres in Menger sponge.

    Science.gov (United States)

    Cieśla, Michał; Barbasz, Jakub

    2013-06-07

    Random packing of spheres inside fractal collectors of dimension 2 algorithm. The paper focuses mainly on the measurement of random packing saturation limit. Additionally, scaling properties of density autocorrelations in the obtained packing are analyzed. The RSA kinetics coefficients are also measured. Obtained results allow to test phenomenological relation between random packing saturation density and collector dimension. Additionally, performed simulations together with previously obtained results confirm that, in general, the known dimensional relations are obeyed by systems having non-integer dimension, at least for d < 3.

  4. SPECTRUM OF DIRECTED KIRKMAN PACKING DESIGNS

    Institute of Scientific and Technical Information of China (English)

    ZhangYan; DuBeiliang

    2003-01-01

    The problem studied in this article is the directed Kirkman packing, the resolvable directed packing which requires all blocks to be of size three except that ,each resolution class should contain either one block of size two(when v=2(mod 3)) or one block of size four (when v=l (mod 3)). A directed Kirkman packing design DKPD(v) is a resolvable directed packing of a v-set by the maximum possible number of resolution classes of this type. This article investigates the spectrum of DKPD(v) and it is found that it contains all positive integers v≥3 and v≠5,6.

  5. Isogyres - Manifestation of Spin-orbit interaction in uniaxial crystal: A closed-fringe Fourier analysis of conoscopic interference.

    Science.gov (United States)

    Samlan, C T; Naik, Dinesh N; Viswanathan, Nirmal K

    2016-09-14

    Discovered in 1813, the conoscopic interference pattern observed due to light propagating through a crystal, kept between crossed polarizers, shows isochromates and isogyres, respectively containing information about the dynamic and geometric phase acquired by the beam. We propose and demonstrate a closed-fringe Fourier analysis method to disentangle the isogyres from the isochromates, leading us to the azimuthally varying geometric phase and its manifestation as isogyres. This azimuthally varying geometric phase is shown to be the underlying mechanism for the spin-to-orbital angular momentum conversion observed in a diverging optical field propagating through a z-cut uniaxial crystal. We extend the formalism to study the optical activity mediated uniaxial-to-biaxial transformation due to a weak transverse electric field applied across the crystal. Closely associated with the phase and polarization singularities of the optical field, the formalism enables us to understand crystal optics in a new way, paving the way to anticipate several emerging phenomena.

  6. Isogyres – Manifestation of Spin-orbit interaction in uniaxial crystal: A closed-fringe Fourier analysis of conoscopic interference

    Science.gov (United States)

    Samlan, C. T.; Naik, Dinesh N.; Viswanathan, Nirmal K.

    2016-01-01

    Discovered in 1813, the conoscopic interference pattern observed due to light propagating through a crystal, kept between crossed polarizers, shows isochromates and isogyres, respectively containing information about the dynamic and geometric phase acquired by the beam. We propose and demonstrate a closed-fringe Fourier analysis method to disentangle the isogyres from the isochromates, leading us to the azimuthally varying geometric phase and its manifestation as isogyres. This azimuthally varying geometric phase is shown to be the underlying mechanism for the spin-to-orbital angular momentum conversion observed in a diverging optical field propagating through a z-cut uniaxial crystal. We extend the formalism to study the optical activity mediated uniaxial-to-biaxial transformation due to a weak transverse electric field applied across the crystal. Closely associated with the phase and polarization singularities of the optical field, the formalism enables us to understand crystal optics in a new way, paving the way to anticipate several emerging phenomena. PMID:27625210

  7. Ideal, best packing, and energy minimizing double helices

    CERN Document Server

    O'Hara, Jun

    2011-01-01

    We study optimal double helices with straight axes (or the fattest tubes around them) computationally using three kinds of functionals; ideal ones using ropelength, best volume packing ones, and energy minimizers using two one-parameter families of interaction energies between two strands of types $r^{-\\alpha}$ and $\\frac1r\\exp(-kr)$. We compare the numerical results with experimental data of DNA.

  8. DHS Internship Summary-Crystal Assembly at Different Length Scales

    Energy Technology Data Exchange (ETDEWEB)

    Mishchenko, L

    2009-08-06

    . In particular, molecular crystals, which are typically dominated by ionic and covalent bonding, are an order of magnitude more strongly bonded than colloidal crystals. In molecular crystals, ordering is driven by the interaction potentials between molecules. By contrast, colloidal assembly is a competition between the repulsive electrostatic forces that prevent aggregation in solution (due to surface charge), and short-range van der Waals and entropic forces that leads to ordering. Understanding atomic crystallization is fundamentally important for fabrication of tailorable crystalline materials, for example for biological or chemical sensors. The transformation of brushite to OCP not only serves as a model system for atomic crystal growth (applicable to many other crystal growth processes), but is also important in bone cements. Colloidal crystals have unique optical properties which respond to chemical and mechanical stimuli, making them very important for sensing applications. The mechanism of colloidal crystal assembly is thus fundamentally important. Our in situ dissolution and regrowth experiments are one good method of analyzing how these crystals pack under different conditions and how defect sites are formed and filled. In these experiments, a silica additive was used to strengthen the colloidal crystal during initial assembly (ex situ) and to increase domain size and long range order. Reversible electrodeposition of colloids onto a conductive substrate (ITO in our case) is another system which can further our knowledge of colloidal assembly. This experiment holds promise of allowing in situ observation of colloidal crystal growth and the influence of certain additives on crystal order. The ultimate goal would be to achieve long range order in these crystals by changing the surface charge or the growth environment.

  9. Frac-and-pack stimulation: Application, design, and field experience

    Energy Technology Data Exchange (ETDEWEB)

    Roodhart, L.P.; Fokker, P.A.; Davies, D.R.; Shlyapobersky, J.; Wong, G.K.

    1994-03-01

    This paper discusses the criteria for selecting wells to be frac-and-packed. The authors show how systematic study of the inflow performance can be used to assess the potential of frac-and-packed wells, to identify the controlling factors, and to optimize design parameters. They also show that fracture conductivity is often the key to successful treatment. This conductivity depends largely on proppant size; formation permeability damage around the created fracture has less effect. Appropriate allowance needs to be made for flow restrictions caused by the presence of the perforations, partial penetration, and non-Darcy effects. They describe the application of the overpressure-calibrated hydraulic fracture model in frac-and-pack treatment design, and discuss some operational considerations with reference to field examples. The full potential of this promising new completion method can be achieved only if the design is tailored to the individual well. This demands high-quality input data, which can be obtained only from a calibration test. This paper presents their strategy for frac-and-pack design, drawing on examples from field experience. They also point out several areas that the industry needs to address, such as the sizing of proppant in soft formations and the interaction between fracturing fluids and resin in resin-coated proppant.

  10. Synthesis, Crystal Structure, and Hirshfeld Surface Analysis of Ciprofloxacin-Salicylic Acid Molecular Salt

    Directory of Open Access Journals (Sweden)

    Ravikumar Nagalapalli

    2014-01-01

    Full Text Available In the present study, ciprofloxacin-salicylic acid molecular salt has been synthesized and preliminarily characterized by FT-IR spectroscopy. The single crystal X-ray diffraction (SCXRD reveals the proton transfer from carboxylic acid group of salicylic acid to piperazine moiety in ciprofloxacin confirming the formation of new molecular salt. The molecular packing of the molecular salt is mainly supported by N+–H⋯O−, O–H⋯O, C–H⋯F, C–H⋯π, and π-π interactions. The 3D Hirshfeld surfaces and the associated 2D fingerprint plots were investigated for intermolecular hydrogen bonding interactions.

  11. Minimally packed phases in holography

    CERN Document Server

    Donos, Aristomenis

    2015-01-01

    We numerically construct asymptotically AdS black brane solutions of $D=4$ Einstein-Maxwell theory coupled to a pseudoscalar. The solutions are holographically dual to $d=3$ CFTs held at constant chemical potential and magnetic field that spontaneously break translation invariance leading to the spontaneous formation of abelian and momentum magnetisation currents flowing around the plaquettes of a periodic Bravais lattice. We analyse the three-dimensional moduli space of lattice solutions, which are generically oblique, and show that the free energy is minimised by the triangular lattice, associated with minimal packing of circles in the plane. The triangular structure persists at low temperatures indicating the existence of novel crystalline ground states.

  12. Confined disordered strictly jammed binary sphere packings

    Science.gov (United States)

    Chen, D.; Torquato, S.

    2015-12-01

    Disordered jammed packings under confinement have received considerably less attention than their bulk counterparts and yet arise in a variety of practical situations. In this work, we study binary sphere packings that are confined between two parallel hard planes and generalize the Torquato-Jiao (TJ) sequential linear programming algorithm [Phys. Rev. E 82, 061302 (2010), 10.1103/PhysRevE.82.061302] to obtain putative maximally random jammed (MRJ) packings that are exactly isostatic with high fidelity over a large range of plane separation distances H , small to large sphere radius ratio α , and small sphere relative concentration x . We find that packing characteristics can be substantially different from their bulk analogs, which is due to what we term "confinement frustration." Rattlers in confined packings are generally more prevalent than those in their bulk counterparts. We observe that packing fraction, rattler fraction, and degree of disorder of MRJ packings generally increase with H , though exceptions exist. Discontinuities in the packing characteristics as H varies in the vicinity of certain values of H are due to associated discontinuous transitions between different jammed states. When the plane separation distance is on the order of two large-sphere diameters or less, the packings exhibit salient two-dimensional features; when the plane separation distance exceeds about 30 large-sphere diameters, the packings approach three-dimensional bulk packings. As the size contrast increases (as α decreases), the rattler fraction dramatically increases due to what we call "size-disparity" frustration. We find that at intermediate α and when x is about 0.5 (50-50 mixture), the disorder of packings is maximized, as measured by an order metric ψ that is based on the number density fluctuations in the direction perpendicular to the hard walls. We also apply the local volume-fraction variance στ2(R ) to characterize confined packings and find that these

  13. Adsorption, Desorption, Surface Diffusion, Lattice Defect Formation, and Kink Incorporation Processes of Particles on Growth Interfaces of Colloidal Crystals with Attractive Interactions

    Directory of Open Access Journals (Sweden)

    Yoshihisa Suzuki

    2016-07-01

    Full Text Available Good model systems are required in order to understand crystal growth processes because, in many cases, precise incorporation processes of atoms or molecules cannot be visualized easily at the atomic or molecular level. Using a transmission-type optical microscope, we have successfully observed in situ adsorption, desorption, surface diffusion, lattice defect formation, and kink incorporation of particles on growth interfaces of colloidal crystals of polystyrene particles in aqueous sodium polyacrylate solutions. Precise surface transportation and kink incorporation processes of the particles into the colloidal crystals with attractive interactions were observed in situ at the particle level. In particular, contrary to the conventional expectations, the diffusion of particles along steps around a two-dimensional island of the growth interface was not the main route for kink incorporation. This is probably due to the number of bonds between adsorbed particles and particles in a crystal; the number exceeds the limit at which a particle easily exchanges its position to the adjacent one along the step. We also found novel desorption processes of particles from steps to terraces, attributing them to the assistance of attractive forces from additionally adsorbing particles to the particles on the steps.

  14. Crystal field properties of Yb2Ti2O7. [Eigenfunctions, quadrupole interactions

    Energy Technology Data Exchange (ETDEWEB)

    Dunlap, B. D.; Shenoy, G. K.; Friedt, J. M.; Meyer, M.; McCarthy, G. J.

    1977-01-01

    Electronic properties of Yb/sup 3 +/ in Yb/sub 2/Ti/sub 2/O/sub 7/ were investigated using the 84.6 keV Mossbauer transition in /sup 170/Yb. The crystal field parameters were deduced by analyzing spectra taken in various externally applied magnetic fields up to 32 kG at temperatures of 4.2 K and 1.6 K. Because of the hexagonal point symmetry at the Yb ion, the crystal field levels are sensitive to the direction of the applied field relative to the c axis. As a result, a proper discussion of the field and temperature dependence of the hyperfine parameters is not possible for a powder sample without a careful average over angles. Such an analysis then yields a value for the crystal field parameter B/sub 2//sup 0/ in the range 15 to 21 K and B/sup 0//sub 4//B/sup 0//sub 2/ approximately equal 0.01. These parameters and the resulting crystal field eigenfunctions were used to explain the small quadrupole interaction present in this material.

  15. Particle-size distribution and packing fraction of geometric random packings

    NARCIS (Netherlands)

    Brouwers, H.J.H.

    2006-01-01

    This paper addresses the geometric random packing and void fraction of polydisperse particles. It is demonstrated that the bimodal packing can be transformed into a continuous particle-size distribution of the power law type. It follows that a maximum packing fraction of particles is obtained when t

  16. Supramolecular assembly of 2,4,5-trifluorobenzoate complex based on weak interactions involving fluorine atoms

    Institute of Scientific and Technical Information of China (English)

    Chun-Hua Ge; Rui Zhang; Ping Fan; Xiang-Dong Zhang; Li-Juan Wang; Fang-Fang Wang

    2013-01-01

    The complex [Cd(tfbz)2(phen)]2 (1) (tfbz =2,4,5-trifluorobenzoate,phen =1,10-phenanthro-line) was synthesized using trifluorobenzoic acid ligand.The single-crystal structure of 1 has been determined by X-ray crystallography.The packing structure is characterized by the formation of an intricate three-dimensional supramolecular network that depends on the C-H…F,F…F, F(lp)…π (lp =lone pair) interactions.

  17. Cloning, expression, purification, crystallization and preliminary crystallographic analysis of pseudo death-effector domain of HIPPI, a molecular partner of Huntingtin-interacting protein HIP-1

    Energy Technology Data Exchange (ETDEWEB)

    Banerjee, Manisha; Majumder, Pritha; Bhattacharyya, Nitai P.; Dattagupta, Jiban K.; Sen, Udayaditya, E-mail: udayaditya.sen@saha.ac.in [Structural Genomics Section, Saha Institute of Nuclear Physics, 1/AF Bidhan Nagar, Kolkata 700064 (India)

    2006-12-01

    A pseudo death-effector domain (pDED) of HIPPI, a partner of Huntingtin-interacting protein HIP1, has been cloned, overexpressed and crystallized. The crystals of pDED-HIPPI diffracted to 2.2 Å. The formation of a heterodimer between Huntingtin-interacting protein-1 (HIP-1) and its novel partner HIPPI (HIP-1 protein interactor) through their pseudo death-effector domains (pDEDs) is a key step that recruits caspase-8 and initiates apoptosis. This could be one of the pathways by which apoptosis is increased in Huntington’s disease (HD). A construct consisting of the pDED of HIPPI has been cloned and overexpressed as 6NH-tagged protein and purified by Ni–NTA affinity chromatography. Crystals of the pDED of HIPPI were grown in space group P4{sub 1}, with unit-cell parameters a = b = 77.42, c = 33.31 Å and a calculated Matthews coefficient of 1.88 Å{sup 3} Da{sup −1} (33% solvent content) with two molecules per asymmetric unit.

  18. Theoretical study on molecular packing and electronic structure of bi-1,3,4-oxadiazole derivatives

    KAUST Repository

    Wang, Haitao

    2014-01-01

    The molecular aggregation structure of 5,5′-bis(naphthalen-2-yl)-2,2′-bi(1,3,4-oxadiazole) (BOXD-NP) was studied by computing the intermolecular interaction potential energy surface (PES) at density functional theory level based on a dimer model. All B3LYP, CAM-B3LYP and M062x functionals can yield a reliable isolated molecular geometry. The conformation of BOXD-NP obtained with all methods is perfectly planar, indicating good conjugation ability between oxadiazole and naphthalene rings. The vibrational frequencies of BOXD-NP were also calculated using the B3LYP/6-311+G∗∗ method, which showed great consistency with the experimental observations and makes the assignments of the IR spectra more solid. It was revealed that the lowest excited state of BOXD-NP should be assigned as a highly allowed π-π∗ state by TD-DFT calculation. Considering the non-covalent interactions in molecular aggregates, the M062x functional was applied in the construction of the PES. Besides the packing structure found in the crystals, PES also predicted several stable structures, indicating that PES has great ability in guiding molecular self-assembly. Symmetry Adapted Perturbation Theory (SAPT) analysis on these energy-minimum molecular stacking structures revealed that London dispersion forces are the strongest attractive component in the binding. This journal is

  19. Development of an effective valve packing program

    Energy Technology Data Exchange (ETDEWEB)

    Hart, K.A.

    1996-12-01

    Current data now shows that graphite valve packing installed within the guidance of a controlled program produces not only reliable stem sealing but predictable running loads. By utilizing recent technological developments in valve performance monitoring for both MOV`s and AOV`s, valve packing performance can be enhanced while reducing maintenance costs. Once known, values are established for acceptable valve packing loads, the measurement of actual valve running loads via the current MOV/AOV diagnostic techniques can provide indication of future valve stem sealing problems, improper valve packing installation or identify the opportunity for valve packing program improvements. At times the full benefit of these advances in material and predictive technology remain under utilized due to simple past misconceptions associated with valve packing. This paper will explore the basis for these misconceptions, provide general insight into the current understanding of valve packing and demonstrate how with this new understanding and current valve diagnostic equipment the key aspects required to develop an effective, quality valve packing program fit together. The cost and operational benefits provided by this approach can be significant impact by the: elimination of periodic valve repacking, reduction of maintenance costs, benefits of leak-free valve operation, justification for reduced Post Maintenance Test Requirements, reduced radiation exposure, improved plant appearance.

  20. On maximum cycle packings in polyhedral graphs

    Directory of Open Access Journals (Sweden)

    Peter Recht

    2014-04-01

    Full Text Available This paper addresses upper and lower bounds for the cardinality of a maximum vertex-/edge-disjoint cycle packing in a polyhedral graph G. Bounds on the cardinality of such packings are provided, that depend on the size, the order or the number of faces of G, respectively. Polyhedral graphs are constructed, that attain these bounds.

  1. BIPP (BISMUTH IODINE PARAFFINE PASTE PACK REVISITED

    Directory of Open Access Journals (Sweden)

    Balasubramanian Thiagarajan

    2011-09-01

    Full Text Available This review article takes a new look at the use of BIPP pack following nasal and ear surgeries. It lists the advantages and pitfalls of using this packing material. Pubmed search revealed very little material on this topic hence I compiled existing data to bring out an article.

  2. Meromorphic Vector Fields and Circle Packings

    DEFF Research Database (Denmark)

    Dias, Kealey

    to structurally stable vector fields, there is an underlying dynamically defined triangulation of the plane. Circle packings are a means to realize such a given combinatorial structure. About 20 years ago, W. Thurston suggested applying circle packings to obtain approximations to Riemann mappings. This gave rise...

  3. Improved lower bound for online strip packing

    NARCIS (Netherlands)

    Harren, Rolf; Kern, Walter

    2012-01-01

    In the two-dimensional strip packing problem a number of rectangles have to be packed without rotation or overlap into a strip such that the height of the strip used is minimal. The width of the rectangles is bounded by 1 and the strip has width 1 and infinite height. We study the online version of

  4. 7 CFR 29.1048 - Packing.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Packing. 29.1048 Section 29.1048 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Type 92) § 29.1048 Packing. A lot of tobacco consisting of a number of packages submitted as...

  5. 7 CFR 29.6031 - Packing.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Packing. 29.6031 Section 29.6031 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... INSPECTION Standards Definitions § 29.6031 Packing. A lot of tobacco consisting of a number of...

  6. 7 CFR 29.3538 - Packing.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Packing. 29.3538 Section 29.3538 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Type 95) § 29.3538 Packing. A lot of tobacco consisting of a number of packages submitted as...

  7. Difference packing arrays and systematic authentication codes

    Institute of Scientific and Technical Information of China (English)

    2004-01-01

    In this paper, a type of combinatorial design (called difference packing array)is proposed and used to give a construction of systematic authentication codes. Taking advantage of this construction, some new series of systematic authentication codes are obtainable in terms of existing difference packing arrays.

  8. 7 CFR 29.2541 - Packing.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Packing. 29.2541 Section 29.2541 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing...-Cured Tobacco (u.s. Types 22, 23, and Foreign Type 96) § 29.2541 Packing. A lot of tobacco consisting...

  9. 7 CFR 29.3048 - Packing.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Packing. 29.3048 Section 29.3048 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Packing. A lot of tobacco consisting of a number of packages submitted as one definite unit for...

  10. 7 CFR 29.2289 - Packing.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Packing. 29.2289 Section 29.2289 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Packing. A lot of tobacco consisting of a number of packages submitted as one definite unit for...

  11. Does Post Septoplasty Nasal Packing Reduce Complications?

    Directory of Open Access Journals (Sweden)

    Bijan Naghibzadeh

    2011-01-01

    Full Text Available The main issues in nasal surgery are to stabilize the nose in the good position after surgery and preserve the cartilages and bones in the favorable situation and reduce the risk of deviation recurrence. Also it is necessary to avoid the synechia formation, nasal valve narrowing, hematoma and bleeding. Due to the above mentioned problems and in order to solve and minimize them nasal packing, nasal splint and nasal mold have been advised. Patients for whom the nasal packing used may faced to some problems like naso-pulmonary reflex, intractable pain, sleep disorder, post operation infection and very dangerous complication like toxic shock syndrome. We have two groups of patients and three surgeons (one of the surgeons used post operative nasal packing in his patients and the two others surgeons did not.Complications and morbidities were compared in these two groups. Comparing the two groups showed that the rate of complication and morbidities between these two groups were same and the differences were not valuable, except the pain and discomfort post operatively and at the time of its removal. Nasal packing has several risks for the patients while its effects are not studied. Septoplasty can be safely performed without postoperative nasal packing. Nasal packing had no main findings that compensated its usage. Septal suture is one of the procedures that can be used as alternative method to nasal packing. Therefore the nasal packing after septoplasty should be reserved for the patients with increased risk of bleeding.

  12. Pack formation in cycling and orienteering.

    Science.gov (United States)

    Ackland, G J; Butler, D

    2001-09-13

    In cycling and orienteering competitions, competitors can become bunched into packs, which may mask an individual's true ability. Here we model this process with a view to determining when competitors' times are determined more by others than by their own ability. Our results may prove useful in helping to stage events so that pack formation can be avoided.

  13. Monitoring three-dimensional packings in microgravity.

    NARCIS (Netherlands)

    Yu, Peidong; Frank-Richter, Stefan; Börngen, Alexander; Sperl, Matthias

    2014-01-01

    We present results from experiments with granular packings in three dimensions in microgravity as realized on parabolic flights. Two different techniques are employed to monitor the inside of the packings during compaction: (1) X-ray radiography is used to measure in transmission the integrated fluc

  14. On contact numbers in random rod packings

    NARCIS (Netherlands)

    Wouterse, A.; Luding, Stefan; Philipse, A.P.

    2009-01-01

    Random packings of non-spherical granular particles are simulated by combining mechanical contraction and molecular dynamics, to determine contact numbers as a function of density. Particle shapes are varied from spheres to thin rods. The observed contact numbers (and packing densities) agree well

  15. Cluster and constraint analysis in tetrahedron packings.

    Science.gov (United States)

    Jin, Weiwei; Lu, Peng; Liu, Lufeng; Li, Shuixiang

    2015-04-01

    The disordered packings of tetrahedra often show no obvious macroscopic orientational or positional order for a wide range of packing densities, and it has been found that the local order in particle clusters is the main order form of tetrahedron packings. Therefore, a cluster analysis is carried out to investigate the local structures and properties of tetrahedron packings in this work. We obtain a cluster distribution of differently sized clusters, and peaks are observed at two special clusters, i.e., dimer and wagon wheel. We then calculate the amounts of dimers and wagon wheels, which are observed to have linear or approximate linear correlations with packing density. Following our previous work, the amount of particles participating in dimers is used as an order metric to evaluate the order degree of the hierarchical packing structure of tetrahedra, and an order map is consequently depicted. Furthermore, a constraint analysis is performed to determine the isostatic or hyperstatic region in the order map. We employ a Monte Carlo algorithm to test jamming and then suggest a new maximally random jammed packing of hard tetrahedra from the order map with a packing density of 0.6337.

  16. 7 CFR 51.1217 - Standard pack.

    Science.gov (United States)

    2010-01-01

    ... be ring faced and tightly packed with sufficient bulge to prevent any appreciable movement of the... the box. (d) Peaches packed in other type boxes such as wire-bound boxes and fiber-board boxes may be... than 10 percent of the packages in any lot may not meet these requirements. (i) “Well filled”...

  17. Crystal structures of bis-(phen-oxy)silicon phthalocyanines: increasing π-π inter-actions, solubility and disorder and no halogen bonding observed.

    Science.gov (United States)

    Lessard, Benoît H; Lough, Alan J; Bender, Timothy P

    2016-07-01

    We report the syntheses and characterization of three solution-processable phen-oxy silicon phthalocyanines (SiPcs), namely bis-(3-methyl-phen-oxy)(phthalocyanine)silicon [(3MP)2-SiPc], C46H30N8O2Si, bis-(2-sec-butyl-phen-oxy)(phthalocyanine)silicon [(2secBP)2-SiPc], C44H24I2N8O2Si, and bis-(3-iodo-phen-oxy)(phthalocyanine)silicon [(3IP)2-SiPc], C52H42N8O2Si. Crystals grown of these compounds were characterized by single-crystal X-ray diffraction and the π-π inter-actions between the aromatic SiPc cores were studied. It was determined that (3MP)2-SiPc has similar inter-actions to previously reported bis-(3,4,5-tri-fluoro-phen-oxy)silicon phthalocyanines [(345 F)2-SiPc] with significant π-π inter-actions between the SiPc groups. (3IP)2-SiPc and (2secBP)2-SiPc both experienced a parallel stacking of two of the peripheral aromatic groups. In all three cases, the solubility of these mol-ecules was increased by the addition of phen-oxy groups while maintaining π-π inter-actions between the aromatic SiPc groups. The solubility of (2secBP)2-SiPc was significantly higher than other bis-phen-oxy-SiPcs and this was exemplified by the higher observed disorder within the crystal structure.

  18. Crystallization of Self-Propelled Hard Discs

    Science.gov (United States)

    Briand, G.; Dauchot, O.

    2016-08-01

    We experimentally study the crystallization of a monolayer of vibrated discs with a built-in polar asymmetry, a model system of active liquids, and contrast it with that of vibrated isotropic discs. Increasing the packing fraction ϕ , the quasicontinuous crystallization reported for isotropic discs is replaced by a transition, or a crossover, towards a "self-melting" crystal. Starting from the liquid phase and increasing the packing fraction, clusters of dense hexagonal-ordered packed discs spontaneously form, melt, split, and merge, leading to a highly intermittent and heterogeneous dynamics. For a packing fraction larger than ϕ*, a few large clusters span the system size. The cluster size distribution is monotonically decreasing for ϕ ϕ*, and is a power law at the transition. The system is, however, never dynamically arrested. The clusters permanently melt from place to place, forming droplets of an active liquid which rapidly propagate across the system. This self-melting crystalline state subsists up to the highest possible packing fraction, questioning the stability of the crystal for active discs unless it is at ordered close packing.

  19. Disordered contact networks in jammed packings of frictionless disks

    Science.gov (United States)

    Ramola, Kabir; Chakraborty, Bulbul

    2016-11-01

    We analyse properties of contact networks formed in packings of soft frictionless disks near the unjamming transition. We construct polygonal tilings and triangulations of the contact network that partitions space into convex regions which are either covered or uncovered. This allows us to characterize the local spatial structure of the packing near the transition using well-defined geometric objects. We construct bounds on the number of polygons and triangulation vectors that appear in such packings. We study these networks using simulations of bidispersed disks interacting via a one-sided linear spring potential. We find that several underlying geometric distributions are reproducible and display self averaging properties. We find that the total covered area is a reliable real space parameter that can serve as a substitute for the packing fraction. We find that the unjamming transition occurs at a fraction of covered area AG\\ast=0.446(1) . We determine scaling exponents of the excess covered area as the energy of the system approaches zero {{E}G}\\to {{0}+} , and the coordination number approaches its isostatic value Δ Z= -{\\text{iso}}\\to {{0}+} . We find Δ {{A}G}∼ Δ {{E}G}0.28(1) and Δ {{A}G}∼ Δ {{Z}1.00(1)} , representing new structural critical exponents. We use the distribution functions of local areas to study the underlying geometric disorder in the packings. We find that a finite fraction of order \\Psi O\\ast=0.369(1) persists as the transition is approached.

  20. INTERACTION OF LASER RADIATION WITH MATTER: Influence of Ca and Pb impurities on the bulk optical strength of ultrapure NaCl and KCl crystals

    Science.gov (United States)

    Vinogradov, An V.; Voszka, R.; Kovalev, Valerii I.; Faĭzullov, F. S.; Janszky, J.

    1987-06-01

    A significant increase (by a factor of about 3) of the bulk damage threshold in the case of interaction of CO2 laser radiation pulses with ultrapure NaCl and KCl crystals grown in a reactive atmosphere was observed on introduction of divalent metal ions Ca and Pb in concentrations of 10-5-10-6 mol/mol. Impurities were introduced in concentrations of 10-8-10-3 and 2×10-7-10-4 mol/mol into the melts of KCl and NaCl, respectively. The concentration of other impurities (including OH) did not exceed ~10-6 mol/mol. A physical model was developed to account for the observed dependence on the basis of an analogy between a system of colloidal particles and F centers in a crystal and a liquid-vapor system.