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Sample records for crystal packing forces

  1. Packing forces in nine crystal forms of cutinase.

    PubMed

    Jelsch, C; Longhi, S; Cambillau, C

    1998-05-15

    During the characterization of mutants and covalently inhibited complexes of Fusarium solani cutinase, nine different crystal forms have been obtained so far. Protein mutants with a different surface charge distribution form new intermolecular salt bridges or long-range electrostatic interactions that are accompanied by a change in the crystal packing. The whole protein surface is involved in the packing contacts and the hydrophobicities of the protein surfaces in mutual contact turned out to be noncorrelated, which indicates that the packing interactions are nonspecific. In the case of the hydrophobic variants, the packing contacts showed some specificity, as the protein in the crystal tends to form either crystallographic or noncrystallographic dimers, which shield the hydrophobic surface from the solvent. The likelihood of surface atoms to be involved in a crystal contact is the same for both polar and nonpolar atoms. However, when taking areas in the 200-600 A2 range, instead of individual atoms, the either highly hydrophobic or highly polar surface regions were found to have an increased probability of establishing crystal lattice contacts. The protein surface surrounding the active-site crevice of cutinase constitutes a large hydrophobic area that is involved in packing contacts in all the various crystalline contexts.

  2. Determining the Molecular Packing Arrangements on Protein Crystal Faces by Atomic Force Microscopy

    NASA Technical Reports Server (NTRS)

    Li, Huayu; Perozzo, Mary A.; Konnert, John H.; Nadarajan, Arunan; Pusey, Marc L.

    1998-01-01

    Periodic Bond Chain (PBC) analysis of the packing of tetragonal lysozyme crystals have revealed that there are two possible molecular packing arrangements for the crystal faces. The analysis also predicted that only one of these, involving the formation of helices about the 4(sub 3) axes, would prevail during crystal growth. In this study high resolution atomic force microscopy (AFM) was employed to verify these predictions for the (110) crystal face. A computer program was developed which constructs the expected AFM image for a given tip shape for each possible molecular packing arrangement. By comparing the actual AFM image with the predicted images the correct packing arrangement was determined. The prediction of an arrangement involving 4(sub 3) helices was confirmed in this manner,"while the alternate arrangement was not observed. The investigation also showed the protein molecules were packed slightly closer about the 4(sub 3) axes than in the crystallographic arrangement of the crystal interior. This study demonstrates a new approach for determining the molecular packing arrangements on protein crystal faces. It also shows the power of combining a theoretical PBC analysis with experimental high resolution AFM techniques in probing protein crystal growth processes at the molecular level.

  3. Crystallization force--a density functional theory concept for revealing intermolecular interactions and molecular packing in organic crystals.

    PubMed

    Li, Tonglei; Ayers, Paul W; Liu, Shubin; Swadley, Matthew J; Aubrey-Medendorp, Clare

    2009-01-01

    Organic molecules are prone to polymorphic formation in the solid state due to the rich diversity of functional groups that results in comparable intermolecular interactions, which can be greatly affected by the selection of solvent and other crystallization conditions. Intermolecular interactions are typically weak forces, such as van der Waals and stronger short-range ones including hydrogen bonding, that are believed to determine the packing of organic molecules during the crystal-growth process. A different packing of the same molecules leads to the formation of a new crystal structure. To disclose the underlying causes that drive the molecule to have various packing motifs in the solid state, an electronic concept or function within the framework of conceptual density functional theory has been developed, namely, crystallization force. The concept aims to describe the local change in electronic structure as a result of the self-assembly process of crystallization and may likely quantify the locality of intermolecular interactions that directs the molecular packing in a crystal. To assess the applicability of the concept, 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile, so-called ROY, which is known to have the largest number of solved polymorphs, has been examined. Electronic calculations were conducted on the seven available crystal structures as well as on the single molecule. The electronic structures were analyzed and crystallization force values were obtained. The results indicate that the crystallization forces are able to reveal intermolecular interactions in the crystals, in particular, the close contacts that are formed between molecules. Strong correlations exist between the total crystallization force and lattice energy of a crystal structure, further suggesting the underlying connection between the crystallization force and molecular packing.

  4. Spontaneous Crystallization in Athermal Polymer Packings

    PubMed Central

    Karayiannis, Nikos Ch.; Foteinopoulou, Katerina; Laso, Manuel

    2013-01-01

    We review recent results from extensive simulations of the crystallization of athermal polymer packings. It is shown that above a certain packing density, and for sufficiently long simulations, all random assemblies of freely-jointed chains of tangent hard spheres of uniform size show a spontaneous transition into a crystalline phase. These polymer crystals adopt predominantly random hexagonal close packed morphologies. An analysis of the local environment around monomers based on the shape and size of the Voronoi polyhedra clearly shows that Voronoi cells become more spherical and more symmetric as the system transits to the ordered state. The change in the local environment leads to an increase in the monomer translational contribution to the entropy of the system, which acts as the driving force for the phase transition. A comparison of the crystallization of hard-sphere polymers and monomers highlights similarities and differences resulting from the constraints imposed by chain connectivity. PMID:23263666

  5. Crystal packing effects on protein loops.

    PubMed

    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.

  6. Trifluoracetic acid-assisted crystallization of vitamin B12 results in protonation of the phosphate group of the nucleotide loop: insight into the influence of crystal packing forces on vitamin B12 structures.

    PubMed

    Marino, Nadia; Rabideau, Amy E; Doyle, Robert P

    2011-01-03

    In the course of experiments concerning our ongoing project on the synthesis of vitamin B(12) (cyanocobalamin, CNCbl) bioconjugates for drug-delivery purposes, we observed the formation of well-shaped red parallelepipeds from a concentrated aqueous solution of the HPLC-purified vitamin. The X-ray structural investigation (MoK(α)) at 98 K on these crystals revealed a CNCbl-TFA salt of formula [CNCbl(H)](TFAc)·14H(2)O (1, where TFA = trifluoracetic acid; TFAc(-) = trifluoracetate anion), in which a proton transfer from the trifluoracetic acid to the phosphate-O4P oxygen atoms is observed. 1 crystallizes in the standard orthorhombic P2(1)2(1)2(1) space group, a = 16.069(2) Å, b = 20.818(2) Å, c = 24.081(2) Å, Z = 4. The final full-matrix least-squares refinements on F(2) converged with R(1) = 4.1% for the 18957 significant reflections, a very low crystallographic residual for cobalamins, which facilitated the analysis of the extensive network of hydrogen bonds within the lattice. To the best of our knowledge, this is the first cobalamin structure to show protonation of the phosphate group of the cobalamin nucleotide loop. In this work, the crystal structure of 1 is analyzed and compared to other CNCbls reported in the literature, namely, CNCbl·3PrOH·12H(2)O (2, PrOH = propyl alcohol), CNCbl·acetone·20H(2)O (3), CNCbl·2LiCl·10.2H(2)O (4), and CNCbl·2KCl·10.6H(2)O (5). The analysis confirmed that protonation of the phosphate leaves the major CNCbl structural parameters unaffected, so that 1 can be considered an "unmodified" Cbl solvate. However, comparison between 1-5 led to interesting findings. In fact, although the cobalt(III) coordination sphere in 1-5 is similar, significant differences could be noted in the upward fold angle of the corrin macrocycle, a parameter commonly related to the steric hindrance of the axial lower "α" nucleotide-base and the electronic trans influence of the upper "β" substituent. This suggests that crystal-packing forces may

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

    PubMed Central

    Jelsch, Christian; Bibila Mayaya Bisseyou, Yvon

    2017-01-01

    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 two phenol groups

  8. Ultratight crystal packing of a 10 kDa protein

    SciTech Connect

    Trillo-Muyo, Sergio; Chruszcz, Maksymilian; Minor, Wladek; Kuisiene, Nomeda

    2013-03-01

    The crystal structure of the C-terminal domain of a putative U32 peptidase from G. thermoleovorans is reported; it is one of the most tightly packed protein structures reported to date. While small organic molecules generally crystallize forming tightly packed lattices with little solvent content, proteins form air-sensitive high-solvent-content crystals. Here, the crystallization and full structure analysis of a novel recombinant 10 kDa protein corresponding to the C-terminal domain of a putative U32 peptidase are reported. The orthorhombic crystal contained only 24.5% solvent and is therefore among the most tightly packed protein lattices ever reported.

  9. An effective packing density of binary cubic crystals

    NASA Astrophysics Data System (ADS)

    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.

  10. Noncontact atomic force microscopy of perfect single crystals of pentacene prepared by crystallization from solution.

    PubMed

    Sato, Kazuya; Sawaguchi, Takahiro; Sakata, Masafumi; Itaya, Kingo

    2007-12-18

    Nearly perfect single crystals of pentacene were grown from trichlorobenzene solution. The surface structure of pentacene single crystals has been investigated by frequency modulation atomic force microscopy. Molecularly flat and extraordinarily wide terraces, extended over the width of more than a few micrometers with monomolecular steps, were consistently observed, suggesting that those pentacene crystals were nearly perfect single crystals. Molecular packing arrangements were revealed by FM-AFM for the first time.

  11. How proteins pack into crystals: nuclei achieve translation symmetries by growing.

    PubMed

    Feng, Dan; Zeng, Zong-Hao

    2004-07-01

    How protein molecules pack into a crystal remains problematic. Packing units are direct materials for packing into crystals. The group generator method is introduced for automatically identifying the packing unit. By introducing deviations into the nucleation stage of crystallization, we proved that these deviations diminish in further packing. This process illustrates how translation symmetries are achieved by the growing of nuclei. Two effects, the size effect and the close up effect, are found to behave differently in this process.

  12. Comparison of generic force fields for packing of concave molecules

    NASA Astrophysics Data System (ADS)

    Del Regno, Annalaura; Siperstein, Flor R.

    2014-09-01

    Organic molecules of intrinsic microporosity (OMIMs) are a new class of highly concave molecules, designed to pack inefficiently and create microporous materials. In this work, OMIM-1 was described with full atomistic models using Dreiding, optimised potentials for liquid simulations (OPLS) and Universal force fields to recognise the features enhanced by each force field and assess their ability in representing the structural properties of this new class of materials. In addition, argon adsorption isotherms were modelled to determine the features observed in the isotherm generated by each force field, for future comparison with experimental data.

  13. Head group effects on molecular packing in lamellar liquid crystals.

    PubMed

    Ishizuka, Chika; Arima, Satoshi; Aramaki, Kenji

    2011-09-01

    In this study, molecular packing in lamellar liquid crystals in poly(oxyethylene) dodecyl ether(C(12)EO(n)) pure systems and the two surfactant mixtures of C(12)EO(8)/1-dodecanol(C(12)EO(0)), C(12)EO(8)/lipophilic sucrose laurate (L-595), hydrophilic sucrose laurate (L-1695)/C(12)EO(2) is investigated in terms of mean molecular area and partial molecular area (PMA). Lamellar liquid crystals formed in the C(12)EO(8)/C(12)EO(0) mixed system show higher melting temperatures than those in the C(12)EO(n) pure systems, even though the average number of EO units in the mixed surfactant system is the same as in the pure system. We compared the mean molecular area at the interface between hydrophilic and lipophilic moieties in the lamellar liquid crystals in each system. In the mixed system, the molecules are packed more tightly than in the pure system. Among the C(12)EO(n) and sucrose laurate mixtures, the L-1695/C(12)EO(2) mixed system showed a smaller mean molecular area per lipophilic chain than the C(12)EO(8)/L-595 mixed system. We investigated the effect of mixing two surfactants with different head group geometry on molecular packing by comparing the PMA of each surfactant. Copyright © 2011 Elsevier Inc. All rights reserved.

  14. Dislocation dynamics in hexagonal close-packed crystals

    DOE PAGES

    Aubry, S.; Rhee, M.; Hommes, G.; ...

    2016-04-14

    Extensions of the dislocation dynamics methodology necessary to enable accurate simulations of crystal plasticity in hexagonal close-packed (HCP) metals are presented. They concern the introduction of dislocation motion in HCP crystals through linear and non-linear mobility laws, as well as the treatment of composite dislocation physics. Formation, stability and dissociation of and other dislocations with large Burgers vectors defined as composite dislocations are examined and a new topological operation is proposed to enable their dissociation. Furthermore, the results of our simulations suggest that composite dislocations are omnipresent and may play important roles both in specific dislocation mechanisms and in bulkmore » crystal plasticity in HCP materials. While fully microscopic, our bulk DD simulations provide wealth of data that can be used to develop and parameterize constitutive models of crystal plasticity at the mesoscale.« less

  15. Dislocation dynamics in hexagonal close-packed crystals

    SciTech Connect

    Aubry, S.; Rhee, M.; Hommes, G.; Bulatov, V. V.; Arsenlis, A.

    2016-04-14

    Extensions of the dislocation dynamics methodology necessary to enable accurate simulations of crystal plasticity in hexagonal close-packed (HCP) metals are presented. They concern the introduction of dislocation motion in HCP crystals through linear and non-linear mobility laws, as well as the treatment of composite dislocation physics. Formation, stability and dissociation of and other dislocations with large Burgers vectors defined as composite dislocations are examined and a new topological operation is proposed to enable their dissociation. Furthermore, the results of our simulations suggest that composite dislocations are omnipresent and may play important roles both in specific dislocation mechanisms and in bulk crystal plasticity in HCP materials. While fully microscopic, our bulk DD simulations provide wealth of data that can be used to develop and parameterize constitutive models of crystal plasticity at the mesoscale.

  16. Dislocation dynamics in hexagonal close-packed crystals

    SciTech Connect

    Aubry, S.; Rhee, M.; Hommes, G.; Bulatov, V. V.; Arsenlis, A.

    2016-04-14

    Extensions of the dislocation dynamics methodology necessary to enable accurate simulations of crystal plasticity in hexagonal close-packed (HCP) metals are presented. They concern the introduction of dislocation motion in HCP crystals through linear and non-linear mobility laws, as well as the treatment of composite dislocation physics. Formation, stability and dissociation of and other dislocations with large Burgers vectors defined as composite dislocations are examined and a new topological operation is proposed to enable their dissociation. Furthermore, the results of our simulations suggest that composite dislocations are omnipresent and may play important roles both in specific dislocation mechanisms and in bulk crystal plasticity in HCP materials. While fully microscopic, our bulk DD simulations provide wealth of data that can be used to develop and parameterize constitutive models of crystal plasticity at the mesoscale.

  17. Nanofluidic crystals: nanofluidics in a close-packed nanoparticle array.

    PubMed

    Ouyang, Wei; Han, Jongyoon; Wang, Wei

    2017-09-12

    With various promising applications demonstrated, nanofluidics has been of broad research interest in the past decade. As nanofluidics matures from a proof of concept towards practical applications, it faces two major barriers: expensive nanofabrication and ultra-low throughput. To date, the only material that enables nanofabrication-free, high-throughput, yet precisely controllable nanofluidic systems is the close-packed nanoparticle array, i.e. nanofluidic crystals. Recently, significant progress in nanofluidics has been made using nanofluidic crystals, including high-current ionic diodes, high-power energy harvesters, efficient biomolecular separation, and facile biosensors. Nanofluidic crystals are seen as a key to applying nanofluidic concepts to real-world applications. In this review, we introduce the key concepts and models in nanofluidic crystals, summarize the fabrication methods, and discuss the various applications of nanofluidic crystals in depth, highlighting their advantages in terms of simple fabrication, low cost, flexibility, and high throughput. Finally, we provide our perspectives on the future of nanofluidic crystals and their potential impacts.

  18. Crystal structure and packing energy calculations of (+)-6-aminopenicillanic acid.

    PubMed

    Saouane, Sofiane; Buth, Gernot; Fabbiani, Francesca P A

    2013-11-01

    The X-ray single-crystal structure of (2S,5R,6R)-6-amino-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid, commonly known as (+)-6-aminopenicillanic acid (C8H12N2O3S) and a precursor of a variety of semi-synthetic penicillins, has been determined from synchrotron data at 150 K. The structure represents an ordered zwitterion and the crystals are nonmerohedrally twinned. The crystal structure is composed of a three-dimensional network built by three charge-assisted hydrogen bonds between the ammonium and carboxylate groups. The complementary analysis of the crystal packing by the PIXEL method brings to light the nature and ranking of the energetically most stabilizing intermolecular interaction energies. In accordance with the zwitterionic nature of the structure, PIXEL lattice energy calculations confirm the predominance of the Coulombic term (-379.1 kJ mol(-1)) ahead of the polarization (-141.4 kJ mol(-1)), dispersion (-133.7 kJ mol(-1)) and repulsion (266.3 kJ mol(-1)) contributions.

  19. Molecular design, crystal packing and TFT performance of novel polythiophenes

    NASA Astrophysics Data System (ADS)

    Pan, Hualong

    This thesis presents the design, synthesis and thin-film-transistor performance of a novel series of polythiophenes. The work can be divided into two parts: (1) study of crystal packing of the alkyl side chains in single crystals of model oligothiophene compounds for soluble polythiophenes; (2) exploration of a new series of polythiophenes to achieve favorable crystal packing and hense high mobility for use in organic thin-film-transistors. The first part is based on the crystal packing of a series of compounds derived from the monomer of a high-performance semiconductor, poly(3,3"didodecylquarter-thiophene), PQT-12. A unique conformational polymorphism arising from side chains was observed when the conjugation of backbone of PQT-monomer was extended with phenyl, methyl-phenyl, trifluoromethyl-phenyl. The alkyl side chains preferred tilting towards the middle and then being parallel with the backbones when crystallized from a poor solvent, whereas, the side chains extended out vertically to the backbones when crystallized from a good solvent. The conformational polymorphism of the side chains in the dip-coated film was also studied. The following chapters focus on the design, characterization and TFT performance test of novel polymer semiconductors. A novel and symmetrical poly(4,8-didodecylbenzo[1,2-b:4,5-b']dithiophene) with alkyl side chains tethered to the middle of the large fused backbone was synthesized from 2,6-dibromo-4,8-didodecylbenzo[1,2-b:4,5-b']dithiophene by a dehalogenative coupling polymerization. The thin-film transistors made from this polymer as a semiconductor produced a field-effect mobility of 0.012 cm2V-1s-1 and current on/off ratio ˜2.5x105 after thermal annealing at 140°C. The performance was greatly enhanced (field-effect mobility ˜0.15 cm 2V-1s-1 and current on/off ratio x10 6) when two 3-methyl-thienylenes were incorporated into the backbone, poly(4,8-dodecyl-2,6-bis-(3-methylthiophen-2-yl)-benzo[1,2-b:4,5-b']dithiophene). Such good

  20. Low solubility in drug development: de-convoluting the relative importance of solvation and crystal packing.

    PubMed

    Docherty, Robert; Pencheva, Klimentina; Abramov, Yuriy A

    2015-06-01

    An increasing trend towards low solubility is a major issue for drug development as formulation of low solubility compounds can be problematic. This paper presents a model which de-convolutes the solubility of pharmaceutical compounds into solvation and packing properties with the intention to understand the solubility limiting features. The Cambridge Crystallographic Database was the source of structural information. Lattice energies were calculated via force-field based approaches using Materials Studio. The solvation energies were calculated applying quantum chemistry models using Cosmotherm software. The solubilities of 54 drug-like compounds were mapped onto a solvation energy/crystal packing grid. Four quadrants were identified were different balances of solvation and packing were defining the solubility. A version of the model was developed which allows for the calculation of the two features even in absence of crystal structure. Although there are significant number of in-silico models, it has been proven very difficult to predict aqueous solubility accurately. Therefore, we have taken a different approach where the solubility is not predicted directly but is de-convoluted into two constituent features. © 2015 Royal Pharmaceutical Society.

  1. Force distribution/transmission in amorphous and crystalline packings of spheres

    NASA Astrophysics Data System (ADS)

    An, Xizhong; Huang, Fei

    2013-06-01

    In this paper, the discrete element modeling (DEM) was used to study the force distributions/transmissions in the packings of amorphous and crystalline states generated by equal spheres subjected to an external load (of a large sphere) applied on the top of a packing. Crystalline packings such as {100}-and {111}-oriented face centered cubic (FCC), hexagonal close packed (HCP) and body centered cubic (BCC) were considered. The results show that the forces among the particles in these packings are quite different, with different force chains identified with different structures. For amorphous packings, the force chain supporting the external load gives a conical shape. The force chain in a crystalline packing is mainly of a pyramid shape and the forces therein are transmitted along the crystalline lattice. For {100}-FCC, {111}-FCC, and BCC other than HCP, the forces transmit along straight lines with different orientations. In crystalline packings, the forces in the chains are uniformly distributed in each layer and decrease linearly with the height. The force distributions in amorphous and crystalline granular packings are structure-dependent.

  2. A structural dissection of large protein-protein crystal packing contacts.

    PubMed

    Luo, Jiesi; Liu, Zhongyu; Guo, Yanzhi; Li, Menglong

    2015-09-15

    With the rapid increase in crystal structures of protein-protein complexes deposited in the Protein Data Bank (PDB), more and more crystal contacts have been shown to have similar or even larger interface areas than biological interfaces. However, little attention has been paid to these large crystal packing contacts and their structural principles remain unknown. To address this issue, we used a comparative feature analysis to analyze the geometric and physicochemical properties of large crystal packing contacts by comparing two types of specific protein-protein interactions (PPIs), weak transient complexes and permanent homodimers. Our results show that although large crystal packing contacts have a similar interface area and contact size as permanent homodimers, they tend to be more planar, loosely packed and less hydrophobic than permanent homodimers and cannot form a central core region that is fully buried during interaction. However, the properties of large crystal packing contacts, except for the interface area and contact size, more closely resemble those of weak transient complexes. The large overlap between biological and large crystal packing contacts indicates that interface properties are not efficient indicators for classification of biological interfaces from large crystal packing contacts and finding other specific features urgently needed.

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

    NASA Astrophysics Data System (ADS)

    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 < c + a > and prismatic < a > 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.

  4. High-pressure mechanical instability in close-packed Hooke's-law crystals

    SciTech Connect

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

    1981-01-15

    Lattice dynamics and molecular dynamics are used to study close-packed crystals with pairwise-additive Hooke's-law interparticle potentials. Lattice dynamics describes a mechanical soft-mode instability at high pressure. In two dimensions molecular dynamics reveals that a thermodynamic transition, from the triangular close-packed lattice to the square lattice, occurs before the soft-mode instability density is reached. Similar phenomena occur in the three-dimensional close-packed lattices.

  5. Packing Interface Energetics in Different Crystal Forms of the λ Cro Dimer

    PubMed Central

    Ahlstrom, Logan S.; Miyashita, Osamu

    2014-01-01

    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. PMID:24218107

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

    PubMed

    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. © 2013 Wiley Periodicals, Inc.

  7. Applications of Atomic Force Microscopy in Macromolecular Crystal Growth

    NASA Astrophysics Data System (ADS)

    McPherson, Alexander

    1997-03-01

    A series of protein and virus crystals was investigated, in situ, using atomic force microscopy. Most of the crystals grew principally on steps generated by two dimensional nucleation on surfaces, though some, such as canavalin, grew by development of spiral dislocations. Apoferritin grew by a rarely encountered mechanism, normal growth, usually associated only with melt or vapor phase crystallization. Cubic crystals of satellite tobacco mosaic virus (STMV) grew, at moderate to high levels of supersaturation, by the direct addition of three- dimensional nuclei followed by their rapid normal growth and lateral expansion, a mechanism not previously described to promote controlled and reproducible crystal growth from solutions. Biological macromolecules apparently utilize a more diverse range of growth mechanisms in their crystallization than any previously studied material. High resolution AFM analyses have allowed us to record the first, real time, in situ atomic force microscope images, on the nanometer scale, of the incorporation of molecules into the growth steps of crystals grown from solution. The molecular structure of the growth step edge and surface layer on the (101) faces of tetragonal thaumatin crystals were resolved. It was shown that, although the growth step height corresponds to the unit cell containing eight thaumatin molecules, its advancement occurs by the addition of individual protein molecules rather than molecular clusters. Models for the packing of molecules on the surface layer, and of the structure of the step edge were developed which agree well with experimental data. Again, using high resolution, in situ atomic force microscopy, the initial stages of the formation and development of two- and three-dimensional nuclei on the surface of protein crystals were recorded. From these we conclude that non crystalline aggregates, with short range order, present both on the crystal-solution interface, and in the volume of the solution, give rise to

  8. Effective discrimination between biologically relevant contacts and crystal packing contacts using new determinants.

    PubMed

    Luo, Jiesi; Guo, Yanzhi; Fu, Yuanyuan; Wang, Yu; Li, Wenling; Li, Menglong

    2014-11-01

    In the structural models determined by X-ray crystallography, contacts between molecules can be divided into two categories: biologically relevant contacts and crystal packing contacts. With the growth in the number and quality of available large crystal packing contacts structures, distinguishing crystal packing contacts from biologically relevant contacts remains a difficult task, which can lead to wrong interpretation of structural models. In this study, we performed a systematic analysis on the biologically relevant contacts and crystal packing contacts. The analysis results reveal that biologically contacts are more tightly packed than crystal packing contacts. This property of biologically contacts may contribute to the formation of their interfacial core region. Meanwhile, the differences between the core and surface region of biologically contacts in amino acid composition and evolutionary measure are more dramatic than crystal packing contacts and these differences appear to be useful in distinguishing these two categories of contacts. On the basis of the features derived from our analysis, we developed a random forest model to classify biological relevant contacts and crystal packing contacts. Our method can achieve a high receiver operating curve of 0.923 in the 5-fold cross-validation and accuracies of 91.4% and 91.7% for two different test sets. Moreover, in a comparison study, our model outperforms other existing methods, such as DiMoVo, Pita, Pisa, and Eppic. We believe that this study will provide useful help in the validation of oligomeric proteins and protein complexes. The model and all data used in this paper are freely available at http://cic.scu.edu.cn/bioinformatics/bio-cry.zip.

  9. Tailor-made force fields for crystal-structure prediction.

    PubMed

    Neumann, Marcus A

    2008-08-14

    A general procedure is presented to derive a complete set of force-field parameters for flexible molecules in the crystalline state on a case-by-case basis. The force-field parameters are fitted to the electrostatic potential as well as to accurate energies and forces generated by means of a hybrid method that combines solid-state density functional theory (DFT) calculations with an empirical van der Waals correction. All DFT calculations are carried out with the VASP program. The mathematical structure of the force field, the generation of reference data, the choice of the figure of merit, the optimization algorithm, and the parameter-refinement strategy are discussed in detail. The approach is applied to cyclohexane-1,4-dione, a small flexible ring. The tailor-made force field obtained for cyclohexane-1,4-dione is used to search for low-energy crystal packings in all 230 space groups with one molecule per asymmetric unit, and the most stable crystal structures are reoptimized in a second step with the hybrid method. The experimental crystal structure is found as the most stable predicted crystal structure both with the tailor-made force field and the hybrid method. The same methodology has also been applied successfully to the four compounds of the fourth CCDC blind test on crystal-structure prediction. For the five aforementioned compounds, the root-mean-square deviations between lattice energies calculated with the tailor-made force fields and the hybrid method range from 0.024 to 0.053 kcal/mol per atom around an average value of 0.034 kcal/mol per atom.

  10. A phenomenological force model of Li-ion battery packs for enhanced performance and health management

    NASA Astrophysics Data System (ADS)

    Oh, Ki-Yong; Epureanu, Bogdan I.

    2017-10-01

    A 1-D phenomenological force model of a Li-ion battery pack is proposed to enhance the control performance of Li-ion battery cells in pack conditions for efficient performance and health management. The force model accounts for multiple swelling sources under the operational environment of electric vehicles to predict swelling-induced forces in pack conditions, i.e. mechanically constrained. The proposed force model not only incorporates structural nonlinearities due to Li-ion intercalation swelling, but also separates the overall range of states of charge into three ranges to account for phase transitions. Moreover, an approach to study cell-to-cell variations in pack conditions is proposed with serial and parallel combinations of linear and nonlinear stiffness, which account for battery cells and other components in the battery pack. The model is shown not only to accurately estimate the reaction force caused by swelling as a function of the state of charge, battery temperature and environmental temperature, but also to account for cell-to-cell variations due to temperature variations, SOC differences, and local degradation in a wide range of operational conditions of electric vehicles. Considering that the force model of Li-ion battery packs can account for many possible situations in actual operation, the proposed approach and model offer potential utility for the enhancement of current battery management systems and power management strategies.

  11. Efficient calculation of the packing density of the crystal lattice of perovskite

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

    The methodology of efficient macroscopic calculation of parameters of the cubic crystal lattice based on the use of the coefficient of structured packing of its elementary cell is considered. The possibility of precision theoretical determination of the numerical values of interatomic distances in crystals of the type under consideration is shown.

  12. Characterization of interparticle forces in the packing of cohesive fine particles.

    PubMed

    Yang, R Y; Zou, R P; Yu, A B; Choi, S K

    2008-09-01

    We numerically investigate force structures in the packing of fine cohesive particles using the discrete element method. By changing the particle size and therefore the van der Waals force, the effect of cohesion on the normal contact force and the total normal force, which is the sum of the normal contact forces and the van der Waals forces, is analyzed. It is shown that, with decreasing particle size, the normal contact forces become more uniform and have a narrower and more symmetric distribution, while the distributions of the total normal forces widen. Spatial correlation between the interparticle forces exists for the packing of coarse noncohesive particles. As the particle size decreases, this correlation becomes weaker for the contact forces but stronger for the total normal forces. A comparison between the effective weight of particles and the internal force structure suggests that there are differences between the particle-particle and particle-wall forces. The bimodal distribution of the effective weight indicates that there may exist two phases in the packings when cohesion is present, governed by the compressive and tensile stresses.

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

    PubMed

    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. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

  14. The crystal packing modes of butane-1,4-diamine salts with acetic, di- and trichloroacetic acids at 100 K

    NASA Astrophysics Data System (ADS)

    Paul, Agnieszka; Kubicki, Maciej

    2010-03-01

    The crystal structures of three salts of butane-1,4-diamine: acetate ((C 4H 14N 22+ · 2(C 2H 3O 2) -), dichloroacetate ((C 4H 14N 22+ · 2(C 2HCl 2O 2) -) and trichloroacetate ((C 4H 14N 22+ · 2(C 2Cl 3O 2) -) were determined by X-ray diffraction at 100 K. In all these cases the dication is either symmetrical and situated at the inversion center or disordered about the inversion center, in the P2 1/ c space group. The conformation of dication is ttt ( t- trans) for acetate and trichloroacetate, or tg -t and tg +t ( g- gauche) - for dichloroacetate, and this last salt undergoes the phase transition in higher temperature. The role of covalently bonded chlorine atoms in the determination of the crystal packing, at least in this case, is only the secondary one. The potential halogen bonds or N sbnd H⋯Cl hydrogen bonds do not compete successfully with the N sbnd H⋯O hydrogen bonds of different strength which - along with the coulombic interactions between the charged species - are certainly the main driving force of the crystal packing along this series of compounds. The different packing modes are pronounced in relative cation-dication arrangement in the layer structure.

  15. Packing and melting of mesoscopically confined two-dimensional Coulomb crystals in straight narrow channels.

    PubMed

    Liu, Kuo-An; I, Lin

    2010-10-01

    The microstructure and melting dynamics of the two-dimensional mesoscopic Coulomb crystal with 1/r-type mutual interaction force and parabolic transverse confining potential, under different degrees of incommensurability, are investigated through molecular-dynamics simulation. To tune the degree of incommensurability, N(a) extra particles are added into the commensurate uniform triangular lattice which has seven-layer structure and 40 particles in each layer with the periodic longitudinal boundary condition, until the system reaches another commensurate packing with eight-layer structure at N(a)=40. It is found that the increasing incommensurability with the increasing N(a) or 40-N(a) gradually deteriorates the structural order with the presence of intrinsic defects and the anisotropic bond-length distribution, except for the defect-free configurations at a few magic N(a)'s. The system prefers the seven- and the eight-layer single structures through the entire crystal for the low- and the high-N(a) regimes, respectively, and the configurations with seven- and eight-layer domain mixtures for 18≤N(a)≤24. The increasing strain or the worse local particle interlocking around the intrinsic defects with the increasing incommensurability also causes the easier structural rearrangement associated with the easier particle hopping and the earlier onset of melting transition. The transverse confinement suppresses the transverse motion, induces nonuniform melting, and sustains the layered structure after melting.

  16. The Strength of Binary Junctions in Hexagonal Close-Packed Crystals

    DTIC Science & Technology

    2014-03-01

    L , Figueiredo RB, Ungár T, Langdon TG. Mater Sci Eng A 2010;528:533. [27] Kuwano N, Tsuruda T, Kida Y, Miyake H, Hiramatsu K, Shibata T. Phys Stat...The Strength of Binary Junctions in Hexagonal Close-Packed Crystals by C.-C. Wu, P. W. Chung, S. Aubry, L . B. Munday, and A. Arsenlis...Packed Crystals C.-C. Wu Oak Ridge Affiliated Universities P. W. Chung and L . B. Munday Computational and Information Sciences Directorate, ARL

  17. A comparison between bridges and force-chains in photoelastic disk packing.

    PubMed

    Zhang, Ling; Cai, Shuxiao; Hu, Zunpeng; Zhang, Jie

    2014-01-07

    In a dense granular material, force-chains form naturally as a backbone to support an external load. Due to the limitation of experimental techniques, the determination of the force-chain network in 3D packing is rather difficult, requiring a precise measurement of contact forces between particles. For 3D packing under gravity, it has long been proposed that bridges form as load-bearing structures. Identification of a bridge is relatively easy, requiring only the geometric information of particles. Although both concepts have existed for years, their relationship remains elusive. In this study, we aim towards resolving such a connection by comparing bridges and force-chains in packing of photoelastic disks. No direct correspondence between bridges and force-chains is observed. In addition, when a bridge grows longer, its probability of being a force-chain or part of the force-chain network decreases exponentially. Nonetheless, both are consistent in distinguishing certain properties of packing of strong hysteresis. To test the load-bearing assumption of bridges, stresses of particles in/out of bridges are analysed and compared and only minor differences are found.

  18. Energetics of Cyclic Dipeptide Crystal Packing and Solvation

    PubMed Central

    Brady, G. Patrick; Sharp, Kim A.

    1997-01-01

    Calculations of the thermodynamics of transfer of the cyclic alanine-alanine (cAA) and glycine-glycine (cGG) dipeptides between the gas, water, and crystal phases were carried out using a combination of molecular mechanics, normal mode analysis, and continuum electrostatics. The experimental gas-to-water solvation free energy and the enthalpy of gas-to-crystal transfer of cGG are accurately reproduced by the calculations. The enthalpies of cGG and cAA crystal-to-water transfer are also close to the experimental values. A combination of experimental data and normal mode analysis of cGG provides an accurate estimate of the association entropy penalty (loss of rotational and translational entropy and gain in vibrational entropy) for “binding” in the crystalline phase of -14.1 cal/mol/K. This is a smaller number than most previous theoretical estimates, but it is similar to previous experimental estimates. Calculated entropies of the crystal phase under-estimate the experimental entropy by about 15 cal/mol/K because of neglect of longe-range lattice motions. Comparison of the intermolecular interactions in the crystals of cGG and cAA provides a possible explanation of the puzzling decrease in enthalpy, with increasing hydrophobicity seen previously for both cyclic dipeptide dissolution and protein unfolding. This decrease arises from a favorable long-range electrostatic interaction between dipeptide molecules in the crystals, which is attenuated by the more hydrophobic side chains. PMID:9017216

  19. Atomic force microscopy on liquid crystals

    NASA Astrophysics Data System (ADS)

    Bahr, Christian; Schulz, Benjamin

    This chapter provides an introduction to the atomic force microscopy (AFM) on thermotropic liquid crystals. We first give a general introduction to the technique of AFM and then describe the special requirements that have to be met for the imaging of liquid-crystalline surfaces. We also discuss the relation between the quality or reliability of the imaging results and various parameters of the scanning conditions. We briey review the existing work on AFM on liquid crystals and finally describe applications beyond the imaging, such as molecular force spectroscopy or manipulation of surface structures.

  20. Crystalline assemblies and densest packings of a family of truncated tetrahedra and the role of directional entropic forces.

    PubMed

    Damasceno, Pablo F; Engel, Michael; Glotzer, Sharon C

    2012-01-24

    Polyhedra and their arrangements have intrigued humankind since the ancient Greeks and are today important motifs in condensed matter, with application to many classes of liquids and solids. Yet, little is known about the thermodynamically stable phases of polyhedrally shaped building blocks, such as faceted nanoparticles and colloids. Although hard particles are known to organize due to entropy alone, and some unusual phases are reported in the literature, the role of entropic forces in connection with polyhedral shape is not well understood. Here, we study thermodynamic self-assembly of a family of truncated tetrahedra and report several atomic crystal isostructures, including diamond, β-tin, and high-pressure lithium, as the polyhedron shape varies from tetrahedral to octahedral. We compare our findings with the densest packings of the truncated tetrahedron family obtained by numerical compression and report a new space-filling polyhedron, which has been overlooked in previous searches. Interestingly, the self-assembled structures differ from the densest packings. We show that the self-assembled crystal structures can be understood as a tendency for polyhedra to maximize face-to-face alignment, which can be generalized as directional entropic forces.

  1. Grain size constraints on twin expansion in hexagonal close packed crystals

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

    Deformation twins are stress-induced transformed domains of lamellar shape that form when polycrystalline hexagonal close packed metals, like Mg, are strained. Several studies have reported that the propensity of deformation twinning reduces as grain size decreases. Here, we use a 3D crystal plasticity based micromechanics model to calculate the effect of grain size on the driving forces responsible for expanding twin lamellae. The calculations reveal that constraints from the neighboring grain where the grain boundary and twin lamella meet induce a stress reversal in the twin lamella. A pronounced grain size effect arises as reductions in grain size cause these stress-reversal fields from twin/grain boundary junctions to affect twin growth. We further show that the severity of this neighboring grain constraint depends on the crystallographic orientation and plastic response of the neighboring grain. We show that these stress-reversal fields from twin/grain boundary junctions will affect twin growth, below a critical parent grain size. These results reveal an unconventional yet influential role that grain size and grain neighbors can play on deformation twinning.

  2. Grain size constraints on twin expansion in hexagonal close packed crystals

    DOE PAGES

    Kumar, Mariyappan Arul; Beyerlein, Irene Jane; Tome, Carlos N.

    2016-10-20

    Deformation twins are stress-induced transformed domains of lamellar shape that form when polycrystalline hexagonal close packed metals, like Mg, are strained. Several studies have reported that the propensity of deformation twinning reduces as grain size decreases. Here, we use a 3D crystal plasticity based micromechanics model to calculate the effect of grain size on the driving forces responsible for expanding twin lamellae. The calculations reveal that constraints from the neighboring grain where the grain boundary and twin lamella meet induce a stress reversal in the twin lamella. A pronounced grain size effect arises as reductions in grain size cause thesemore » stress-reversal fields from twin/grain boundary junctions to affect twin growth. We further show that the severity of this neighboring grain constraint depends on the crystallographic orientation and plastic response of the neighboring grain. We show that these stress-reversal fields from twin/grain boundary junctions will affect twin growth, below a critical parent grain size. Finally, these results reveal an unconventional yet influential role that grain size and grain neighbors can play on deformation twinning.« less

  3. Grain size constraints on twin expansion in hexagonal close packed crystals

    SciTech Connect

    Kumar, Mariyappan Arul; Beyerlein, Irene Jane; Tome, Carlos N.

    2016-10-20

    Deformation twins are stress-induced transformed domains of lamellar shape that form when polycrystalline hexagonal close packed metals, like Mg, are strained. Several studies have reported that the propensity of deformation twinning reduces as grain size decreases. Here, we use a 3D crystal plasticity based micromechanics model to calculate the effect of grain size on the driving forces responsible for expanding twin lamellae. The calculations reveal that constraints from the neighboring grain where the grain boundary and twin lamella meet induce a stress reversal in the twin lamella. A pronounced grain size effect arises as reductions in grain size cause these stress-reversal fields from twin/grain boundary junctions to affect twin growth. We further show that the severity of this neighboring grain constraint depends on the crystallographic orientation and plastic response of the neighboring grain. We show that these stress-reversal fields from twin/grain boundary junctions will affect twin growth, below a critical parent grain size. Finally, these results reveal an unconventional yet influential role that grain size and grain neighbors can play on deformation twinning.

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

    NASA Astrophysics Data System (ADS)

    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.

  5. Force chains and contact network topology in sheared packings of elongated particles

    NASA Astrophysics Data System (ADS)

    Azéma, Emilien; Radjaï, Farhang

    2012-03-01

    By means of contact dynamic simulations, we investigate the contact network topology and force chains in two-dimensional packings of elongated particles subjected to biaxial shearing. The morphology of large packings of elongated particles in quasistatic equilibrium is complex due to the combined effects of local nematic ordering of the particles and orientations of contacts between particles. The effect of elongation on shear behavior and dilatancy was investigated in detail in a previous paper [Azéma and Radjai, Phys. Rev. EPLEEE81539-375510.1103/PhysRevE.81.051304 81, 051304 (2010)]. Here, we show how particle elongation affects force distributions and force-fabric anisotropy via various local structures allowed by steric exclusions and the requirement of force balance. We find that the force distributions become increasingly broader as particles become more elongated. Interestingly, the weak force network transforms from a passive stabilizing agent with respect to strong force chains to an active force-transmitting network for the whole system. The strongest force chains are carried by side-side contacts oriented along the principal stress direction.

  6. Molecular structures and crystal packings of 2-styrylquinoline and its derivatives

    SciTech Connect

    Kuz'mina, L. G.; Sitin, A. G.; Gulakova, E. N.; Fedorova, O. A.; Lermontova, E. Kh.; Churakov, A. V.

    2011-07-15

    The crystal and molecular structures of five styrylheterocycles of the quinoline series are studied. All molecules are planar. The double bond in the ethylene fragment is essentially localized. In the molecule of 2-(4-methylstyryl)quinoline, the ethylene fragment is disordered by the bicycle-pedal pattern. In four of the five compounds, the crystal packings do not contain stacking dimers prearranged for the [2+2] photocycloaddition (PCA) reaction. In the crystal of 2-(3-nitrostyryl)quinoline, pairs of crystallographically independent molecules form stacking dimers. In a dimer, the ethylene fragments have a twist orientation, which is incompatible with the PCA reaction. An attempt to initiate a temperature-dependent process of bicyclepedal isomerization in the crystal and, as a consequence, the PCA reaction by means of simultaneous irradiation and heating of a single crystal is unsuccessful.

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

    PubMed Central

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

    2014-01-01

    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. PMID:25178812

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

    PubMed

    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.

  9. Crystallographic Structure, Intermolecular Packing Energetics, Crystal Morphology and Surface Chemistry of Salmeterol Xinafoate (Form I).

    PubMed

    Moldovan, Alexandru A; Rosbottom, Ian; Ramachandran, Vasuki; Pask, Christopher M; Olomukhoro, Oboroghene; Roberts, Kevin J

    2017-03-01

    Single crystals of salmeterol xinafoate (form I), prepared from slow cooled supersaturated propan-2-ol solutions, crystallize in a triclinic P1¯ symmetry with 2 closely related independent salt pairs within the asymmetric unit, with an approximately double-unit cell volume compared with the previously published crystal structure. Synthonic analysis of the bulk intermolecular packing confirms the similarity in packing energetics between the 2 salt pairs. The strongest synthons, as expected, are dominated by coulombic interactions. Morphologic prediction reveals a plate-like morphology, dominated by the {001}, {010}, and {100} surfaces, consistent with experimentally grown crystals. Although surface chemistry of the slow-growing {001} face comprises large sterically hindering phenyl groups, although weaker coulombic interactions still prevail from the alcohol group present on the phenyl and hydroxymethyl groups. The surface chemistry of the faster growing {010} and {100} faces are dominated by the significantly stronger cation/anion interactions occurring between the carboxylate and protonated secondary ammonium ion groups. The importance of understanding the cohesive and adhesive nature of the crystal surfaces of an active pharmaceutical ingredient, with respect to their interaction with other active pharmaceutical ingredient crystals and how that may affect formulation design, is highlighted.

  10. Columnar/herringbone dual crystal packing of pyrenylsumanene and its photophysical properties

    PubMed Central

    Shrestha, Binod Babu

    2014-01-01

    Summary A single crystal of pyrenylsumanene was found to exhibit both columnar and herringbone crystal packing. The sumanene moieties form unidirectional columnar structures based on π–π stacking while the pyrene moieties generate herringbone structures due to CH–π interactions. The absorption and emission maxima of pyrenylsumanene were both red-shifted relative to those of sumanene and pyrene, owing to the extension of π-conjugation. Monomer emission with high quantum yield (0.82) was observed for pyrenylsumanene in solution, while excimer-type red-shifted emission was evident in the crystalline phase. PMID:24778739

  11. Dependence of crystallization of Brownian particles by sedimentation on the force direction

    NASA Astrophysics Data System (ADS)

    Sato, Masahide; Yusuf Hakim Widianto, Muhammad; Kanatsu, Youhei

    2015-11-01

    The formation of a large close-packed colloidal crystal with the fcc structure was observed during the sedimentation of colloidal particles in an inverted pyramidal pit [S. Matsuo et al., Appl. Phys. Lett. 82, 4285 (2003)]. Carrying out Brownian dynamics simulations, we confirmed that large grains with the fcc structure are formed when the apex angle of the inverted pyramidal container is suitable and the force direction is parallel to the the center axis [Y. Kanatsu and M. Sato, J. Phys. Soc. Jpn. 84, 044601 (2015)]. To form a high-quality colloidal crystal without defects, it is important to investigate in detail how the quality of a colloidal crystal is affected by the force direction and container shape. In this paper, we focus on the effect of the force direction on crystal quality and investigate how the ratio of the number of the hcp structured particles, Nhcp, to that of fcc structured particles, Nfcc, is affected by the force direction. In our simulation, the ratio of Nfcc to Nhcp is hardly changed when the force direction deviates from the central axis: Nfcc is much larger than Nhcp irrespective of the force direction. Thus, our results show that the crystal structure is insensitive to the force direction in forming a colloidal crystal by sedimentation in an inverted pyramidal container.

  12. Effect of packing fraction on shear band formation in a granular material forced by a penetrometer

    NASA Astrophysics Data System (ADS)

    Tapia, Franco; Espíndola, David; Hamm, Eugenio; Melo, Francisco

    2013-01-01

    Granular ensembles subjected to confinement forces can reach metastable states that often break down via formation of shear bands for sufficiently high deviatoric stress. In this article we investigate the flow induced in a granular ensemble that is perturbed by a vertically moving finger in a quasiplanar geometry. The flow exhibits spiral-like shear bands and evolves discontinuously in time, in concert with an oscillating penetration force. We characterize the nature of this nucleation-relaxation type process for loose to dense packing fractions. The nucleation dynamics is reasonably well described by a simple Mohr-Coulomb failure criterium in which the friction coefficient is a function of packing fraction. We contrast our findings with the recent work of Gravish [Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.105.128301 105, 128301 (2010)].

  13. Effect of packing fraction on shear band formation in a granular material forced by a penetrometer.

    PubMed

    Tapia, Franco; Espíndola, David; Hamm, Eugenio; Melo, Francisco

    2013-01-01

    Granular ensembles subjected to confinement forces can reach metastable states that often break down via formation of shear bands for sufficiently high deviatoric stress. In this article we investigate the flow induced in a granular ensemble that is perturbed by a vertically moving finger in a quasiplanar geometry. The flow exhibits spiral-like shear bands and evolves discontinuously in time, in concert with an oscillating penetration force. We characterize the nature of this nucleation-relaxation type process for loose to dense packing fractions. The nucleation dynamics is reasonably well described by a simple Mohr-Coulomb failure criterium in which the friction coefficient is a function of packing fraction. We contrast our findings with the recent work of Gravish et al. [Phys. Rev. Lett. 105, 128301 (2010)].

  14. Tris(hydroxymethyl)aminomethane induces conformational change and crystal-packing contraction of porcine pancreatic elastase

    PubMed Central

    Kinoshita, Takayoshi; Yamaguchi, Asako; Tada, Toshiji

    2006-01-01

    Porcine pancreatic elastase (PPE) was crystallized under new sulfate-free conditions containing 0.3 M NaCl and 50 mM tris(hydroxymethyl)aminomethane–HCl at pH 7.0. The crystal structure determined at 1.5 Å resolution had a unique conformation in four regions which contained loop portions. A chloride ion was bound near the catalytic triad instead of the sulfate ion in PDB entry 1qnj, a typical PPE crystal structure. However, the chloride ion did not affect the configuration of the catalytic triad. A tris(hydroxymethyl)aminomethane (Tris) molecule was bound to the S4 and S5 subsites in place of the adjacent molecule in the 1qnj crystal and played a significant role in the structural change of the region. The distortion in this region may subsequently have induced conformational changes in the other three regions. The fact that Tris and these four regions make a diagonal line in the ac plane may have affected the crystal-packing contraction along the a and c axes in the crystal compared with the typical crystal. PMID:16820677

  15. Tris(hydroxymethyl)aminomethane induces conformational change and crystal-packing contraction of porcine pancreatic elastase.

    PubMed

    Kinoshita, Takayoshi; Yamaguchi, Asako; Tada, Toshiji

    2006-07-01

    Porcine pancreatic elastase (PPE) was crystallized under new sulfate-free conditions containing 0.3 M NaCl and 50 mM tris(hydroxymethyl)aminomethane-HCl at pH 7.0. The crystal structure determined at 1.5 angstroms resolution had a unique conformation in four regions which contained loop portions. A chloride ion was bound near the catalytic triad instead of the sulfate ion in PDB entry 1qnj, a typical PPE crystal structure. However, the chloride ion did not affect the configuration of the catalytic triad. A tris(hydroxymethyl)aminomethane (Tris) molecule was bound to the S4 and S5 subsites in place of the adjacent molecule in the 1qnj crystal and played a significant role in the structural change of the region. The distortion in this region may subsequently have induced conformational changes in the other three regions. The fact that Tris and these four regions make a diagonal line in the ac plane may have affected the crystal-packing contraction along the a and c axes in the crystal compared with the typical crystal.

  16. A crystal plasticity model for slip in hexagonal close packed metals based on discrete dislocation simulations

    NASA Astrophysics Data System (ADS)

    Messner, Mark C.; Rhee, Moono; Arsenlis, Athanasios; Barton, Nathan R.

    2017-06-01

    This work develops a method for calibrating a crystal plasticity model to the results of discrete dislocation (DD) simulations. The crystal model explicitly represents junction formation and annihilation mechanisms and applies these mechanisms to describe hardening in hexagonal close packed metals. The model treats these dislocation mechanisms separately from elastic interactions among populations of dislocations, which the model represents through a conventional strength-interaction matrix. This split between elastic interactions and junction formation mechanisms more accurately reproduces the DD data and results in a multi-scale model that better represents the lower scale physics. The fitting procedure employs concepts of machine learning—feature selection by regularized regression and cross-validation—to develop a robust, physically accurate crystal model. The work also presents a method for ensuring the final, calibrated crystal model respects the physical symmetries of the crystal system. Calibrating the crystal model requires fitting two linear operators: one describing elastic dislocation interactions and another describing junction formation and annihilation dislocation reactions. The structure of these operators in the final, calibrated model reflect the crystal symmetry and slip system geometry of the DD simulations.

  17. Structure of finite sphere packings via exact enumeration: Implications for colloidal crystal nucleation

    NASA Astrophysics Data System (ADS)

    Hoy, Robert S.; Harwayne-Gidansky, Jared; O'Hern, Corey S.

    2012-05-01

    We analyze the geometric structure and mechanical stability of a complete set of isostatic and hyperstatic sphere packings obtained via exact enumeration. The number of nonisomorphic isostatic packings grows exponentially with the number of spheres N, and their diversity of structure and symmetry increases with increasing N and decreases with increasing hyperstaticity H≡Nc-NISO, where Nc is the number of pair contacts and NISO=3N-6. Maximally contacting packings are in general neither the densest nor the most symmetric. Analyses of local structure show that the fraction f of nuclei with order compatible with the bulk (rhcp) crystal decreases sharply with increasing N due to a high propensity for stacking faults, five- and near-fivefold symmetric structures, and other motifs that preclude rhcp order. While f increases with increasing H, a significant fraction of hyperstatic nuclei for N as small as 11 retain non-rhcp structure. Classical theories of nucleation that consider only spherical nuclei, or only nuclei with the same ordering as the bulk crystal, cannot capture such effects. Our results provide an explanation for the failure of classical nucleation theory for hard-sphere systems of N≲10 particles; we argue that in this size regime, it is essential to consider nuclei of unconstrained geometry. Our results are also applicable to understanding kinetic arrest and jamming in systems that interact via hard-core-like repulsive and short-ranged attractive interactions.

  18. Predicting transmembrane helix packing arrangements using residue contacts and a force-directed algorithm.

    PubMed

    Nugent, Timothy; Jones, David T

    2010-03-19

    Alpha-helical transmembrane proteins constitute roughly 30% of a typical genome and are involved in a wide variety of important biological processes including cell signalling, transport of membrane-impermeable molecules and cell recognition. Despite significant efforts to predict transmembrane protein topology, comparatively little attention has been directed toward developing a method to pack the helices together. Here, we present a novel approach to predict lipid exposure, residue contacts, helix-helix interactions and finally the optimal helical packing arrangement of transmembrane proteins. Using molecular dynamics data, we have trained and cross-validated a support vector machine (SVM) classifier to predict per residue lipid exposure with 69% accuracy. This information is combined with additional features to train a second SVM to predict residue contacts which are then used to determine helix-helix interaction with up to 65% accuracy under stringent cross-validation on a non-redundant test set. Our method is also able to discriminate native from decoy helical packing arrangements with up to 70% accuracy. Finally, we employ a force-directed algorithm to construct the optimal helical packing arrangement which demonstrates success for proteins containing up to 13 transmembrane helices. This software is freely available as source code from http://bioinf.cs.ucl.ac.uk/memsat/mempack/.

  19. Predicting Transmembrane Helix Packing Arrangements using Residue Contacts and a Force-Directed Algorithm

    PubMed Central

    Nugent, Timothy; Jones, David T.

    2010-01-01

    Alpha-helical transmembrane proteins constitute roughly 30% of a typical genome and are involved in a wide variety of important biological processes including cell signalling, transport of membrane-impermeable molecules and cell recognition. Despite significant efforts to predict transmembrane protein topology, comparatively little attention has been directed toward developing a method to pack the helices together. Here, we present a novel approach to predict lipid exposure, residue contacts, helix-helix interactions and finally the optimal helical packing arrangement of transmembrane proteins. Using molecular dynamics data, we have trained and cross-validated a support vector machine (SVM) classifier to predict per residue lipid exposure with 69% accuracy. This information is combined with additional features to train a second SVM to predict residue contacts which are then used to determine helix-helix interaction with up to 65% accuracy under stringent cross-validation on a non-redundant test set. Our method is also able to discriminate native from decoy helical packing arrangements with up to 70% accuracy. Finally, we employ a force-directed algorithm to construct the optimal helical packing arrangement which demonstrates success for proteins containing up to 13 transmembrane helices. This software is freely available as source code from http://bioinf.cs.ucl.ac.uk/memsat/mempack/. PMID:20333233

  20. Crystal structure and packing analysis of nitrofurantoin N,N-dimethylformamide solvate

    NASA Astrophysics Data System (ADS)

    Cvetkovski, A.; Ferretti, V.

    2016-07-01

    The N, N'-dimethylformamide solvated crystal of the drug nitrofurantoin has been prepared and analysed by single-crystal X-ray diffraction. The two co-crystallized molecules, in the 1 : 1 stoichiometric ratio, are linked by a medium/strong N-H···O hydrogen bond (N···O is 2.759 (3) Å) and a weaker C-H···O interaction to form isolated supramolecular adducts, that in turn are packed into the lattice framework mainly through C-H···O hydrogen bonds. Two-dimensional fingerprint plots of Hirshfeld surfaces are used to visualize, analyze and compare intermolecular interactions found in the title compound and in similar structures.

  1. The effect of crystal shape, size and bimodality on the maximum packing and the rheology of crystal bearing magma

    NASA Astrophysics Data System (ADS)

    Moitra, Pranabendu; Gonnermann, Helge

    2014-05-01

    Magma often contains crystals of various shapes and sizes. We present experimental results on the effect of the shape- and size-distribution of solid particles on the rheological properties of solid-liquid suspensions, which are hydrodynamically analogous to crystal-bearing magmas. The suspensions were comprised of either a single particle shape and size (unimodal) or a mixture of two different particle shapes and sizes (bimodal). For each type of suspension we characterized the dry maximum packing fraction of the particle mixture using the tap density method. We then systematically varied the total volume fraction of particles in the suspension, as well as the relative proportion of the two different particle types in the bimodal suspensions. For each of the resultant mixtures (suspensions) we performed controlled shear stress experiments using a rotational rheometer in parallel-plate geometry spanning 4 orders of magnitude in shear stress. The resultant data curves of shear stress as a function of shear rate were fitted using a Herschel-Bulkley rheological model. We find that the dry maximum packing decreases with increasing particle aspect ratio (ar) and decreasing particle size ratio (Λ). The highest dry maximum packing was obtained at 60-75% volume of larger particles for bimodal spherical particle mixture. Normalized consistency, Kr, defined as the ratio of the consistency of the suspension and the viscosity of the suspending liquid, was fitted using a Krieger-Dougherty model as a function of the total solid volume fraction (φ). The maximum packing fractions (φm) obtained from the shear experimental data fitting of the unimodal suspensions were similar in magnitude with the dry maximum packing fractions of the unimodal particles. Subsequently, we used the dry maximum packing fractions of the bimodal particle mixtures to fit Kr as a function of φ for the bimodal suspensions. We find that Kr increases rapidly for suspensions with larger ar and smaller

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

    PubMed Central

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

    2016-01-01

    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. PMID:27640812

  3. Hydrogen bonds in the crystal packings of mesalazine and mesalazine hydrochloride

    NASA Astrophysics Data System (ADS)

    Banić-Tomišić, Z.; Kojić-Prodić, B.; Širola, I.

    1997-10-01

    The crystal structures of pharmaceutical product mesalazine (marketed also under different proprietary names as Salofalk, Asacol, Asacolitin, and Claversal) and its hydrochloride are reported. In the crystal mesalazine is in zwitterion form as 5-ammoniosalicylate ( 1) whereas mesalazine hydrochloride crystallizes in an ionized form as 5-ammoniosalicylium chloride ( 2). Compound 1 (C 7H 7O 3N) crystallizes in the monoclinic space group {P2 1}/{n} with a = 3.769(1) Å, b = 7.353(2) Å, c = 23.475(5) Å, β = 94.38(2)°, V = 648.7(8) Å3, Z = 4, Dc = 1.568 g cm -3 and μ( MoKα) = 1.2 cm -1. Compound 2 (C 7H 8O 3NCl) crystallizes in the triclinic space group P 1¯ with a = 4.4839(2) Å, b = 5.7936(2) Å, c = 15.6819(5) Å, α = 81.329(3)°, β = 88.026(3)°, γ = 79.317(4)°, V = 395.74(3) Å3, Z = 2, Dc = 1.591 g cm -3 and μ(CuK α) = 40.8 cm -1. The crystal structures were solved by direct methods and refined to R = 0.041 for 1 and 0.028 for 2, using 607 and 1374 observed reflections, respectively. The configuration of both molecules, with the ortho hydroxyl to a carboxyl group, favours the intramolecular hydrogen bonds. Very complex systems of intermolecular hydrogen bonds were observed in both crystal packings. They are discussed in terms of graph-set notation. The mesalazine crystal structure is characterized by two-dimensional network of hydrogen bonds in the ab plane. The crystal structure pattern of mesalazine hydrochloride is a three-dimensional network significantly supported by N +H⋯Cl - interactions.

  4. Multicore photonic crystal fiber force meters

    NASA Astrophysics Data System (ADS)

    Reimlinger, M.; Colalillo, A.; Coompson, J.; Wynne, R.

    2011-04-01

    A silica based three core photonic crystal fiber (PCF) force meter with fast response times (<30μs) for low wind speed detection is presented. Results are provided for PCF structures containing cores with varied lattice spacing. Force meters with high spatial resolution (sample regions <10cm) specially outfitted for extreme environmental conditions are of interest to both industry and basic research institutions. The featured PCF force meter exhibited sensitivities that agreed with theoretical predictions that are useful for the detection of minimum displacements for wind speeds <30m/s. The results of this investigation are relevant to civil engineering applications including urban sensing technologies that involve air quality monitoring. The deflection of the PCF detection interface was measured as a function of the fiber deflection or the applied force (e.g. wind speed). The three core PCF has a core diameter of 3.9μm, outer diameter of 132.5μm and 7.56μm core-core spacing. A 4cm length of the PCF is attached to the surface of a thin metal beam. One end of the PCF section is fusion spliced to a single mode fiber (SMF) at the fiber input. The remaining fiber end is coupled to a CCD camera with a lens at the PCF output. The applied force deflects the supported PCF such that the intensity distribution of the optical field for the multiple cores changes as a function of displacement. Experimental results from static deflection measurements are in agreement with coupled-mode theory and simple beam deflection theory models.

  5. Crystallization and Crystal-Packing Studies of Chlorella Virus Deoxyuridine Triphosphatase

    SciTech Connect

    Homma, K.; Moriyama, H

    2009-01-01

    The 141-amino-acid deoxyuridine triphosphatase (dUTPase) from the algal Chlorella virus IL-3A and its Glu81Ser/Thr84Arg-mutant derivative Mu-22 were crystallized using the hanging-drop vapor-diffusion method at 298 K with polyethylene glycol as the precipitant. An apo IL-3A dUTPase with an amino-terminal T7 epitope tag and a carboxy-terminal histidine tag yielded cubic P2{sub 1}3 crystals with unit-cell parameter a = 106.65 {angstrom}. In the presence of dUDP, the enzyme produced thin stacked orthorhombic P222 crystals with unit-cell parameters a = 81.0, b = 96.2, c = 132.8 {angstrom}. T7-histidine-tagged Mu-22 dUTPase formed thin stacked rectangular crystals. Amino-terminal histidine-tagged dUTPases did not crystallize but formed aggregates. Glycyl-seryl-tagged dUTPases yielded cubic P2{sub 1}3 IL-3A crystals with unit-cell parameter a = 105.68 {angstrom} and hexagonal P6{sub 3} Mu-22 crystals with unit-cell parameters a = 132.07, c = 53.45 {angstrom}, {gamma} = 120{sup o}. Owing to the Thr84Arg mutation, Mu-22 dUTPase had different monomer-to-monomer interactions to those of IL-3A dUTPase.

  6. Manipulation of an existing crystal form unexpectedly results in interwoven packing networks with pseudo-translational symmetry

    PubMed Central

    Reimer, Janice M.; Aloise, Martin N.; Powell, Harold R.; Schmeing, T. Martin

    2016-01-01

    Nonribosomal peptide synthetases (NRPSs) are multimodular enzymes that synthesize a myriad of diverse molecules. Tailoring domains have been co-opted into NRPSs to introduce further variety into nonribosomal peptide products. Linear gramicidin synthetase contains a unique formylation-tailoring domain in its initiation module (F-A-PCP). The structure of the F-A di-domain has previously been determined in a crystal form which had large solvent channels and no density for the minor Asub subdomain. An attempt was made to take advantage of this packing by removing the Asub subdomain from the construct (F-AΔsub) in order to produce a crystal that could accommodate the PCP domain. In the resulting crystal the original packing network was still present, but a second network with the same packing and almost no contact with the original network took the place of the solvent channels and changed the space group of the crystal. PMID:27710934

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

    PubMed

    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.

  8. Preliminary investigations into mooring forces on a semisubmersible and a turret moored tanker in pack ice, current and waves

    SciTech Connect

    Murray, J.J.; Spencer, D.

    1996-12-01

    Physical model tests were carried out on a scale model of a semisubmersible and a monohull tanker in drifting pack ice. The tests covered a range of drift velocities, directions and ice concentrations. The models were tested in both a fully restrained and moored condition. Data from the experiments were used to develop a semi-empirical numerical model to predict maximum global loads on the mooring system. These results were compared with the maximum loads on the mooring system caused by hydrodynamic forces (waves and current) predicted from a linear numerical model for waves. Analysis results showed that the maximum mooring loads due to the pack ice on the semisubmersible were considerably higher than those caused by the hydrodynamic forces on the same vessel. Also, the maximum mooring loads due to pack ice on the tanker were close to the maximum mooring loads caused by the hydrodynamic forces. Maximum mooring loads related to pack ice forces were realized in ice concentrations of 10/10 coverage while for concentrations less than 6/10 coverage loads attributed to pack ice were negligible in comparison to the hydrodynamic forces. The paper also presents a number of recommendations, based on these findings, to improve the performance of both vessel types and to advance the general state-of-the-art for analysis procedures related to offshore vessel moored in pack ice.

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

    NASA Astrophysics Data System (ADS)

    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.

  10. Hard-sphere solids near close packing: testing theories for crystallization

    PubMed

    Groh; Mulder

    2000-04-01

    The freezing transition of hard spheres has been well described by various versions of density-functional theory (DFT). These theories should possess the close-packed crystal as a special limit, which represents an extreme testing ground for the quality of such liquid-state based theories. We therefore study the predictions of DFT for the structure and thermodynamics of the hard-sphere crystal in this limit. We examine the Ramakrishnan-Yussouff (RY) approximation and two variants of the fundamental-measure theory (FMT) developed by Rosenfeld and co-workers. We allow for general shapes of the density peaks, going beyond the common Gaussian approximation. In all cases we find that upon approaching close packing, the peak width vanishes proportionally to the free distance a between the particles and the free energy depends logarithmically on a. However, different peak shapes and next-to-leading contributions to the free energy result from the different approximate functionals. For the RY theory, within the Gaussian approximation, we establish that the crystalline solutions form a closed loop with a stable and an unstable branch both connected to the close-packing point at a=0, consistent with the absence of a liquid-solid spinodal. That version of FMT that has previously been applied to freezing, predicts asymptotically steplike density profiles confined to the cells of self-consistent cell theory. But a recently suggested improved version which employs tensor weighted densities yields wider and almost Gaussian peaks that are shown to be in very good agreement with computer simulations.

  11. Designing better diffracting crystals of biotin carboxyl carrier protein from Pyrococcus horikoshii by a mutation based on the crystal-packing propensity of amino acids

    PubMed Central

    Yamada, Kazunori D.; Kunishima, Naoki; Matsuura, Yoshinori; Nakai, Koshiro; Naitow, Hisashi; Fukasawa, Yoshinori; Tomii, Kentaro

    2017-01-01

    An alternative rational approach to improve protein crystals by using single-site mutation of surface residues is proposed based on the results of a statistical analysis using a compiled data set of 918 independent crystal structures, thereby reflecting not only the entropic effect but also other effects upon protein crystallization. This analysis reveals a clear difference in the crystal-packing propensity of amino acids depending on the secondary-structural class. To verify this result, a systematic crystallization experiment was performed with the biotin carboxyl carrier protein from Pyrococcus horikoshii OT3 (PhBCCP). Six single-site mutations were examined: Ala138 on the surface of a β-sheet was mutated to Ile, Tyr, Arg, Gln, Val and Lys. In agreement with prediction, it was observed that the two mutants (A138I and A138Y) harbouring the residues with the highest crystal-packing propensities for β-sheet at position 138 provided better crystallization scores relative to those of other constructs, including the wild type, and that the crystal-packing propensity for β-sheet provided the best correlation with the ratio of obtaining crystals. Two new crystal forms of these mutants were obtained that diffracted to high resolution, generating novel packing interfaces with the mutated residues (Ile/Tyr). The mutations introduced did not affect the overall structures, indicating that a β-sheet can accommodate a successful mutation if it is carefully selected so as to avoid intramolecular steric hindrance. A significant negative correlation between the ratio of obtaining amorphous precipitate and the crystal-packing propensity was also found. PMID:28876239

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

    NASA Astrophysics Data System (ADS)

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

  14. Charge Stabilized Crystalline Colloidal Arrays As Templates For Fabrication of Non-Close-Packed Inverted Photonic Crystals

    PubMed Central

    Bohn, Justin J.; Ben-Moshe, Matti; Tikhonov, Alexander; Qu, Dan; Lamont, Daniel N.

    2010-01-01

    We developed a straightforward method to form non close-packed highly ordered fcc direct and inverse opal silica photonic crystals. We utilize an electrostatically self assembled crystalline colloidal array (CCA) template formed by monodisperse, highly charged polystyrene particles. We then polymerize a hydrogel around the CCA (PCCA) and condense the silica to form a highly ordered silica impregnated (siPCCA) photonic crystal. Heating at 450 °C removes the organic polymer leaving a silica inverse opal structure. By altering the colloidal particle concentration we independently control the particle spacing and the wall thickness of the inverse opal photonic crystals. This allows us to control the optical dielectric constant modulation in order to optimize the diffraction; the dielectric constant modulation is controlled independently of the photonic crystal periodicity. These fcc photonic crystals are better ordered than typical close-packed photonic crystals because their self assembly utilizes soft electrostatic repulsive potentials. We show that colloidal particle size and charge polydispersity has modest impact on ordering, in contrast to that for close-packed crystals. PMID:20163800

  15. Charge stabilized crystalline colloidal arrays as templates for fabrication of non-close-packed inverted photonic crystals.

    PubMed

    Bohn, Justin J; Ben-Moshe, Matti; Tikhonov, Alexander; Qu, Dan; Lamont, Daniel N; Asher, Sanford A

    2010-04-15

    We developed a straightforward method to form non-close-packed highly ordered fcc direct and inverse opal silica photonic crystals. We utilize an electrostatically self assembled crystalline colloidal array (CCA) template formed by monodisperse, highly charged polystyrene particles. We then polymerize a hydrogel around the CCA (PCCA) and condense silica to form a highly ordered silica impregnated (siPCCA) photonic crystal. Heating at 450 degrees C removes the organic polymer leaving a silica inverse opal structure. By altering the colloidal particle concentration we independently control the particle spacing and the wall thickness of the inverse opal photonic crystals. This allows us to control the optical dielectric constant modulation in order to optimize the diffraction; the dielectric constant modulation is controlled independently of the photonic crystal periodicity. These fcc photonic crystals are better ordered than typical close-packed photonic crystals because their self assembly utilizes soft electrostatic repulsive potentials. We show that colloidal particle size and charge polydispersity has modest impact on ordering, in contrast to that for close-packed crystals. 2010 Elsevier Inc. All rights reserved.

  16. Scattering Forces within a Left-Handed Photonic Crystal

    NASA Astrophysics Data System (ADS)

    Ang, Angeleene S.; Sukhov, Sergey V.; Dogariu, Aristide; Shalin, Alexander S.

    2017-01-01

    Electromagnetic waves are known to exert optical forces on particles through radiation pressure. It was hypothesized previously that electromagnetic waves inside left-handed metamaterials produce negative radiation pressure. Here we numerically examine optical forces inside left-handed photonic crystals demonstrating negative refraction and reversed phase propagation. We demonstrate that even though the direction of force might not follow the flow of energy, the positive radiation pressure is maintained inside photonic crystals.

  17. Scattering Forces within a Left-Handed Photonic Crystal

    PubMed Central

    Ang, Angeleene S.; Sukhov, Sergey V.; Dogariu, Aristide; Shalin, Alexander S.

    2017-01-01

    Electromagnetic waves are known to exert optical forces on particles through radiation pressure. It was hypothesized previously that electromagnetic waves inside left-handed metamaterials produce negative radiation pressure. Here we numerically examine optical forces inside left-handed photonic crystals demonstrating negative refraction and reversed phase propagation. We demonstrate that even though the direction of force might not follow the flow of energy, the positive radiation pressure is maintained inside photonic crystals. PMID:28112217

  18. Scattering Forces within a Left-Handed Photonic Crystal.

    PubMed

    Ang, Angeleene S; Sukhov, Sergey V; Dogariu, Aristide; Shalin, Alexander S

    2017-01-23

    Electromagnetic waves are known to exert optical forces on particles through radiation pressure. It was hypothesized previously that electromagnetic waves inside left-handed metamaterials produce negative radiation pressure. Here we numerically examine optical forces inside left-handed photonic crystals demonstrating negative refraction and reversed phase propagation. We demonstrate that even though the direction of force might not follow the flow of energy, the positive radiation pressure is maintained inside photonic crystals.

  19. Determining the Molecular Growth Mechanisms of Protein Crystal faces by Atomic Force Microscopy

    NASA Technical Reports Server (NTRS)

    Li, Huayu; Nadarajah, Arunan; Pusey, Marc L.

    1998-01-01

    A high resolution atomic force microscopy (AFM) study had shown that the molecular packing on the tetragonal lysozyme (110) face corresponded to only one of two possible packing arrangements, suggesting that growth layers on this face were of bimolecular height (Li et al., 1998). Theoretical analyses of the packing had also indicated that growth of this face should proceed by the addition of growth units of at least tetramer size corresponding to the 43 helices in the crystal. In this study an AFM linescan technique was devised to measure the dimensions of individual growth units on protein crystal faces. The growth process of tetragonal lysozyme crystals was slowed down by employing very low supersaturations. As a result images of individual growth events on the (110) face were observed, shown by jump discontinuities in the growth step in the linescan images. The growth unit dimension in the scanned direction was obtained by suitably averaging these images. A large number of scans in two directions on the (110) face were performed and the distribution of lysozyme aggregate sizes were obtained. A variety of growth units, all of which were 43 helical lysozyme aggregates, were shown to participate in the growth process with a 43 tetramer being the minimum observed size. This technique represents a new application for AFM allowing time resolved studies of molecular process to be carried out.

  20. Determining the Molecular Growth Mechanisms of Protein Crystal Faces by Atomic Force Microscopy

    NASA Technical Reports Server (NTRS)

    Nadarajah, Arunan; Li, Huayu; Pusey, Marc L.

    1999-01-01

    A high resolution atomic force microscopy (AFM) study had shown that the molecular packing on the tetragonal lysozyme (110) face corresponded to only one of two possible packing arrangements, suggesting that growth layers on this face were of bimolecular height. Theoretical analyses of the packing also indicated that growth of this face should proceed by the addition of growth units of at least tetramer size corresponding to the 43 helices in the crystal. In this study an AFM linescan technique was devised to measure the dimensions of individual growth units on protein crystal faces as they were being incorporated into the lattice. Images of individual growth events on the (110) face of tetragonal lysozyme crystals were observed, shown by jump discontinuities in the growth step in the linescan images as shown in the figure. The growth unit dimension in the scanned direction was obtained from these images. A large number of scans in two directions on the (110) face were performed and the distribution of lysozyme growth unit sizes were obtained. A variety of unit sizes corresponding to 43 helices, were shown to participate in the growth process, with the 43 tetramer being the minimum observed size. This technique represents a new application for AFM allowing time resolved studies of molecular process to be carried out.

  1. Determining the Molecular Growth Mechanisms of Protein Crystal Faces by Atomic Force Microscopy

    NASA Technical Reports Server (NTRS)

    Nadarajah, Arunan; Li, Huayu; Pusey, Marc L.

    1999-01-01

    A high resolution atomic force microscopy (AFM) study had shown that the molecular packing on the tetragonal lysozyme (110) face corresponded to only one of two possible packing arrangements, suggesting that growth layers on this face were of bimolecular height. Theoretical analyses of the packing also indicated that growth of this face should proceed by the addition of growth units of at least tetramer size corresponding to the 43 helices in the crystal. In this study an AFM linescan technique was devised to measure the dimensions of individual growth units on protein crystal faces as they were being incorporated into the lattice. Images of individual growth events on the (110) face of tetragonal lysozyme crystals were observed, shown by jump discontinuities in the growth step in the linescan images as shown in the figure. The growth unit dimension in the scanned direction was obtained from these images. A large number of scans in two directions on the (110) face were performed and the distribution of lysozyme growth unit sizes were obtained. A variety of unit sizes corresponding to 43 helices, were shown to participate in the growth process, with the 43 tetramer being the minimum observed size. This technique represents a new application for AFM allowing time resolved studies of molecular process to be carried out.

  2. Determining the Molecular Growth Mechanisms of Protein Crystal faces by Atomic Force Microscopy

    NASA Technical Reports Server (NTRS)

    Li, Huayu; Nadarajah, Arunan; Pusey, Marc L.

    1998-01-01

    A high resolution atomic force microscopy (AFM) study had shown that the molecular packing on the tetragonal lysozyme (110) face corresponded to only one of two possible packing arrangements, suggesting that growth layers on this face were of bimolecular height (Li et al., 1998). Theoretical analyses of the packing had also indicated that growth of this face should proceed by the addition of growth units of at least tetramer size corresponding to the 43 helices in the crystal. In this study an AFM linescan technique was devised to measure the dimensions of individual growth units on protein crystal faces. The growth process of tetragonal lysozyme crystals was slowed down by employing very low supersaturations. As a result images of individual growth events on the (110) face were observed, shown by jump discontinuities in the growth step in the linescan images. The growth unit dimension in the scanned direction was obtained by suitably averaging these images. A large number of scans in two directions on the (110) face were performed and the distribution of lysozyme aggregate sizes were obtained. A variety of growth units, all of which were 43 helical lysozyme aggregates, were shown to participate in the growth process with a 43 tetramer being the minimum observed size. This technique represents a new application for AFM allowing time resolved studies of molecular process to be carried out.

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

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    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

  6. Colloid-probe AFM studies of the interaction forces of proteins adsorbed on colloidal crystals.

    PubMed

    Singh, Gurvinder; Bremmell, Kristen E; Griesser, Hans J; Kingshott, Peter

    2015-04-28

    In recent years, colloid-probe AFM has been used to measure the direct interaction forces between colloidal particles of different size or surface functionality in aqueous media, as one can study different forces in symmerical systems (i.e., sphere-sphere geometry). The present study investigates the interaction between protein coatings on colloid probes and hydrophilic surfaces decorated with hexagonally close packed single particle layers that are either uncoated or coated with proteins. Controlled solvent evaporation from aqueous suspensions of colloidal particles (coated with or without lysozyme and albumin) produces single layers of close-packed colloidal crystals over large areas on a solid support. The measurements have been carried out in an aqueous medium at different salt concentrations and pH values. The results show changes in the interaction forces as the surface charge of the unmodified or modified particles, and ionic strength or pH of the solution is altered. At high ionic strength or pH, electrostatic interactions are screened, and a strong repulsive force at short separation below 5 nm dominates, suggesting structural changes in the absorbed protein layer on the particles. We also study the force of adhesion, which decreases with an increment in the salt concentration, and the interaction between two different proteins indicating a repulsive interaction on approach and adhesion on retraction.

  7. Crystal-Packing Trends for a Series of 6,9,12,15,18-Pentaaryl-1-hydro[60]fullerenes

    SciTech Connect

    Kennedy, Robert D.; Halim, Merissa; Khan, Saeed I.; Schwartz, Benjamin J.; Tolbert, Sarah H.; Rubin, Yves

    2012-06-11

    The relationship between the size of the substituents of aryl groups in a series of fifteen 6,9,12,15,18-pentaaryl-1-hydro[60]fullerenes and the solid-state structures and packing motifs of these compounds has been analyzed. Pentaarylfullerenes have a characteristic “badminton shuttlecock” shape that causes several derivatives to crystallize into columnar stacks. However, many pentaarylfullerenes form non-stacked structures with, for example, dimeric, layered, diamondoid, or feather-in-cavity relationships between molecules. Computational modeling gave a qualitative estimate of the best shape match between the ball and socket surfaces of each pentaarylfullerene. The best match was for pentaarylfullerenes with large, spherically shaped para-substituents on the aryl groups. The series of pentaarylfullerenes was characterized by single-crystal X-ray diffraction. A total of 34 crystal structures were obtained as various solvates and were categorized by their packing motifs.

  8. Dancing Crystals: A Dramatic Illustration of Intermolecular Forces

    ERIC Educational Resources Information Center

    Mundell, Donald W.

    2007-01-01

    Crystals of naphthalene form on the surface of an acetone solution and dance about in an animated fashion illustrating surface tension, crystallization, and intermolecular forces. Additional experiments reveal the properties of the solution. Flows within the solutions can be visualized by various means. Previous demonstrations of surface motion…

  9. Dancing Crystals: A Dramatic Illustration of Intermolecular Forces

    ERIC Educational Resources Information Center

    Mundell, Donald W.

    2007-01-01

    Crystals of naphthalene form on the surface of an acetone solution and dance about in an animated fashion illustrating surface tension, crystallization, and intermolecular forces. Additional experiments reveal the properties of the solution. Flows within the solutions can be visualized by various means. Previous demonstrations of surface motion…

  10. Probing biomechanical properties with a centrifugal force quartz crystal microbalance.

    PubMed

    Webster, Aaron; Vollmer, Frank; Sato, Yuki

    2014-10-21

    Application of force on biomolecules has been instrumental in understanding biofunctional behaviour from single molecules to complex collections of cells. Current approaches, for example, those based on atomic force microscopy or magnetic or optical tweezers, are powerful but limited in their applicability as integrated biosensors. Here we describe a new force-based biosensing technique based on the quartz crystal microbalance. By applying centrifugal forces to a sample, we show it is possible to repeatedly and non-destructively interrogate its mechanical properties in situ and in real time. We employ this platform for the studies of micron-sized particles, viscoelastic monolayers of DNA and particles tethered to the quartz crystal microbalance surface by DNA. Our results indicate that, for certain types of samples on quartz crystal balances, application of centrifugal force both enhances sensitivity and reveals additional mechanical and viscoelastic properties.

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

    PubMed

    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.

  12. Highly organized smectic-like packing in vapor-deposited glasses of a liquid crystal

    DOE PAGES

    Gujral, Ankit; Gomez, Jaritza; Jiang, Jing; ...

    2016-12-26

    Glasses of a model smectic liquid crystal-forming molecule, itraconazole, were prepared by vapor deposition onto substrates with temperatures ranging from Tsubstrate = 0.78Tg to 1.02Tg, where Tg (=330 K) is the glass transition temperature. The films were characterized using X-ray scattering techniques. For Tsubstrate near and below Tg, glasses with layered smectic-like structures can be prepared and the layer spacing can be tuned by 16% through the choice of Tsubstrate. Remarkably, glasses prepared with Tsubstrate values above Tg exhibit levels of structural organization much higher than that of a thermally annealed film. These results are explained by a mechanism basedmore » upon a preferred molecular orientation and enhanced molecular motion at the free surface, indicating that molecular organization in the glass is independent of the anchoring preferred at the substrate. Furthermore, these results suggest new strategies for optimizing molecular packing within active layers of organic electronic and optoelectronic devices.« less

  13. Highly organized smectic-like packing in vapor-deposited glasses of a liquid crystal

    SciTech Connect

    Gujral, Ankit; Gomez, Jaritza; Jiang, Jing; Huang, Chengbin; O’Hara, Kathryn A.; Toney, Michael F.; Chabinyc, Michael L.; Yu, Lian; Ediger, M. D.

    2016-12-26

    Glasses of a model smectic liquid crystal-forming molecule, itraconazole, were prepared by vapor deposition onto substrates with temperatures ranging from Tsubstrate = 0.78Tg to 1.02Tg, where Tg (=330 K) is the glass transition temperature. The films were characterized using X-ray scattering techniques. For Tsubstrate near and below Tg, glasses with layered smectic-like structures can be prepared and the layer spacing can be tuned by 16% through the choice of Tsubstrate. Remarkably, glasses prepared with Tsubstrate values above Tg exhibit levels of structural organization much higher than that of a thermally annealed film. These results are explained by a mechanism based upon a preferred molecular orientation and enhanced molecular motion at the free surface, indicating that molecular organization in the glass is independent of the anchoring preferred at the substrate. Furthermore, these results suggest new strategies for optimizing molecular packing within active layers of organic electronic and optoelectronic devices.

  14. Binary dislocation junction formation and strength in hexagonal close-packed crystals

    DOE PAGES

    Wu, Chi -Chin; Aubry, Sylvie; Arsenlis, Athanasios; ...

    2015-12-17

    This work examines binary dislocation interactions, junction formation and junction strengths in hexagonal close-packed (hcp ) crystals. Through a line-tension model and dislocation dynamics (DD) simulations, the interaction and dissociation of different sets of binary junctions are investigated involving one dislocation on the (011¯0) prismatic plane and a second dislocation on one of the following planes: (0001) basal, (11¯00) prismatic, (11¯01) primary pyramidal, or (2¯112) secondary pyramidal. Varying pairs of Burgers vectors are chosen from among the common types the basal type < a > 1/3 < 112¯0 >, prismatic type < c > <0001>, and pyramidal type < a+cmore » > 1/3 < 112¯3¯ >. For binary interaction due to dislocation intersection, both the analytical results and DD-simulations indicate a relationship between symmetry of interaction maps and the relative magnitude of the Burgers vectors that constitute the junction. Using analytical formulae, a simple regressive model is also developed to represent the junction yield surface. The equation is treated as a degenerated super elliptical equation to quantify the aspect ratio and tilting angle. Lastly, the results provide analytical insights on binary dislocation interactions that may occur in general hcp metals.« less

  15. Binary dislocation junction formation and strength in hexagonal close-packed crystals

    SciTech Connect

    Wu, Chi -Chin; Aubry, Sylvie; Arsenlis, Athanasios; Chung, Peter C.

    2015-12-17

    This work examines binary dislocation interactions, junction formation and junction strengths in hexagonal close-packed (hcp ) crystals. Through a line-tension model and dislocation dynamics (DD) simulations, the interaction and dissociation of different sets of binary junctions are investigated involving one dislocation on the (011¯0) prismatic plane and a second dislocation on one of the following planes: (0001) basal, (11¯00) prismatic, (11¯01) primary pyramidal, or (2¯112) secondary pyramidal. Varying pairs of Burgers vectors are chosen from among the common types the basal type < a > 1/3 < 112¯0 >, prismatic type < c > <0001>, and pyramidal type < a+c > 1/3 < 112¯3¯ >. For binary interaction due to dislocation intersection, both the analytical results and DD-simulations indicate a relationship between symmetry of interaction maps and the relative magnitude of the Burgers vectors that constitute the junction. Using analytical formulae, a simple regressive model is also developed to represent the junction yield surface. The equation is treated as a degenerated super elliptical equation to quantify the aspect ratio and tilting angle. Lastly, the results provide analytical insights on binary dislocation interactions that may occur in general hcp metals.

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

    PubMed

    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.

  17. Self-force on dislocation segments in anisotropic crystals.

    PubMed

    Fitzgerald, S P; Aubry, S

    2010-07-28

    A dislocation segment in a crystal experiences a 'self-force', by virtue of the orientation dependence of its elastic energy. If the crystal is elastically isotropic, this force is manifested as a couple acting to rotate the segment toward the lower energy of the pure screw orientation (i.e. acting to align the dislocation line with its Burgers vector). If the crystal is anisotropic, there are additional contributions to the couple, arising from the more complex energy landscape of the lattice itself. These effects can strongly influence the dynamic evolution of dislocation networks, and via their governing role in dislocation multiplication phenomena, control plastic flow in metals. In this paper we develop a model for dislocation self-forces in a general anisotropic crystal, and briefly consider the technologically important example of α-iron, which becomes increasingly anisotropic as the temperature approaches that of the α-γ phase transition at 912 °C.

  18. Conformational change of the hexagonally packed intermediate layer of Deinococcus radiodurans monitored by atomic force microscopy.

    PubMed Central

    Müller, D J; Baumeister, W; Engel, A

    1996-01-01

    Both surfaces of the hexagonally packed intermediate (HPI) layer of Deinococcus radiodurans were imaged in buffer solution by atomic force microscopy. When adsorbed to freshly cleaved mica, the hydrophilic outer surface of the HPI layer was attached to the substrate and the hydrophobic inner surface was exposed to the stylus. The height of a single HPI layer was 7.0 nm, while overlapping edges of adjacent single layers adsorbed to mica had a height of 14.7 nm. However, double-layered stacks with inner surfaces facing each other exhibited a height of 17.4 nm. These stacks exposed the outer surface to the stylus. The different heights of overlapping layers and stacks are attributed to differences in the interaction between inner and outer surfaces. At high resolution, the inner surface revealed a protruding core with a central pore connected by six emanating arms. The pores exhibited two conformations, one with and the other without a central plug. Individual pores were observed to switch from one state to the other. PMID:8655475

  19. Two-phase Computerized Planning of Cryosurgery Using Bubble-packing and Force-field Analogy

    PubMed Central

    Tanaka, Daigo; Shimada, Kenji; Rabin, Yoed

    2007-01-01

    Background: Cryosurgery is the destruction of undesired tissues by freezing, as in prostate cryosurgery, for example. Minimally-invasive cryosurgery is currently performed by means of an array of cryoprobes, each in the shape of a long hypodermic needle. The optimal arrangement of the cryoprobes, which is known to have a dramatic effect on the quality of the cryoprocedure, remains an art held by the cryosurgeon, based on the cryosurgeon's experience and “rules of thumb.” An automated computerized technique for cryosurgery planning is the subject matter of the current report, in an effort to improve the quality of cryosurgery. Method of Approach: A two-phase optimization method is proposed for this purpose, based on two previous and independent developments by this research team. Phase I is based on a bubble-packing method, previously used as an efficient method for finite elements meshing. Phase II is based on a force-field analogy method, which has proven to be robust at the expense of a typically long runtime. Results: As a proof-of-concept, results are demonstrated on a 2D case of a prostate cross-section. The major contribution of this study is to affirm that in many instances cryosurgery planning can be performed without extremely expensive simulations of bioheat transfer, achieved in Phase I. Conclusions: This new method of planning has proven to reduce planning runtime from hours to minutes, making automated planning practical in a clinical time frame. PMID:16532617

  20. Crystallogenesis in tRNA aminoacylation systems: how packing accounts for crystallization drawbacks with yeast aspartyl-tRNA synthetase

    NASA Astrophysics Data System (ADS)

    Sauter, C.; Lorber, B.; Théobald-Dietrich, A.; Giegé, R.

    2001-11-01

    Two active forms of homodimeric aspartyl-tRNA synthetase from Saccharomyces cerevisiae differing in length at their N-terminus crystallize in the same orthorhombic space group (P4 12 12) with identical cell parameters. Initial studies were hampered by the poor and anisotropic diffraction of the crystals of enzyme extracted from yeast cells. Isotropic diffraction at higher resolution was obtained when crystals were grown from an engineered protein deprived of its 70 N-terminal amino acids. The present work describes the packing contacts in crystals of the shortened protein whose structure was solved at 2.3 Å resolution. Each subunit of the enzyme develops two lattice interactions covering a surface of 670 Å 2, about 7-fold smaller than that of the interface between monomers. The smallest lattice interaction, covering 150 Å 2, brings the anticodon binding domain adjacent to the N-terminus of one monomer in contact with a loop from the active-site domain of a neighboring monomer. Modeling of the extension in the solvent channels shows that the 150 Å 2 intermolecular contact is perturbed in protein molecules possessing a floppy appendix while their second and larger 520 Å 2 contact area is unaffected. Altogether the packing organization explains the poor diffraction properties of the native enzyme crystals and the enhanced diffraction of the crystals of shortened synthetase.

  1. Co-axial association of recombinant eye lens aquaporin-0 observed in loosely packed 3D crystals.

    PubMed

    Palanivelu, Dinesh V; Kozono, David E; Engel, Andreas; Suda, Kitaru; Lustig, Ariel; Agre, Peter; Schirmer, Tilman

    2006-01-27

    Aquaporin-0 (AQP0) is the major membrane protein in vertebrate eye lenses. It has been proposed that AQP0 tetramers mediate contact between membranes of adjacent lens fiber cells, which would be consistent with the extraordinarily narrow inter-cellular spacing. We have obtained 3D crystals of recombinant bovine AQP0 that diffract to 7.0 A resolution. The crystal packing was determined by molecular replacement and shows that, within the cubic lattice, AQP0 tetramers are associated head-to-head along their 4-fold axes. Oligomeric states larger than the tetramer were also observed in solution by native gel electrophoresis and analytical ultracentrifugation methods. In the crystals, there are no direct contacts between octamers, and it can thus be inferred that crystalline order is mediated solely by the detergent belts surrounding the membrane protein. Across the tetramer-tetramer interface, extracellular loops A and C interdigitate at the center and the perimeter of the octamer, respectively. The octamer structure is compared with that of the recently determined structure of truncated ovine AQP0 derived from electron diffraction of 2D crystals. Intriguingly, also in these crystals, octamers are observed, but with significantly different relative tetramer-tetramer orientations. The interactions observed in the loosely packed 3D crystals reported here may in fact represent an in vivo association mode between AQP0 tetramers from juxtaposed membranes in the eye lens.

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

    PubMed

    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.

  3. β-Cyclodextrin dimethylformamide 12.5 hydrate: a deeper insight into β-cyclodextrin crystal packing.

    PubMed

    Granero-García, Rubén; Fabbiani, Francesca P A

    2014-06-01

    The structure of a 1:1 β-cyclodextrin-dimethylformamide hydrated complex has been determined from single-crystal X-ray diffraction data. A complete study of the structure is presented herein, including invariom refinement and interaction energy calculations. The structure has unit-cell parameters that are different from those of other β-cyclodextrin complexes crystallizing in the same space group, but exhibits the known herringbone packing type. A structural comparison of these complexes has been carried out with XPac in order to understand the origin of the differences in packing and unit-cell parameters. The results show that the differences are most likely ascribed to variations in hydration and in the hydrogen-bonded network.

  4. Force-controlled inorganic crystallization lithography.

    PubMed

    Cheng, Chao-Min; LeDuc, Philip R

    2006-09-20

    Lithography plays a key role in integrated circuits, optics, information technology, biomedical applications, catalysis, and separation technologies. However, inorganic lithography techniques remain of limited utility for applications outside of the typical foci of integrated circuit manufacturing. In this communication, we have developed a novel stamping method that applies pressure on the upper surface of the stamp to regulate the dewetting process of the inorganic buffer and the evaporation rate of the solvent in this buffer between the substrate and the surface of the stamp. We focused on generating inorganic microstructures with specific locations and also on enabling the ability to pattern gradients during the crystallization of the inorganic salts. This approach utilized a combination of lithography with bottom-up growth and assembly of inorganic crystals. This work has potential applications in a variety of fields, including studying inorganic material patterning and small-scale fabrication technology.

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

    NASA Astrophysics Data System (ADS)

    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.

  6. Thermodynamic forces in single crystals with dislocations

    NASA Astrophysics Data System (ADS)

    Van Goethem, Nicolas

    2014-06-01

    A simple model for the evolution of macroscopic dislocation regions in a single crystal is presented. This model relies on maximal dissipation principle within Kröner's geometric description of the dislocated crystal. Mathematical methods and tools from shape optimization theory provide equilibrium relations at the dislocation front, similarly to previous work achieved on damage modelling (J Comput Phys 33(16):5010-5044, 2011). The deformation state variable is the incompatible strain as related to the dislocation density tensor by a relation involving the Ricci curvature of the crystal underlying elastic metric. The time evolution of the model variables follows from a novel interpretation of the Einstein-Hilbert flow in terms of dislocation microstructure energy. This flow is interpreted as the dissipation of non-conservative dislocations, due to the climb mechanism, modelled by an average effect of mesoscopic dislocations moving normal to their glide planes by adding or removing points defects. The model equations are a fourth-order tensor parabolic equation involving the operator "incompatibility," here appearing as a tensorial counterpart of the scalar Laplacian. This work encompasses and generalizes results previously announced (C R Acad Sci Paris Ser I 349:923-927, 2011), with in addition a series of physical interpretations to give a meaning to the newly introduced concepts.

  7. Energetics of the lattice: packing elements in crystals of four-stranded intercalated cytosine-rich DNA molecules

    NASA Technical Reports Server (NTRS)

    Berger, I.; Cai, L.; Chen, L.; Rich, A.

    1997-01-01

    Condensation of single molecules from solution into crystals represents a transition between distinct energetic states. In solution, the atomic interactions within the molecule dominate. In the crystalline state, however, a set of additional interactions are formed between molecules in close contact in the lattice--these are the packing interactions. The crystal structures of d(CCCT), d(TAACCC), d(CCCAAT), and d(AACCCC) have in common a four-stranded intercalated cytosine segment, built by stacked layers of cytosine.cytosine+ (C.C+) base pairs coming from two parallel duplexes that intercalate into each other with opposite polarity. The intercalated cytosine segments in these structures are similar in their geometry, even though the sequences crystallized in different space groups. In the crystals, adenine and thymine residues of the sequences are used to build the three-dimensional crystal lattice by elaborately interacting with symmetry-related molecules. The packing elements observed provide novel insight about the copious ways in which nucleic acid molecules can interact with each other--for example, when folded in more complicated higher order structures, such as mRNA and chromatin.

  8. Energetics of the lattice: packing elements in crystals of four-stranded intercalated cytosine-rich DNA molecules

    NASA Technical Reports Server (NTRS)

    Berger, I.; Cai, L.; Chen, L.; Rich, A.

    1997-01-01

    Condensation of single molecules from solution into crystals represents a transition between distinct energetic states. In solution, the atomic interactions within the molecule dominate. In the crystalline state, however, a set of additional interactions are formed between molecules in close contact in the lattice--these are the packing interactions. The crystal structures of d(CCCT), d(TAACCC), d(CCCAAT), and d(AACCCC) have in common a four-stranded intercalated cytosine segment, built by stacked layers of cytosine.cytosine+ (C.C+) base pairs coming from two parallel duplexes that intercalate into each other with opposite polarity. The intercalated cytosine segments in these structures are similar in their geometry, even though the sequences crystallized in different space groups. In the crystals, adenine and thymine residues of the sequences are used to build the three-dimensional crystal lattice by elaborately interacting with symmetry-related molecules. The packing elements observed provide novel insight about the copious ways in which nucleic acid molecules can interact with each other--for example, when folded in more complicated higher order structures, such as mRNA and chromatin.

  9. Preliminary analysis of crystals of panicum mosaic virus (PMV) by X-ray diffraction and atomic force microscopy.

    PubMed

    Makino, Debora L; Larson, Steven B; McPherson, Alexander

    2005-02-01

    Panicum mosaic virus (PMV), a spherical virus of diameter about 300 A, has been crystallized in a form suitable for high-resolution structural analysis. The crystals were grown from 15% PEG 400 at room temperature and could be flash-frozen directly from their mother liquor. The crystals diffracted to beyond 2.7 A resolution. A data set was collected at 100 K to an effective resolution of 3.2 A [Weiss (2001), J. Appl. Cryst. 34, 130-135]. The crystals belonged to space group P2(1), with unit-cell parameters a=411.7, b=403.9, c=412.5 A, beta=89.7 degrees . Self-rotation functions and molecular replacement with tobacco necrosis virus as the probe model yielded tentative positions and orientations for the two entire virus particles comprising the asymmetric unit and implied a pseudo-face-centered cubic packing arrangement. Investigation of lightly glutaraldehyde-fixed crystals in water using atomic force microscopy confirms the packing arrangement given by the molecular-replacement result. The images also show that contaminating virions of the satellite virus to PMV, known as satellite panicum mosaic virus (SPMV), can be incorporated into the PMV crystals by insertion into the interstices between PMV virions in the lattice. This is the first observation of such a phenomenon in macromolecular crystals.

  10. Cooling crystallization experiments observed by in situ scanning force microscopy

    NASA Astrophysics Data System (ADS)

    Kipp, S.; Lacmann, R.

    1996-03-01

    The change in surface morphology of potassium nitrate and potassium alum has been studied in situ by means of scanning force microscopy. The supersaturation and undersaturation were varied in a cooling crystallizer under flow conditions. To keep the crystal growth rate of potassium nitrate low, the specific additive DOW FAX 3B2 had been used in different concentrations. The crystal growth rate of both systems could be determined and the growth and dissolution surface morphologies of potassium alum exhibited structures similar to those of microscopic measurements.

  11. Mechanisms of Topologically Close-Packed Phase Suppression in an Experimental Ruthenium-Bearing Single-Crystal Nickel-Base Superalloy at 1100 °C

    NASA Astrophysics Data System (ADS)

    Hobbs, R. A.; Zhang, L.; Rae, C. M. F.; Tin, S.

    2008-05-01

    Ruthenium (Ru) suppresses the precipitation of deleterious topologically close-packed (TCP) phases in high refractory content single-crystal Ni-base superalloys. The effectiveness of Ru as a TCP suppressant appears to be the net effect of its limited solubility in the TCP phase, a lower density of structural growth ledges for atomic attachment at the TCP/matrix interface, and destabilization of the γ' phase at elevated temperatures. These characteristics combine to limit the growth rates of precipitates and decrease the driving force for TCP precipitation, which has the secondary effect of reducing the TCP nucleation rate. The reduction in γ' volume fraction upon the addition of Ru is particularly potent due to the sensitivity of the rhenium (Re) content in the γ matrix to changes in the γ' volume fraction.

  12. Tip-to-tip interaction in the crystal packing of PACSIN 2 is important in regulating tubulation activity.

    PubMed

    Bai, Xiaoyun; Zheng, Xiaofeng

    2013-09-01

    The F-BAR domain containing proteins PACSINs are cytoplasmic phosphoproteins involved in various membrane deformations, such as actin reorganization, vesicle transport and microtubule movement. Our previous study shows that all PACSINs are composed of crescent shaped dimers with two wedge loops, and the wedge loop-mediated lateral interaction between neighboring dimers is important for protein packing and tubulation activity. Here, from the crystal packing of PACSIN 2, we observed a tight tip-to-tip interaction, in addition to the wedge loop-mediated lateral interaction. With this tip-to-tip interaction, the whole packing of PACSIN 2 shows a spiral-like assembly with a central hole from the top view. Elimination of this tip-to-tip connection inhibited the tubulation function of PACSIN 2, indicating that tip-to-tip interaction plays an important role in membrane deformation activity. Together with our previous study, we proposed a packing model for the assembly of PACSIN 2 on membrane, where the proteins are connected by tip-to-tip and wedge loop-mediated lateral interactions on the surface of membrane to generate various diameter tubules.

  13. Resonance-enhanced optical forces between coupled photonic crystal slabs.

    PubMed

    Liu, Victor; Povinelli, Michelle; Fan, Shanhui

    2009-11-23

    The behaviors of lateral and normal optical forces between coupled photonic crystal slabs are analyzed. We show that the optical force is periodic with displacement, resulting in stable and unstable equilibrium positions. Moreover, the forces are strongly enhanced by guided resonances of the coupled slabs. Such enhancement is particularly prominent near dark states of the system, and the enhancement effect is strongly dependent on the types of guided resonances involved. These structures lead to enhancement of light-induced pressure over larger areas, in a configuration that is directly accessible to externally incident, free-space optical beams.

  14. A signature of a thermodynamic phase transition in jammed granular packings: growing correlations in force space

    NASA Astrophysics Data System (ADS)

    Mailman, M.; Chakraborty, B.

    2011-07-01

    An outstanding question in the physics of jammed packings concerns the nature of the correlations that arise near the unjamming transition. In this work, we study unjamming in an assembly of frictionless grains that are hard but not infinitely rigid. We demonstrate that a static correlation function, which probes sensitivity to boundary conditions, exhibits a diverging correlation length as the packing is decompressed. An analytical expression for the length scale divergence is obtained from a scaling relation of the entropy, and shown to have logarithmic corrections to mean-field results.

  15. Piconewton force measurement using a nanometric photonic crystal diaphragm.

    PubMed

    Jo, Wonuk; Digonnet, Michel J F

    2014-08-01

    A compact force fiber sensor capable of measuring forces at the piconewton level is reported. It consists of a miniature Fabry-Perot cavity fabricated at the tip a single-mode fiber, in which the external reflector is a compliant photonic-crystal diaphragm that deflects when subjected to a force. In the laboratory environment, this sensor was able to detect a force of only ∼4  pN generated by the radiation pressure of a laser beam. Its measured minimum detectable force (MDF) at 3 kHz was as weak as 1.3  pN/√Hz. In a quiet environment, the measured noise was ∼16 times lower, and the MDF predicted to be ∼76  fN/√Hz.

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

    NASA Astrophysics Data System (ADS)

    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.

  17. Mechanisms of protein and virus crystal growth: An atomic force microscopy study of Canavalin crystallization

    SciTech Connect

    Land, T.A.; De Yoreo, J.J.; Malkin, A.J.; Kutznesov, Y.G.; McPherson, A.

    1995-03-10

    The evolution of surface morphology and step dynamics during growth of single crystals of the protein Canavalin and of the cubic satellite tobacco mosaic virus crystals (STMV) have been investigated by in situ atomic force microscopy. These two crystals were observed to grow by very different mechanisms. Growth of Canavalin occurs on complex vicinal hillocks formed by multiple, independently acting screw dislocations. Small cluster were observed on the terraces. STMV on the other hand, was observed to grow by 2D nucleation of islands. No dislocations were found on the crystal. The results are used to determine the growth mechanisms and estimate fundamental materials parameters. The images also illustrate the important mechanism of defect incorporation and provide insight to the processes that limit the growth rate and uniformity of these crystals.

  18. Year-Round Pack Ice in the Weddell Sea, Antarctica: Response and Sensitivity to Atmospheric and Oceanic Forcing

    NASA Technical Reports Server (NTRS)

    Geiger, Cathleen A.; Ackley, Stephen F.; Hibler, William D., III

    1997-01-01

    Using a dynamic-thermodynamic numerical sea-ice model, external oceanic and atmospheric forcings on sea ice in the Weddell Sea are examined to identify physical processes associated with the seasonal cycle of pack ice, and to identify further the parameters that coupled models need to consider in predicting the response of the pack ice to climate and ocean-circulation changes. In agreement with earlier studies, the primary influence on the winter ice-edge maximum extent is air temperature. Ocean heat flux has more impact on the minimum-ice-edge extent and in reducing pack-ice thickness, especially in the eastern-Weddell Sea. Low relative humidity enhances ice growth in thin ice and open-water regions, producing a more realistic ice edge along the coastal areas of the western-Weddell Sea where dry continental air has an impact. The modeled extent of the Weddell summer pack is equally sensitive to ocean heat flux and atmospheric relative humidity variations with the more dynamic responses being from the atmosphere. Since the atmospheric regime in the eastern Weddell is dominated by marine intrusions from lower latitudes, with high humidity already, it is unlikely that either the moisture trans- port could be further raised or that it could be significantly lowered because of its distance from the continent (the lower humidity source). Ocean heat-transport variability is shown to lead to overall ice thinning in the model response and is a known feature of the actual system, as evidenced by the occurrence of the Weddell Polynya in the mid 1970s.

  19. New molecular packing in a crystal of pseudoazurin from Alcaligenes faecalis: a double-helical arrangement of blue copper.

    PubMed

    Fukuda, Yohta; Mizohata, Eiichi; Inoue, Tsuyoshi

    2017-03-01

    Pseudoazurin from the denitrifying bacterium Alcaligenes faecalis (AfPAz) is a blue copper protein and functions as an electron donor to copper-containing nitrite reductase (CuNIR). Conventionally, AfPAz has been crystallized using highly concentrated ammonium sulfate as a precipitant. Here, a needle-like crystal of AfPAz grown in a solution containing a macromolecular precipitant, polyethylene glycol 8000 (PEG 8000), is reported. The crystal belonged to space group P61, with unit-cell parameters a = b = 68.7, c = 94.2 Å. The structure has been determined and refined at 2.6 Å resolution. The asymmetric unit contained two AfPAz molecules contacting each other on negatively charged surfaces. The molecular packing of the crystal showed a right-handed double-helical arrangement of AfPAz molecules and hence of blue copper sites. This structure provides insight into the excluded-volume effect of PEG and the manner of assembly of AfPAz.

  20. A study of drag forces on attached colloidal particles in a packed bed using multiscale numerical modeling

    NASA Astrophysics Data System (ADS)

    Mirsaeidi-Farahani, A.; Thompson, K. E.

    2012-12-01

    Fluid and particle transport in granular porous media is significant in many areas of science and technology including ground-water transport, oil production, and granular filtration processes. Using numerical methods to solve flow equations in disordered porous domain has significantly improved our understanding of the flow behavior in complex materials. However, significant limitations in applying numerical techniques still exist. Issues include computational limitations, generating accurate numerical meshes of complex structures, and the impact of numerical approximations on the accuracy of simulations. In the context of colloid and nanoparticle transport, modeling the hydrodynamics near these particles is difficult because of the large discrepancy in length scale between the small particles and the pore dimensions. In this work, we use multiscale finite-element method (FEM) simulations to study the hydrodynamic forces on small particles which are attached to the surface of spherical grains in a packed bed. Quantifying these forces is important for combining with electrostatic force computations for the modeling of colloidal transport behavior. Particles, which are 100 times smaller in size than the average size of constituent grains of a granular packed bed, are studied in this work, and we continue to reduce their size. A novel meshing algorithm is used to resolve the colloidal particles at a mesh resolution appropriate for their size, while at the same time transitioning to a coarser mesh that fills the surrounding pore space. Validation of the computations are performed by comparing to known solutions in idealized geometries (simple & body-centered cubic arrays and particles in a cylindrical tube) prior to working with more realistic porous media. Results presented here include an analysis of the distribution of hydrodynamic forces experienced by attached colloidal particles in a random packing of spheres. Visualization of local structure, pressure, and

  1. Single molecule force spectroscopy reveals critical roles of hydrophobic core packing in determining the mechanical stability of protein GB1.

    PubMed

    Bu, Tianjia; Wang, Hui-Chuan Eileen; Li, Hongbin

    2012-08-21

    Understanding molecular determinants of protein mechanical stability is important not only for elucidating how elastomeric proteins are designed and functioning in biological systems but also for designing protein building blocks with defined nanomechanical properties for constructing novel biomaterials. GB1 is a small α/β protein and exhibits significant mechanical stability. It is thought that the shear topology of GB1 plays an important role in determining its mechanical stability. Here, we combine single molecule atomic force microscopy and protein engineering techniques to investigate the effect of side chain reduction and hydrophobic core packing on the mechanical stability of GB1. We engineered seven point mutants and carried out mechanical φ-value analysis of the mechanical unfolding of GB1. We found that three mutations, which are across the surfaces of two subdomains that are to be sheared by the applied stretching force, in the hydrophobic core (F30L, Y45L, and F52L) result in significant decrease in mechanical unfolding force of GB1. The mechanical unfolding force of these mutants drop by 50-90 pN compared with wild-type GB1, which unfolds at around 180 pN at a pulling speed of 400 nm/s. These results indicate that hydrophobic core packing plays an important role in determining the mechanical stability of GB1 and suggest that optimizing hydrophobic interactions across the surfaces that are to be sheared will likely be an efficient method to enhance the mechanical stability of GB1 and GB1 homologues.

  2. Six-membered metalla-coronands. synthesis and crystal packing: columns, compartments, and 3D-networks.

    PubMed

    Saalfrank, Rolf W; Deutscher, Christian; Sperner, Stefan; Nakajima, Takayuki; Ako, Ayuk M; Uller, Eveline; Hampel, Frank; Heinemann, Frank W

    2004-07-12

    Reaction of various N-substituted diethanolamines H(2)L(3) (4) with calcium hydride and iron(III) chloride leads to the self-assembly of six-membered ferric wheels [Fe(6)X(6)(L(3))(6)] (5). Principally, all the iron coronands are isostructural; however, they differ fundamentally with respect to their crystal packing. Exemplarily, this is discussed for selected members of the space groups R, P, P2(1)/c, P2(1)/n, C2/c, and P. Depending on the nature of their sidearms, the ferric wheels create various substructures. For instance, the ferric wheels 5a-i of space group R or P are piled in parallel in cylindrical columns, which are surrounded by six parallel columns alternately dislocated by (1)/(3)c and (2)/(3)c against the central one. Pronounced van der Waals interactions give rise to compartmentation and incarceration of guest molecules as seen for 5e,g. However, in 5h strong pi-pi interactions create a three-dimensional scaffold. The most significant difference of the ferric wheels 5j-p of space groups P2(1)/c, P2(1)/n, and C2/c is that these ferric wheels are arranged in parallel in two orientations. They differ mainly only by the included angle of the two groups of parallel wheels. In the case of 5l, molecular chains are formed in the crystal due to pi-pi interactions. The ferric wheels 5q-y of space group P are packed in the crystal most simply, with all the ferric wheels piled in parallel.

  3. Molecular packing and magnetic properties of lithium naphthalocyanine crystals: hollow channels enabling permeability and paramagnetic sensitivity to molecular oxygen

    PubMed Central

    Pandian, Ramasamy P.; Dolgos, Michelle; Marginean, Camelia; Woodward, Patrick M.; Hammel, P. Chris; Manoharan, Periakaruppan T.; Kuppusamy, Periannan

    2009-01-01

    The synthesis, structural framework, magnetic and oxygen-sensing properties of a lithium naphthalocyanine (LiNc) radical probe are presented. LiNc was synthesized in the form of a microcrystalline powder using a chemical method and characterized by electron paramagnetic resonance (EPR) spectroscopy, magnetic susceptibility, powder X-ray diffraction analysis, and mass spectrometry. X-Ray powder diffraction studies revealed a structural framework that possesses long, hollow channels running parallel to the packing direction. The channels measured approximately 5.0 × 5.4 Å2 in the two-dimensional plane perpendicular to the length of the channel, enabling diffusion of oxygen molecules (2.9 × 3.9 Å2) through the channel. The powdered LiNc exhibited a single, sharp EPR line under anoxic conditions, with a peak-to-peak linewidth of 630 mG at room temperature. The linewidth was sensitive to surrounding molecular oxygen, showing a linear increase in pO2 with an oxygen sensitivity of 31.2 mG per mmHg. The LiNc microcrystals can be further prepared as nano-sized crystals without the loss of its high oxygen-sensing properties. The thermal variation of the magnetic properties of LiNc, such as the EPR linewidth, EPR intensity and magnetic susceptibility revealed the existence of two different temperature regimes of magnetic coupling and hence differing columnar packing, both being one-dimensional antiferromagnetic chains but with differing magnitudes of exchange coupling constants. At a temperature of ∼50 K, LiNc crystals undergo a reversible phase transition. The high degree of oxygen-sensitivity of micro- and nano-sized crystals of LiNc, combined with excellent stability, should enable precise and accurate measurements of oxygen concentration in biological systems using EPR spectroscopy. PMID:19809598

  4. Formation of closely packed Cu nanoparticle films by capillary immersion force for preparing low-resistivity Cu films at low temperature

    NASA Astrophysics Data System (ADS)

    Yokoyama, Shun; Motomiya, Kenichi; Takahashi, Hideyuki; Tohji, Kazuyuki

    2016-11-01

    Films made of closely packed Cu nanoparticles (NPs) were obtained by drop casting Cu NP inks. The capillary immersion force exerted during the drying of the inks caused the Cu NPs to attract each other, resulting in closely packed Cu NP films. The apparent density of the films was found to depend on the type of solvent in the ink because the capillary immersion force is affected by the solvent surface tension and dispersibility of Cu NPs in the solvent. The closely packed particulate structure facilitated the sintering of Cu NPs even at low temperature, leading to low-resistivity Cu films. The sintering was also enhanced with a decrease in the size of NPs used. We demonstrated that a closely packed particulate structure using Cu NPs with a mean diameter 61.7 nm showed lower resistivity (7.6 μΩ cm) than a traditionally made Cu NP film (162 μΩ cm) after heat treatment.

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

    PubMed

    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.

  6. Observation of steric hindrance effect controlling crystal packing structures and physical properties in three new isomeric nitronyl nitroxide radicals

    NASA Astrophysics Data System (ADS)

    Zhao, Hai-Rong; Sun, Jia-Sen; Sui, Yun-Xia; Ren, Xiao-Ming; Yao, Bin-Qian; Shen, Lin-Jiang; Meng, Qing-Jin

    2009-07-01

    Three isomeric nitronyl nitroxide radical compounds, 2-[ n-( N-benzyl)pyridinium]-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide bromide ( n = 2, 3 and 4 for 1, 2 and 3, respectively), have been synthesized and structurally characterized. The influence of steric hindrance on the molecular packing structures and physical properties has been observed. In the radical 1, such steric hindrance leads to a folding conformation of the imidazoline and benzene rings and the intramolecular C-H…π interaction between the methyl group and the benzene ring. There is no such effect in 2 and 3. In crystal of 2, there are the intermolecular C-H…π between methyl groups and benzene ring and intermolecular π…π stacking interaction between pyridine and benzene rings. Crystal of 2 with a chiral space group P2 12 12 1 shows the SHG response about 0.4 times as that of urea. In crystal of 3, there are three symmetry-independent radical molecules, which form an unusually six-membered supramolecular ring via intermolecular O…π interactions. For the solid sample of 3, the X-band EPR exhibits an axially symmetric signal and magnetic susceptibility data suggest intermolecular antiferromagnetic (AFM) coupling interactions and very weak intermolecular ferromagnetic (FM) coupling interactions which is more likely caused by magnetic anisotropy, while measurements of both 1 and 2 show isotropic X-band EPR signals and simple Currie-Weiss magnetic behavior.

  7. A master equation for the probability distribution functions of forces in soft particle packings.

    PubMed

    Saitoh, Kuniyasu; Magnanimo, Vanessa; Luding, Stefan

    2015-02-04

    We study the microscopic response of force-chain networks in jammed soft particles to quasi-static isotropic (de)compressions by molecular dynamics simulations. We show that not only contacts but also interparticle gaps between the nearest neighbors must be considered for the stochastic evolution of the probability distribution functions (PDFs) of forces, where the mutual exchange of contacts and interparticle gaps, i.e. opening and closing contacts, are also crucial to the incremental system behavior. By numerically determining the transition rates for all changes of contacts and gaps, we formulate a Master equation for the PDFs of forces, where the insight one gets from the transition rates is striking: the mean change of forces reflects non-affine system responses, while their fluctuations obey uncorrelated Gaussian statistics. In contrast, interparticle gaps react mostly affine in average, but imply multi-scale correlations according to a much wider stable distribution function.

  8. Role of hydrogen bonds in molecular packing of photoreactive crystals: templating photodimerization of protonated stilbazoles in crystalline state with a combination of water molecules and chloride ions.

    PubMed

    Mondal, Barnali; Zhang, Tingting; Prabhakar, Rajeev; Captain, Burjor; Ramamurthy, V

    2014-11-01

    A difference in photobehavior and molecular packing between hydrated and anhydrous crystals of protonated trans-stilbazoles has been identified. While stilbazoles are not photoreactive in the crystalline state, upon protonation with HCl in the solid state they dimerized to a single dimer (anti-head-tail) when exposed to UV light. In these photoreactive crystals the protonated stilbazole molecules are arranged in a ladder-like format with the rungs made up of water molecules and chloride ions. A combination of water and chloride ion holds the protonated trans-stilbazoles through either N-HO or N-HCl(-) interactions. Anhydrous protonated stilbazole crystals prepared by heating the 'wet' crystals under reduced pressure were inert upon exposure to UV light. As per X-ray crystal structure analyses these light stable crystals did not contain water molecules in their lattice. The current investigation has established that water molecules are essential for photodimerization of crystalline protonated trans-stilbazoles. To compare the reactivity of protonated trans-stilbazoles with that of protonated cis-stilbazoles, photoreactivity and packing arrangement of cis-4-iodo stilbazole·HCl salt was examined. This molecule in the crystalline state only isomerized to the trans isomer and did not dimerize. Thus, while the trans isomer dimerized and did not isomerize, the cis isomer only isomerized and did not dimerize in the crystalline state. To probe the role of cationπ interaction in the packing of protonated trans-stilbazoles, energies of various types of packing in the gas phase were estimated by MP-2 calculations and cationπ interaction was found to be unimportant in the packing of protonated trans-stilbazole crystals investigated here.

  9. Normal and lateral forces between lipid covered solids in solution: correlation with layer packing and structure.

    PubMed Central

    Grant, L M; Tiberg, F

    2002-01-01

    We report on the normal and lateral forces between controlled-density mono- and bilayers of phospholipid co-adsorbed onto hydrophobic and hydrophilic solid supports, respectively. Interactions between 1,2-dioleoyl-sn-glycero-3-phosphocholine layers were measured using an atomic force microscope. Notable features of the normal force curves (barrier heights and widths) were found to correlate with the thickness and density of the supported lipid layers. The friction and normal force curves were also found interrelated. Thus, very low friction values were measured as long as the supported layer(s) resisted the normal pressure of the tip. However, as the applied load exceeded the critical value needed for puncturing the layers, the friction jumped to values close to those recorded between bare surfaces. The lipid layers were self-healing between measurements, but a significant hysteresis was observed in the force curves measured on approach and retraction, respectively. The study shows the potential of using atomic force microscopy for lipid layer characterization both with respect to structure and interactions. It further shows the strong lubricating effect of adsorbed lipid layers and how this varies with surface density of lipids. The findings may have important implications for the issue of joint lubrication. PMID:11867453

  10. Crystal Structures of IAPP Amyloidogenic Segments Reveal a Novel Packing Motif of Out-of-Register Beta Sheets.

    PubMed

    Soriaga, Angela B; Sangwan, Smriti; Macdonald, Ramsay; Sawaya, Michael R; Eisenberg, David

    2016-07-07

    Structural studies of amyloidogenic segments by X-ray crystallography have revealed a novel packing motif, consisting of out-of-register β sheets, which may constitute one of the toxic species in aggregation related diseases. Here we sought to determine the presence of such a motif in islet amyloid polypeptide (IAPP), whose amyloidogenic properties are associated with type 2 diabetes. We determined four new crystal structures of segments within IAPP, all forming steric zippers. Most interestingly, one of the segments in the fibril core of IAPP forms an out-of-register steric zipper. Analysis of this structure reveals several commonalities with previously solved out-of-register fibrils. Our results provide additional evidence of out-of-register β sheets as a common structural motif in amyloid aggregates.

  11. Mesosized Crystal-like Structure of Hexagonally Packed Hollow Hoops by Solution Self-Assembly of Diblock Copolymers

    NASA Astrophysics Data System (ADS)

    Zhang, Lifeng; Bartels, Carl; Yu, Yisong; Shen, Hongwei; Eisenberg, Adi

    1997-12-01

    Mesosize crystal-like aggregates with an internal structure of hexagonally packed hollow hoops (HHH) in a polystyrene matrix have been prepared in solution by self-assembly of asymmetric polystyrene-b-poly(acrylic acid) diblock copolymers. Most of the aggregates are cylindrical or in the shape of truncated cones. The external surface of the aggregates and the internal surface of the hollow hoops are lines with short poly(acrylic acid) chains. The hoop morphology is imposed because the end-capping energy of a rod on this size scale is more important than the curvature energy. A strong interdependence between the external shape and the internal structure in these mesosize particles is demonstrated.

  12. Bioremediation of crystal violet using air bubble bioreactor packed with Pseudomonas aeruginosa.

    PubMed

    El-Naggar, Manal A; El-Aasar, Samy A; Barakat, Khlood I

    2004-12-01

    Seven water and sediment samples were collected and tested for decolorizing crystal violet. Pseudomonas aeruginosa was the most effective isolate for dye decolorization. The LC(50) of the crystal violet (115 mg/l) was measured using Artemia salina as a biomarker. The effect of different heavy metals on crystal violet decolorization was investigated. Cd(2+) and Fe(3+) ions showed marginal enhancement of the decolorization process, the rate was 1.35 mg/l/h compared to 1.25 mg/l/h for the control. Phenol and m-cresol showed no effect on crystal violet decolorization, meanwhile p-cresol and p-nitrophenol reduced the decolorization rate to 1.07 and 0.01 mg/l/h, respectively. P. aeruginosa cells were immobilized by entrapment in agar-alginate beads. The beads were cultivated and reused in Erlenmeyer flask and in an air bubble column bioreactor and they enhanced the crystal violet decolorization rate to 3.33 and 7.5 mg/l/h, respectively.

  13. Atomic force microscopy of lead iodide crystal surfaces

    NASA Astrophysics Data System (ADS)

    George, M. A.; Azoulay, M.; Jayatirtha, H. N.; Biao, Y.; Burger, A.; Collins, W. E.; Silberman, E.

    1994-03-01

    Atomic force microscopy (AFM) was used to characterize the surface of lead iodide crystals. The high vapor pressure of lead iodide prohibits the use of traditional high resolution surface study techniques that require high vacuum conditions. AFM was used to image numerous insulating surface in various ambients, with very little sample preparation techniques needed. Freshly cleaved and modified surfaces, including, chemical and vacuum etched, and air aged surfaces, were examined. Both intrinsic and induced defects were imaged with high resolution. The results were compared to a similar AFM study of mercuric iodide surfaces and it was found that, at ambient conditions, lead iodide is significantly more stable than mercuric iodide.

  14. Pack Artillery, A Bibliography

    DTIC Science & Technology

    1980-03-01

    Washington, DC: American Untv Soro, 1965. UC300 Parrino , Michael Francis. An Introduction to Pack P3 Transport and Pack Artillery; the Role of the Mule...Field for the Territorial Force," JORAj 37:15, 1910. " Parrino , Michael F. "Development of Pack Artillery and Its Signi- ficance in Modern Warfare

  15. Dislocation Dynamics Simulations of Junctions in Hexagonal Close-Packed Crystals

    SciTech Connect

    Wu, C; Aubry, S; Chung, P; Arsenlis, A

    2011-12-05

    The formation and strength of dislocations in the hexagonal closed packed material beryllium are studied through dislocation junctions and the critical stress required to break them. Dislocation dynamics calculations (using the code ParaDiS) of junction maps are compared to an analytical line tension approximation in order to validate our model. Results show that the two models agree very well. Also the critical shear stress necessary to break 30{sup o} - 30{sup o} and 30{sup o} - 90{sup o} dislocation junctions is computed numerically. Yield surfaces are mapped out for these junctions to describe their stability regions as function of resolved shear stresses on the glide planes. The example of two non-coplanar binary dislocation junctions with slip planes [2-1-10] (01-10) and [-12-10] (0001) corresponding to a prismatic and basal slip respectively is chosen to verify and validate our implementation.

  16. New opportunities in crystal engineering--the role of atomic force microscopy in studies of molecular crystals.

    PubMed

    Chow, Ernest H H; Bučar, Dejan-Krešimir; Jones, William

    2012-09-25

    Here, we highlight recent research involving atomic force microscopy investigations of molecular crystals, and focus particularly on the latest relevant advances in our knowledge of crystal-growth mechanisms and structure-property relationships in organic crystals. This brief survey features the importance of incorporating AFM into solid-state research as an essential tool for the informed design and construction of crystalline materials.

  17. Conformational stability and crystal packing: polymorphism in Neurospora crassa CAT-3.

    PubMed

    Zárate-Romero, Andrés; Stojanoff, Vivian; Rojas-Trejo, Sonia Patricia; Hansberg, Wilhelm; Rudiño-Piñera, Enrique

    2013-07-01

    Polymorphism is frequently observed from different crystallization conditions. In proteins, the effect on conformational variability is poorly documented, with only a few reported examples. Here, three polymorphic crystal structures determined for a large-subunit catalase, CAT-3 from Neurospora crassa, are reported. Two of them belonged to new space groups, P1 and P43212, and a third structure belonged to the same space group, P212121, as the previously deposited 2.3 Å resolution structure (PDB entry 3ej6), but had a higher resolution (1.95 Å). Comparisons between these polymorphic structures highlight the conformational stability of tetrameric CAT-3 and reveal a distortion in the tetrameric structure that has not previously been described.

  18. Conformational stability and crystal packing: polymorphism in Neurospora crassa CAT-3

    PubMed Central

    Zárate-Romero, Andrés; Stojanoff, Vivian; Rojas-Trejo, Sonia Patricia; Hansberg, Wilhelm; Rudiño-Piñera, Enrique

    2013-01-01

    Polymorphism is frequently observed from different crystallization conditions. In proteins, the effect on conformational variability is poorly documented, with only a few reported examples. Here, three polymorphic crystal structures determined for a large-subunit catalase, CAT-3 from Neurospora crassa, are reported. Two of them belonged to new space groups, P1 and P43212, and a third structure belonged to the same space group, P212121, as the previously deposited 2.3 Å resolution structure (PDB entry 3ej6), but had a higher resolution (1.95 Å). Comparisons between these polymorphic structures highlight the conformational stability of tetrameric CAT-3 and reveal a distortion in the tetrameric structure that has not previously been described. PMID:23832201

  19. Mode conversion enables optical pulling force in photonic crystal waveguides

    NASA Astrophysics Data System (ADS)

    Zhu, Tongtong; Novitsky, Andrey; Cao, Yongyin; Mahdy, M. R. C.; Wang, Lin; Sun, Fangkui; Jiang, Zehui; Ding, Weiqiang

    2017-08-01

    We propose a robust scheme to achieve optical pulling force using the guiding modes supported in a hollow core double-mode photonic crystal waveguide instead of the structured optical beams in free space investigated earlier. The waveguide under consideration supports both the 0th order mode with a larger forward momentum and the 1st order mode with a smaller forward momentum. When the 1st order mode is launched, the scattering by the object inside the waveguide results in the conversion from the 1st order mode to the 0th order mode, thus creating the optical pulling force according to the conservation of linear momentum. We present the quantitative agreement between the results derived from the mode conversion analysis and those from rigorous simulation using the finite-difference in the time-domain numerical method. Importantly, the optical pulling scheme presented here is robust and broadband with naturally occurred lateral equilibriums and has a long manipulation range. Flexibilities of the current configuration make it valuable for the optical force tailoring and optical manipulation operation, especially in microfluidic channel systems.

  20. Transferability of coarse-grained force field for nCB liquid crystal systems.

    PubMed

    Zhang, Jianguo; Guo, Hongxia

    2014-05-01

    In this paper, the transferability of the coarse-grained (CG) force field originally developed for the liquid crystal (LC) molecule 5CB ( Zhang et al. J. Phys. Chem. B 2012 , 116 , 2075 - 2089 ) was investigated by its homologues 6CB and 8CB molecules. Note that, to construct the 5CB CG force field, we combined the structure-based and thermodynamic quantities-based methods and at the same time attempted to use several fragment molecular systems to derive the CG nonbonded interaction parameters. The resultant 5CB CG force field exhibits a good transferability to some extent. For example, not only the experimental densities, the local packing of atom groups, and the antiparallel arrangements of nearest neighboring molecules, but also the unique LC mesophases as well as the nematic-isotropic phase transition temperatures of 6CB and 8CB were reproduced. Meanwhile, the limitations of this 5CB CG force field were also observed, such as the phase transition from nematic to smectic was postponed to the lower temperature and the resulting smectic phase structure is single-layer-like instead of partially interdigitated bilayer-like as observed in underlying atomistic model. Apparently, more attention should be paid when applying a CG force field to the state point which is quite different from which the force field is explicitly parametrized for. The origin of the above limitations can be potentially traced back to the inherent simplifications and some approximations often adopted in the creation process of CG force field, for example, choosing symmetric CG potentials which do not explicitly include electrostatic interactions and are parametrized by reproducing the target properties of the specific nematic 5CB phase at 300 K and 1 atm, as well as using soft nonbonded potential and excluding torsion barriers. Moreover, although by construction this CG force field could inevitably incorporate both thermodynamic and local structural information on the nematic 5CB phase, the

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

    PubMed

    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.

  2. Effect of filler particles morphology of resin-composites on cavity packing force for repeated condensation.

    PubMed

    Kaleem, Muhammad; Watts, David C

    2017-03-29

    Effect of variation in morphology and size of filler particles, temperature and increase in condensation speed on packability of resincomposites was investigated. Eight experimental light-cured resin-composites (RZDn series) were tested. Each material was placed in a cylindrical mould at 26 or 32ºC. A flat-ended stainless-steel probe (φ=6 mm) was mechanically lowered with two different speeds 2 and 8 mm/s onto and into at the surface of the unset sample until a compressive force of 1 N was reached. This was repeated for five cycles, and from each cycle Fp was calculated. All spherical and irregular filler particle resin-composites showed a decrease in Fp with increase in number of compressions. Increase in temperature also decreased Fp, but this effect was not very prominent in the case of irregular filler resin-composites. Filler particle morphology, increase in temperature and compression cycle speed has a prominent effect on packability of resin-composites.

  3. Crystal packing in three related disaccharides: precursors to heparan sulfate oligosaccharides

    PubMed Central

    Gainsford, Graeme J.; Schwörer, Ralf; Tyler, Peter C.; Zubkova, Olga V.

    2015-01-01

    The three title compounds form part of a set of important precursor dissacharides which lead to novel therapeutics, in particular for Alzheimer’s disease. All three crystallize as poorly diffracting crystals with one independent mol­ecule in the asymmetric unit. Two of them are isostructural: 4-meth­oxy­phenyl 4-O-[6-O-acetyl-2-azido-3-O-benzyl-2-de­oxy-4-O-(9-fluor­en­yl­methyl­oxycarbon­yl)-α-d-gluco­pyranos­yl]-2-O-benzoyl-3-O-benzyl-6-O-chloro­acetyl-α-l-ido­pyran­oside, C59H56ClN3O16, (I), the ido-relative of a reported gluco-disaccharide [Gainsford et al., 2013 ▸). Acta Cryst. C69, 679–682] and 4-meth­oxy­phenyl 4-O-[6-O-acetyl-2-azido-3-O-benzyl-2-de­oxy-4-O-(9-fluorenyl­methyl­oxycarbon­yl)-α-d-gluco­pyranos­yl]-2-O-benzoyl-3-O-benzyl-6-O-meth­oxy­acetyl-α-l-ido­pyran­oside, C60H59N3O17, (II). Both exhibit similar conformational disorder of pendant groups. The third compound 4-meth­oxy­phenyl 4-O-[6-O-acetyl-2-azido-3,4-di-O-benzyl-2-de­oxy-α-d-gluco­pyranos­yl]-2-O-benzoyl-3-O-benzyl-6-O-meth­oxy­oacetyl-β-d-gluco­pyran­oside, C52H55N3O15, (III), illustrates that a slightly larger set of weak inter­molecular inter­actions can result in a less disordered mol­ecular arrangement. The mol­ecules are bound by weak C—H⋯O(ether) hydrogen bonds in (I) and (II), augmented by C—H⋯π inter­actions in (III). The absolute configurations were determined, although at varying levels of significance from the limited observed data. PMID:26090127

  4. In-situ detection of growth striations by crystallization electromotive force measurement during Czochralski crystal growth

    NASA Astrophysics Data System (ADS)

    Zhu, Yunzhong; Ma, Decai; Long, Siwei; Tang, Feng; Lin, Shaopeng; Wang, Biao

    2017-10-01

    Growth striations, as macrodefects of crystalline materials, are mainly caused by convection and temperature fluctuations in growth interface. For decades, striations have been widely regarded as an inherent problem. Even in the well-developed Czochralski method, the striation formation process is difficult to inspect in situ. In view of this long-standing issue, after systematically studying the temperature, weight, and output power during crystal growth and numerically modeling the growth process, we found that the regularity of the growth interface electromotive force (GEMF) is related to the distribution of striations. Furthermore, the GEMF quantifies interface fluctuations (711.2 s, 16.6 μm) and thermal hysteresis (107 s), presenting finer details than those provided by a thermocouple and a load cell. In this paper, GEMF is found to be an outstanding choice for monitoring the crystal growth status in real time. As an additional feedback, a new automatic control method could be developed for reducing growth striations and promoting crystal quality.

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

    PubMed

    Miller, Nichole Cates; Cho, Eunkyung; Junk, Matthias J N; Gysel, Roman; Risko, Chad; Kim, Dongwook; Sweetnam, Sean; Miller, Chad E; Richter, Lee J; Kline, R Joseph; Heeney, Martin; McCulloch, Iain; Amassian, Aram; Acevedo-Feliz, Daniel; Knox, Christopher; Hansen, Michael Ryan; Dudenko, Dmytro; Chmelka, Bradley F; Toney, Michael F; Brédas, Jean-Luc; McGehee, Michael D

    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.

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

    SciTech Connect

    McMahon, Roisin M. Coinçon, Mathieu; Tay, Stephanie; Heras, Begoña; Morton, Craig J.; Scanlon, Martin J.; Martin, Jennifer L.

    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.

  7. Influence of quadrupolar interactions on the crystal packing of organic compounds: the pentafluorophenyl ester of a tricyclic α,β-unsaturated-γ-amino acid

    NASA Astrophysics Data System (ADS)

    Mann, Enrique; Mahía, José; Maestro, Miguel A.; Herradón, Bernardo

    2002-10-01

    The single crystal X-ray diffraction structure of (-)-pentafluorophenyl( Z, S, S)-2-(6-oxo-1,3,4,6,11,11a-hexahydro-2 H-pyrido[1,2- b]isoquinolin-11-yliden)acetate ( 1) is reported. We have found that the crystal packing of the α,β-unsaturated-γ-amino acid derivative 1 is mainly determined by the interaction between the two aromatic rings, namely the benzenic type and the pentafluorinated ring. The crystal packing of 1 shows a herringbone (zig-zag) structure, that is quite typical of aromatic compound with intermolecular arene-arene interactions. The benzenic and the fluorinated phenyl rings in 1 are in a matched face-to-face arrangement. The origin of this interaction can be ascribed to a favourably quadrupolar interaction between both types of aromatic ring. The results reported in the present paper indicate that the pentafluorophenyl ester functionality can be a useful building block in crystal engineering.

  8. The advancement and structure of growth steps on thaumatin crystals visualized by atomic force microscopy at molecular resolution

    NASA Astrophysics Data System (ADS)

    Kuznetsov, Yurii G.; Konnert, John; Malkin, Alexander J.; McPherson, Alexander

    1999-10-01

    Using in situ atomic force microscopy (AFM) we have recorded the incorporation, on the nanometer scale, of molecules into growth steps of macromolecular crystals grown from solution. From these investigations we were able to deduce the fine structure of the growth step edges and the surface layer of the {101} faces of tetragonal thaumatin crystals. Although the height of the growth step corresponds to unit cells of eight molecules, step advancement occurs by ordered addition of individual protein molecules rather than molecular clusters. Advancement of growth steps in specific directions, which is anisotropic, occurs by formation of one-dimensional nuclei of varying sizes which generate subkinks on the step edges. Incorporation of molecules into kinks occurs through the same kind of nucleation process. The crystal surface as a whole is created from molecular chains parallel with the surface. Models for the packing of protein molecules comprising the surface layer, the structure of the step edges, and the structure of two-dimensional nuclei were developed which are consistent with the AFM images.

  9. The role of the "Casimir force analogue" at the microscopic processes of crystallization and melting

    NASA Astrophysics Data System (ADS)

    Chuvildeev, V. N.; Semenycheva, A. V.

    2016-10-01

    Melting (crystallization), a phase transition from a crystalline solid to a liquid state, is a common phenomenon in nature. We suggest a new factor, "the Casimir force analogue", to describe mechanisms of melting and crystallization. The Casimir force analogue is a force occurring between the surfaces of solid and liquid phases of metals caused by different energy density of phonons of these phases. It explains abrupt changes in geometry and thermodynamic parameters at a melting point. "The Casimir force analogue" helps to estimate latent melting heat and to gain an insight into a solid-liquid transition problem.

  10. Image forces on 3d dislocation structures in crystals of finite volume

    SciTech Connect

    El-Azab, A.

    1999-07-01

    The present work aims at studying the image stress and image Peach-Koehler force fields for three-dimensional dislocation configurations in a single crystal of finite volume. It is shown that the image stress field is significant within the entire crystal volume, and that the image Peach-Koehler force can be of the same order of magnitude as the direct interaction force calculated from the infinite domain solution. The results demonstrate that image stress gives rise to long-range interaction forces that are important in meso-scale dynamics of dislocation structures.

  11. Image Forces on 3-D Dislocation Structures in Crystals of Finite Volume

    SciTech Connect

    El-Azab, Anter ); V.V. Bulatov

    1999-01-01

    The present work aims at studying the image stress and image Peach-Koehler force fields for three-dimensional dislocation configurations in a single crystal of finite volume. It is shown that the image stress field is significant within the entire crystal volume, and that the image Peach-Koehler force can be of the same order of magnitude as the direct interaction force calculated from the infinite domain solution. The results demonstrate that image stress gives rise to long-range interaction forces that are important in meso-scale dynamics of dislocation structures.

  12. Packed-Tower Aeration Study to Remove Volatile Organics from Groundwater at Wurtsmith Air Force Base, Michigan.

    DTIC Science & Technology

    1985-06-01

    Materials at a Water Irrigation Rate of 3.56 ft3/min/ft 2 as a Function of Air Flow Rate .......... ........................ 72 23 Comparison of Benzene...the pilot system for any of the packings at the maximum well pump capacity of 85 gpm (322 L/min), three water rates spanning the range from...Well A only. This limited the maximum water -loading rate in the packed tower to the pumping capacity of the Well A pump . Although the pump was rated at

  13. Mechanisms of protein and virus crystal growth: An atomic force microscopy study of canavalin and STMV crystallization

    SciTech Connect

    Land, T.A.; De Yoreo, J.J.; Malkin, A.J.; Kutznesov, Yu.G.; McPherson, A.

    1996-05-01

    The evolution of surface morphology and step dynamics during growth of rhombohedral crystals of the protein canavalin and crystals of the cubic satellite tobacco mosaic virus (STMV) have been investigated for the first time by in situ atomic force microscopy. These two crystals were observed to grow by very different mechanisms. Growth of canavalin occurs on complex vicinal hillocks formed by multiple, independently acting screw dislocations. Small clusters were observed on the terraces. STMV on the other hand, was observed to grow by 2D nucleation of islands. No dislocations were found on the crystal. The results are used to determine the growth mechanisms and estimate the fundamental materials parameters. The images also illustrate the important mechanism of defect incorporation and provide insight to the processes that limit the growth rate and uniformity of these crystals.

  14. Direct measurements of forces induced by Bloch surface waves in a one-dimensional photonic crystal.

    PubMed

    Shilkin, Daniil A; Lyubin, Evgeny V; Soboleva, Irina V; Fedyanin, Andrey A

    2015-11-01

    An experimental study of the interaction between a single dielectric microparticle and the evanescent field of the Bloch surface wave in a one-dimensional (1D) photonic crystal is reported. The Bloch surface wave-induced forces on a 1 μm polystyrene sphere were measured by photonic force microscopy. The results demonstrate the potential of 1D photonic crystals for the optical manipulation of microparticles and suggest a novel approach for utilizing light in lab-on-a-chip devices.

  15. Comparison of the simulations of cellulosic crystals with three carbohydrate force fields.

    PubMed

    Miyamoto, Hitomi; Schnupf, Udo; Crowley, Michael F; Brady, John W

    2016-03-03

    Three independently developed molecular mechanics force fields for carbohydrates have been used to simulate a suite of small molecule analogs of cellulose for which crystal structures have been reported, as a test to determine which might be best for simulations of cellulose itself. Such evaluation is necessary since the reported cellulose crystal structure is not stable in molecular dynamics simulations with any available force field. The present simulations found that all three resulted in small deviations from the reported crystal structures, but that all were reasonably accurate and none was clearly superior to the others for the entire suite of structures examined. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Atomic force microscopy of three-dimensional membrane protein crystals. Ca-ATPase of sarcoplasmic reticulum.

    PubMed Central

    Lacapère, J J; Stokes, D L; Chatenay, D

    1992-01-01

    We have observed three-dimensional crystals of the calcium pump from sarcoplasmic reticulum by atomic force microscopy (AFM). From AFM images of dried crystals, both on graphite and mica, we measured steps in the crystal thickness, corresponding to the unit cell spacing normal to the substrate. It is known from transmission electron microscopy that crystal periodicity in the plane of the substrate is destroyed by drying, and it was therefore not surprising that we were unable to observe this periodicity by AFM. Thus, we were motivated to use the AFM on hydrated crystals. In this case, crystal adsorption appeared to be a limiting factor, and our studies indicate that adsorption is controlled by the composition of the medium and by the physical-chemical properties of the substrate. We used scanning electron microscopy to determine the conditions yielding the highest adsorption of crystals, and, under these conditions, we have obtained AFM images of hydrated crystals with a resolution similar to that observed with dried samples (i.e., relatively poor). In the same preparations, we have observed lipid bilayers with a significantly better resolution, indicating that the poor quality of crystal images was not due to instrumental limitations. Rather, we attribute poor images to the intrinsic flexibility of these multilamellar crystals, which apparently allow movement of one layer relative to another in response to shear forces from the AFM tip. We therefore suggest some general guidelines for future studies of membrane proteins with AFM. Images FIGURE 1 FIGURE 2 FIGURE 3 FIGURE 4 PMID:1420878

  17. Surface Polarity Of Beta-hmx Crystal And The Related Adhesive Forces With Estane Binder

    SciTech Connect

    Yang, Lu; Hanson, David E

    2008-01-01

    Here we present the results on the study of surface properties of {beta}-HMX crystal utilizing molecular simulations. The surface polarity of three principal crystal surfaces are investigated by measuring the water contact angles. The calculated contact angles agree excellently with the values measured by experiment and show that the surface polarity of three crystal surfaces are different. The free energies and forces of detaching an Estane chain with and without nitroplasticizer from the three principal crystal surfaces were calculated using umbrella sampling technique. We find that the detaching free energy/force increases with the increasing HMX surface polarity. In addition, our results also show that nitroplasticizer plays an important role in the adhesion forces between Estane and HMX surfaces.

  18. Synthesis, structure and crystal packing of a clothespin-shaped binuclear trans-bis(2-amino- troponato)palladium(II) complex bearing m-xylidene linkers

    NASA Astrophysics Data System (ADS)

    Naito, Masaya; Komiya, Naruyoshi; Naota, Takeshi

    2015-12-01

    A clothespin-shaped binuclear trans-bis(2-aminotroponato)palladium(II) complex doubly linked with m-xylidene spacers [Pd2(C22H18N2O2)2] (1), has been synthesized and fully characterized using 1H and 13C NMR, FT-IR, high-resolution mass spectrometry and nuclear Overhauser effect spectroscopy (NOESY). Single-crystal X-ray diffraction analysis unequivocally established the specific structure of 1, including its trans-coordination, anti-conformation and three-dimensional clothespin-like shape, and confirmed highly regular crystal packing resulting from consecutive intermolecular π-stacking and CH-π interactions between the coordination platforms and the linkers.

  19. A new constitutive analysis of hexagonal close-packed metal in equal channel angular pressing by crystal plasticity finite element method

    NASA Astrophysics Data System (ADS)

    Li, Hejie; Öchsner, Andreas; Yarlagadda, Prasad K. D. V.; Xiao, Yin; Furushima, Tsuyoshi; Wei, Dongbin; Jiang, Zhengyi; Manabe, Ken-ichi

    2017-07-01

    Most of hexagonal close-packed (HCP) metals are lightweight metals. With the increasing application of light metal products, the production of light metal is increasingly attracting the attentions of researchers worldwide. To obtain a better understanding of the deformation mechanism of HCP metals (especially for Mg and its alloys), a new constitutive analysis was carried out based on previous research. In this study, combining the theories of strain gradient and continuum mechanics, the equal channel angular pressing process is analyzed and a HCP crystal plasticity constitutive model is developed especially for Mg and its alloys. The influence of elevated temperature on the deformation mechanism of the Mg alloy (slip and twin) is novelly introduced into a crystal plasticity constitutive model. The solution for the new developed constitutive model is established on the basis of the Lagrangian iterations and Newton Raphson simplification.

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

    ERIC Educational Resources Information Center

    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…

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

    ERIC Educational Resources Information Center

    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…

  2. Structural characterization of an MJ1267 ATP-binding cassette crystal with a complex pattern of twinning caused by promiscuous fiber packing.

    PubMed

    Yuan, Yu-Ren; Martsinkevich, Oskana; Hunt, John F

    2003-02-01

    ATP-binding cassettes represent the motor domains in ABC transporters, a superfamily of integral membrane-protein pumps that couple the hydrolysis of ATP to transmembrane solute translocation. A crystal of a Mg-ADP complex of the MJ1267 ATP-binding cassette was obtained that produced a diffraction pattern characterized by pathological streaking of the spots in the a* x b* plane. While the Laue symmetry of the diffraction pattern was P3;1m, the crystal was determined to be twinned based on intensity statistics, molecular-replacement analysis and difference Fourier analysis of an engineered single-site methylmercury derivative. The unit cell contains three similar 3(1) fibers, with two of them related by primarily translational non-crystallographic symmetry (NCS) and the third related to the first two by approximate twofold screw operations whose rotational components are very similar to the twinning operator. The promiscuous packing of these 3(1) fibers, which make both parallel and antiparallel interactions in the primary crystal lattice, can explain the twinning tendency based on the ability of the twin-related lattices to interact with one another while making only one slightly sub-optimal intermolecular contact per unit cell in the boundary region. The promiscuous fiber packing can also explain the streaking in the diffraction pattern based on the ability to form a variety of different lattices with similar inter-fiber packing interactions. The crystal structure was refined as a twin in space group P3(1) using the program CNS, yielding a free R factor of 28.9% at 2.6 A and a refined twin fraction of 0.50. The structure shows a rigid-body rotation of the ABC-transporter-specific alpha-helical subdomain (ABCalpha subdomain) in MJ1267 compared with the conformation observed for the same protein in a C2 crystal lattice; this observation suggests that the ABCalpha subdomain is flexibly attached to the F1-type ATP-binding core of the ATP-binding cassette when Mg

  3. Chiral Asymmetric Structures in Aspartic Acid and Valine Crystals Assessed by Atomic Force Microscopy.

    PubMed

    Teschke, Omar; Soares, David Mendez

    2016-03-29

    Structures of crystallized deposits formed by the molecular self-assembly of aspartic acid and valine on silicon substrates were imaged by atomic force microscopy. Images of d- and l-aspartic acid crystal surfaces showing extended molecularly flat sheets or regions separated by single molecule thick steps are presented. Distinct orientation surfaces were imaged, which, combined with the single molecule step size, defines the geometry of the crystal. However, single molecule step growth also reveals the crystal chirality, i.e., growth orientations. The imaged ordered lattice of aspartic acid (asp) and valine (val) mostly revealed periodicities corresponding to bulk terminations, but a previously unreported molecular hexagonal lattice configuration was observed for both l-asp and l-val but not for d-asp or d-val. Atomic force microscopy can then be used to identify the different chiral forms of aspartic acid and valine crystals.

  4. A test of improved force field parameters for urea: molecular-dynamics simulations of urea crystals.

    PubMed

    Özpınar, Gül Altınbaş; Beierlein, Frank R; Peukert, Wolfgang; Zahn, Dirk; Clark, Timothy

    2012-08-01

    Molecular-dynamics (MD) simulations of urea crystals of different shapes (cubic, rectangular prismatic, and sheet) have been performed using our previously published force field for urea. This force field has been validated by calculating values for the cohesive energy, sublimation temperature, and melting point from the MD data. The cohesive energies computed from simulations of cubic and rectangular prismatic urea crystals in vacuo at 300 K agreed very well with the experimental sublimation enthalpies reported at 298 K. We also found very good agreement between the melting points as observed experimentally and from simulations. Annealing the crystals just below the melting point leads to reconstruction to form crystal faces that are consistent with experimental observations. The simulations reveal a melting mechanism that involves surface (corner/edge) melting well below the melting point, and rotational disordering of the urea molecules in the corner/edge regions of the crystal, which then facilitates the translational motion of these molecules.

  5. Evaluation of interactive forces between alkaline earth metal fluoride particles and single crystal substrate using atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Tsai, Yi-Yang; Nalladega, Vijay; Sathish, Shamachary; Stanford, Malcolm K.

    2004-07-01

    Interactive forces between particles play an important role in diverse fields of science and technology. With the advent of Atomic Force Microscopy, investigation of interactive forces has been extended to micro and nano-scale particles with new applications. These forces are known to vary with the dimension of the particles and with the different levels of humidity. In the present paper we have investigated the interactive forces between a spherical particle probes of eutectic BaF2-CaF2 and a single crystal surface of CaF2 using an Atomic Force Microscope. The effect of humidity on the interactive forces has been examined by analyzing the force-displacement curves at controlled levels of humidity. Force distance curves obtained with two different probes, 5 μm and 17 μm in diameter, and have been examined to investigate the effect of probe dimensions. The results are discussed in view of the application of eutectic BaF2-CaF2 particles in self-lubricating coatings for aerospace applications.

  6. Effect of compression force on the crystal properties of erythromycin acistrate tablets.

    PubMed

    Riippi, M; Tanninen, V; Yliruusi, J

    2000-11-01

    The crystal properties of compressed and powdered erythromycin acistrate tablets were studied by the X-ray powder diffraction (XRPD) method. Detailed analysis of X-ray powder diffraction line profiles was performed. Diffraction peak intensities and full width at half maximum (FWHM) values of the peaks corresponding to three different crystal lattice directions were determined. Crystallite size was calculated by Scherrer's equation using the data of integral breadth of the peaks. The preferred orientation of the crystallites is also discussed. According to the results, the crystallite size increased on the tablet surface after a small compression force (4 kN) in all crystal lattice directions studied. Even small compression forces caused recrystallization. With higher compression forces (8-18 kN) the crystallite size and the FWHM values remained rather constant. After the compression force of 18 kN the peaks in different crystal lattice directions behaved differently. In the lattice directions of diffraction maxima 2 and 3, the effect was the same with the small (4 kN) and the high compression force (22 kN). Further recrystallization occurred with 22 kN. However, in the crystal lattice direction of diffraction maximum 1 at the compression force of 8 kN the crystallite broke and crystallinity decreased. These were not seen in the powdered tablet samples. It could be concluded that the effect of compression force on the crystal properties of erythromycin acistrate tablets was seen on the tablet surface but not in the powdered tablets. Compression force also affected the preferred orientation of crystallites on the tablet surface and especially in the lattice direction of diffraction maximum 3. This was not seen in the powdered tablets.

  7. Elasticity of two-dimensional crystals of polydisperse hard disks near close packing: surprising behavior of the Poisson's ratio.

    PubMed

    Tretiakov, Konstantin V; Wojciechowski, Krzysztof W

    2012-05-28

    The equation of state, elastic constants, and Poisson's ratio of a crystalline two-dimensional polydisperse hard disk system were determined in the close packing limit. Monte Carlo simulations in the NpT ensemble with variable shape of the periodic box reveal that the pressure and elastic constants grow with increasing polydispersity. The equation of state and the bulk modulus are well described by the free volume approximation. The latter approximation fails, however, for the shear modulus. The simulations also show that the introduction of any amount of size polydispersity in the hard disk systems causes a discontinuous "jump" of the Poisson's ratio in the close packing limit from the value ν(δ=0) = 0.1308(22), obtained for equidiameter hard disks, to ν(δ>0) ≈ 1, estimated for the polydisperse disks.

  8. Accurate force fields and methods for modelling organic molecular crystals at finite temperatures.

    PubMed

    Nyman, Jonas; Pundyke, Orla Sheehan; Day, Graeme M

    2016-06-21

    We present an assessment of the performance of several force fields for modelling intermolecular interactions in organic molecular crystals using the X23 benchmark set. The performance of the force fields is compared to several popular dispersion corrected density functional methods. In addition, we present our implementation of lattice vibrational free energy calculations in the quasi-harmonic approximation, using several methods to account for phonon dispersion. This allows us to also benchmark the force fields' reproduction of finite temperature crystal structures. The results demonstrate that anisotropic atom-atom multipole-based force fields can be as accurate as several popular DFT-D methods, but have errors 2-3 times larger than the current best DFT-D methods. The largest error in the examined force fields is a systematic underestimation of the (absolute) lattice energy.

  9. An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics.

    PubMed

    Pyzer-Knapp, Edward O; Thompson, Hugh P G; Day, Graeme M

    2016-08-01

    We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%.

  10. An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics

    PubMed Central

    Pyzer-Knapp, Edward O.; Thompson, Hugh P. G.; Day, Graeme M.

    2016-01-01

    We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%. PMID:27484370

  11. Crystallization behavior of single isotactic poly(methyl methacrylate) chains visualized by atomic force microscopy.

    PubMed

    Anzai, Takahiro; Kawauchi, Mariko; Kawauchi, Takehiro; Kumaki, Jiro

    2015-01-08

    We have, for the first time, successfully visualized the crystallization behavior of a single isolated polymer chain at the molecular level by atomic force microscopy (AFM). Previously, we found that isotactic poly(methyl methacrylate) (it-PMMA) formed two-dimensional folded chain crystals composed of double-stranded helices upon compression of its Langmuir monolayer on a water surface, and the molecular images of the crystals deposited on mica were clearly visualized by AFM (Kumaki, J.; et al. J. Am. Chem. Soc. 2005, 127, 5788). In the present study, a high-molecular-weight it-PMMA was diluted in a monolayer of an it-PMMA oligomer which cannot crystallize at the experimental temperature due to its low molecular weight. At a low surface pressure, isolated amorphous chains of the high-molecular-weight it-PMMA solubilized in the oligomer monolayer were observed. On compression, the isolated chains converted to crystals composed of a single chain, typically some small crystallites linked by an amorphous chain like a necklace. Detailed AFM observations of the crystals indicated that the crystalline nuclei preferentially formed at the ends of the chains, and the size of the nuclei was almost independent of the molecular weight of it-PMMA over a wide range. At an extremely slow compression, crystallization was promoted, resulting in crystallization of the whole chain. The crystallization behavior of a single isolated chain provides new insights in understanding the polymer crystallization process.

  12. Surface polarity of beta-HMX crystal and the related adhesive forces with Estane binder.

    PubMed

    Yang, Lu

    2008-12-02

    Here I present the results on the study of surface properties of beta-HMX crystal utilizing molecular dynamics simulations. The surface polarity of three principal crystal surfaces, (011), (010), and (110), is investigated by measuring the water contact angles. The calculated contact angles are in excellent agreement with the values measured by experiment and show that the surface polarity of three crystal surfaces are different. The free energies and forces of detaching an Estane chain (with and without surrounding nitroplasticizer molecules) from the three principal crystal surfaces are also calculated using the umbrella sampling method. I find that the force for Estane detachment increases with the increasing HMX surface polarity. In addition, my results show that the nitroplasticizer also plays an important role in the adhesion between Estane and HMX surfaces.

  13. Tracking traction force changes of single cells on the liquid crystal surface.

    PubMed

    Soon, Chin Fhong; Tee, Kian Sek; Youseffi, Mansour; Denyer, Morgan C T

    2015-01-05

    Cell migration is a key contributor to wound repair. This study presents findings indicating that the liquid crystal based cell traction force transducer (LCTFT) system can be used in conjunction with a bespoke cell traction force mapping (CTFM) software to monitor cell/surface traction forces from quiescent state in real time. In this study, time-lapse photo microscopy allowed cell induced deformations in liquid crystal coated substrates to be monitored and analyzed. The results indicated that the system could be used to monitor the generation of cell/surface forces in an initially quiescent cell, as it migrated over the culture substrate, via multiple points of contact between the cell and the surface. Future application of this system is the real-time assaying of the pharmacological effects of cytokines on the mechanics of cell migration.

  14. Tracking Traction Force Changes of Single Cells on the Liquid Crystal Surface

    PubMed Central

    Soon, Chin Fhong; Tee, Kian Sek; Youseffi, Mansour; Denyer, Morgan C. T.

    2015-01-01

    Cell migration is a key contributor to wound repair. This study presents findings indicating that the liquid crystal based cell traction force transducer (LCTFT) system can be used in conjunction with a bespoke cell traction force mapping (CTFM) software to monitor cell/surface traction forces from quiescent state in real time. In this study, time-lapse photo microscopy allowed cell induced deformations in liquid crystal coated substrates to be monitored and analyzed. The results indicated that the system could be used to monitor the generation of cell/surface forces in an initially quiescent cell, as it migrated over the culture substrate, via multiple points of contact between the cell and the surface. Future application of this system is the real-time assaying of the pharmacological effects of cytokines on the mechanics of cell migration. PMID:25808839

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

    PubMed

    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.

  16. Single-Crystal Diamond Nanowire Tips for Ultrasensitive Force Microscopy.

    PubMed

    Tao, Y; Degen, C L

    2015-12-09

    We report the fabrication, integration, and assessment of sharp diamond tips for ultrasensitive force microscopy experiments. Two types of tips, corresponding to the upper and lower halves of a diamond nanowire, were fabricated by top-down plasma etching from a single-crystalline substrate. The lower, surface-attached halves can be directly integrated into lithographically defined nanostructures, like cantilevers. The upper, detachable halves result in diamond nanowires with a tunable diameter (50-500 nm) and lengths of a few microns. Tip radii were around 10 nm and tip apex angles around 15°. We demonstrate the integration of diamond nanowires for use as scanning tips onto ultrasensitive pendulum-style silicon cantilevers. We find the noncontact friction and frequency jitter to be exceptionally low, with no degradation in the intrinsic mechanical quality factor (Q ≈ 130,000) down to tip-to-surface distances of about 10 nm. Our results are an encouraging step toward further improvement of the sensitivity and resolution of force-detected magnetic resonance imaging.

  17. Computational and Experimental Characterization of Five Crystal Forms of Thymine: Packing Polymorphism, Polytypism/Disorder and Stoichiometric 0.8-Hydrate

    PubMed Central

    Braun, Doris E.; Gelbrich, Thomas; Wurst, Klaus; Griesser, Ulrich J.

    2017-01-01

    New polymorphs of thymine emerged in an experimental search for solid forms, which was guided by the computationally generated crystal energy landscape. Three of the four anhydrates (AH) are homeoenergetic (A° – C) and their packing modes differ only in the location of oxygen and hydrogen atoms. AHs A° and B are ordered phases, whereas AH C shows disorder (X-ray diffuse scattering). Anhydrates AHs A° and B are ordered phases, whereas AH C shows disorder (X-ray diffuse scattering). Analysis of the crystal energy landscape for alternative AH C hydrogen bonded ribbon motifs identified a number of different packing modes, whose 3D structures were calculated to deviate by less than 0.24 kJ mol–1 in lattice energy. These structures provide models for stacking faults. The three anhydrates A° – C show strong similarity in their powder X-ray diffraction, thermoanalytical and spectroscopic (IR and Raman) characteristics. The already known anhydrate AH A° was identified as the thermodynamically most stable form at ambient conditions; AH B and AH C are metastable but show high kinetic stability. The hydrate of thymine is stable only at water activities (aw) > 0.95 at temperatures ≤ 25 °C. It was found to be a stoichiometric hydrate despite being a channel hydrate with an unusual water:thymine ratio of 0.8:1. Depending on the dehydration conditions, either AH C or AH D is obtained. The hydrate is the only known precursor to AH D. This study highlights the value and complementarity of simultaneous explorations of computationally and experimentally generated solid form landscapes of a small molecule anhydrate ↔ hydrate system. PMID:28663717

  18. Kinetic Roughening and Energetics of Tetragonal Lysozyme Crystal Growth: A Preliminary Atomic Force Microscopy Investigation

    NASA Technical Reports Server (NTRS)

    Gorti, Sridhar; Forsythe, Elizabeth L.; Pusey, Marc L.

    2004-01-01

    We examined particulars of crystal growth from measurements obtained at both microscopic and molecular levels. The crystal growth measurements performed at the microscopic level are well characterized by a model that balances the flux of macromolecules towards the crystal surface with the flux of the crystal surface. Numerical evaluation of model with measurements of crystal growth, in time, provided accurate estimates for the average growth velocities. Growth velocities thus obtained were also interpreted using well-established phenomenological theories. Moreover, we find that microscopic measurements of growth velocity measurements obtained as a function of temperature best characterizes changes in crystal growth modes, when present. We also examined the possibility of detecting a change in crystal growth modes at the molecular level using atomic force microscopy, AFM. From preliminary AFM measurements performed at various supersaturations, we find that magnitude of surface height fluctuations, h(x), increases with supersaturation. Further examination of surface height fluctuations using methods established for fluctuation spectroscopy also enabled the discovery of the existence of a characteristic length, c, which may possibly determine the mode of crystal growth. Although the results are preliminary, we establish the non- critical divergence of 5 and the root-mean-square (rms) magnitude of height-height fluctuations as the kinetic roughening transition temperatures are approached. Moreover, we also examine approximate models for interpreting the non-critical behavior of both 6 and rms magnitude of height-height fluctuations, as the solution supersaturation is increased towards the kinetic roughening supersaturation.

  19. Kinetic Roughening and Energetics of Tetragonal Lysozyme Crystal Growth: A Preliminary Atomic Force Microscopy Investigation

    NASA Technical Reports Server (NTRS)

    Gorti, Sridhar; Forsythe, Elizabeth L.; Pusey, Marc L.

    2004-01-01

    We examined particulars of crystal growth from measurements obtained at both microscopic and molecular levels. The crystal growth measurements performed at the microscopic level are well characterized by a model that balances the flux of macromolecules towards the crystal surface with the flux of the crystal surface. Numerical evaluation of model with measurements of crystal growth, in time, provided accurate estimates for the average growth velocities. Growth velocities thus obtained were also interpreted using well-established phenomenological theories. Moreover, we find that microscopic measurements of growth velocity measurements obtained as a function of temperature best characterizes changes in crystal growth modes, when present. We also examined the possibility of detecting a change in crystal growth modes at the molecular level using atomic force microscopy, AFM. From preliminary AFM measurements performed at various supersaturations, we find that magnitude of surface height fluctuations, h(x), increases with supersaturation. Further examination of surface height fluctuations using methods established for fluctuation spectroscopy also enabled the discovery of the existence of a characteristic length, c, which may possibly determine the mode of crystal growth. Although the results are preliminary, we establish the non- critical divergence of 5 and the root-mean-square (rms) magnitude of height-height fluctuations as the kinetic roughening transition temperatures are approached. Moreover, we also examine approximate models for interpreting the non-critical behavior of both 6 and rms magnitude of height-height fluctuations, as the solution supersaturation is increased towards the kinetic roughening supersaturation.

  20. Exfoliation of two-dimensional polymer single crystals into thin sheets and investigations of their surface structure by high-resolution atomic force microscopy.

    PubMed

    Beyer, Hannes; Kory, Max J; Hofer, Gregor; Stemmer, Andreas; Schlüter, A Dieter

    2017-07-13

    The acid-assisted wet-chemical and the adhesive-tape induced micromechanical exfoliation of differently sized single crystals of a 2D polymer (approx. 20 μm and 100 μm) is shown to result in thin sheet stacks. Tuning of the thickness is achieved via duration and frequency of the exfoliation, respectively. A color code is established that correlates interference colors of sheet stacks on SiO2(300 nm)/Si as observed under an optical microscope with their thicknesses measured by atomic force microscopy. This facilitates reliable monitoring of the exfoliation and quick identification of sheet stacks of a desired thickness. Furthermore, high resolution atomic force microscopy is applied to investigate the surfaces of starting crystals and both wet-chemically and micromechanically exfoliated sheet stacks aiming at exploring whether exfoliation proceeds with preservation of surface periodicity and with a low frequency of sheet rupturing. These investigations also aimed at uncovering possible point defects and domain (grain) boundaries in the surfaces. It appears that all investigated objects have a high molecular scale perfection and that both exfoliation methods proceed mild enough to largely preserve the molecular structure of the 2D polymer including the not covalently bonded template molecules being part of the crystal packing.

  1. Crystal structures of two bis­(iodo­meth­yl)benzene derivatives: similarities and differences in the crystal packing

    PubMed Central

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

    2015-01-01

    The isomeric derivatives 1,2-bis­(iodo­meth­yl)benzene, (I), and 1,3-bis­(iodo­meth­yl)benzene (II), both C8H8I2, were prepared by metathesis from their di­bromo analogues. The ortho-derivative, (I), lies about a crystallographic twofold axis that bis­ects the C—C bond between the two iodo­methyl substituents. The packing in (I) relies solely on C—H⋯I hydrogen bonds supported by weak parallel slipped π–π stacking inter­actions [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. PMID:26870415

  2. Nature of packs used in propellant modeling.

    PubMed

    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.

  3. A three-dimensional photonic crystal model: Hollow-spherical non-closed-packed face-centered cubic structure

    NASA Astrophysics Data System (ADS)

    Chen, Hong-Bo; Cao, Yan-Ling; Zhu, Yong-Zheng; Wang, Yan-Ping; Chi, Yuan-Bin

    2006-05-01

    We report a photonic crystal model, which consists of hollow spheres located at face-centered cubic lattice sites and each sphere connected to all of its 12 nearest neighbors by cylindrical rods. Theoretical calculations show that this kind of structure exhibits two large complete photonic band gaps. The maximum relative gap sizes reach 17.3% between the eighth and ninth bands, and 15.1% between the 13th and 14th bands for a dielectric contrast of 11.9, and the minimal dielectric contrasts needed to open the two gaps are 5.8 and 7.3, respectively, which are lower than that of other face-centered cubic photonic crystal structures.

  4. Li18Na2Ge17--a compound demonstrating cation effects on cluster shapes and crystal packing in ternary Zintl phases.

    PubMed

    Scherf, Lavinia M; Zeilinger, Michael; Fässler, Thomas F

    2014-02-17

    The novel ternary Zintl phase Li18Na2Ge17 was synthesized from a stoichiometric melt and characterized crystallographically. It crystallizes in the trigonal space group P31m (No. 157) with a = 17.0905(4) Å, c = 8.0783(2) Å, and V = 2043.43(8) Å(3) (final R indices R1 = 0.0212 and wR2 = 0.0420 for all data). The structure contains three different Zintl anions in a 1:1:1 ratio: isolated anions Ge(4-), tetrahedra [Ge4](4-), and truncated, Li-centered tetrahedra [Li@Ge12](11-), whose hexagonal faces are capped by four Li cations, resulting in the Friauf polyhedra [Li@Li4Ge12](7-). According to the Zintl-Klemm concept, Li18Na2Ge17 is an electronically balanced Zintl phase, as experimentally verified by its diamagnetism. The compound is structurally related to Li7RbGe8, which also contains [Ge4](4-) and [Li@Li4Ge12](7-) in its anionic substructure. However, exchanging the heavier alkali metal cation Rb for Na in the mixed-cation germanides leads to drastic changes in stoichiometry and crystal packing, demonstrating the great effects that cations exert on such Zintl phases through optimized cluster sheathing and space filling.

  5. Understanding shape entropy through local dense packing

    PubMed Central

    van Anders, Greg; Klotsa, Daphne; Ahmed, N. Khalid; Engel, Michael; Glotzer, Sharon C.

    2014-01-01

    Entropy drives the phase behavior of colloids ranging from dense suspensions of hard spheres or rods to dilute suspensions of hard spheres and depletants. Entropic ordering of anisotropic shapes into complex crystals, liquid crystals, and even quasicrystals was demonstrated recently in computer simulations and experiments. The ordering of shapes appears to arise from the emergence of directional entropic forces (DEFs) that align neighboring particles, but these forces have been neither rigorously defined nor quantified in generic systems. Here, we show quantitatively that shape drives the phase behavior of systems of anisotropic particles upon crowding through DEFs. We define DEFs in generic systems and compute them for several hard particle systems. We show they are on the order of a few times the thermal energy (kBT) at the onset of ordering, placing DEFs on par with traditional depletion, van der Waals, and other intrinsic interactions. In experimental systems with these other interactions, we provide direct quantitative evidence that entropic effects of shape also contribute to self-assembly. We use DEFs to draw a distinction between self-assembly and packing behavior. We show that the mechanism that generates directional entropic forces is the maximization of entropy by optimizing local particle packing. We show that this mechanism occurs in a wide class of systems and we treat, in a unified way, the entropy-driven phase behavior of arbitrary shapes, incorporating the well-known works of Kirkwood, Onsager, and Asakura and Oosawa. PMID:25344532

  6. Understanding shape entropy through local dense packing

    DOE PAGES

    van Anders, Greg; Klotsa, Daphne; Ahmed, N. Khalid; ...

    2014-10-24

    Entropy drives the phase behavior of colloids ranging from dense suspensions of hard spheres or rods to dilute suspensions of hard spheres and depletants. Entropic ordering of anisotropic shapes into complex crystals, liquid crystals, and even quasicrystals was demonstrated recently in computer simulations and experiments. The ordering of shapes appears to arise from the emergence of directional entropic forces (DEFs) that align neighboring particles, but these forces have been neither rigorously defined nor quantified in generic systems. In this paper, we show quantitatively that shape drives the phase behavior of systems of anisotropic particles upon crowding through DEFs. We definemore » DEFs in generic systems and compute them for several hard particle systems. We show they are on the order of a few times the thermal energy (kBT) at the onset of ordering, placing DEFs on par with traditional depletion, van der Waals, and other intrinsic interactions. In experimental systems with these other interactions, we provide direct quantitative evidence that entropic effects of shape also contribute to self-assembly. We use DEFs to draw a distinction between self-assembly and packing behavior. We show that the mechanism that generates directional entropic forces is the maximization of entropy by optimizing local particle packing. Finally, we show that this mechanism occurs in a wide class of systems and we treat, in a unified way, the entropy-driven phase behavior of arbitrary shapes, incorporating the well-known works of Kirkwood, Onsager, and Asakura and Oosawa.« less

  7. Understanding shape entropy through local dense packing

    SciTech Connect

    van Anders, Greg; Klotsa, Daphne; Ahmed, N. Khalid; Engel, Michael; Glotzer, Sharon C.

    2014-10-24

    Entropy drives the phase behavior of colloids ranging from dense suspensions of hard spheres or rods to dilute suspensions of hard spheres and depletants. Entropic ordering of anisotropic shapes into complex crystals, liquid crystals, and even quasicrystals was demonstrated recently in computer simulations and experiments. The ordering of shapes appears to arise from the emergence of directional entropic forces (DEFs) that align neighboring particles, but these forces have been neither rigorously defined nor quantified in generic systems. In this paper, we show quantitatively that shape drives the phase behavior of systems of anisotropic particles upon crowding through DEFs. We define DEFs in generic systems and compute them for several hard particle systems. We show they are on the order of a few times the thermal energy (kBT) at the onset of ordering, placing DEFs on par with traditional depletion, van der Waals, and other intrinsic interactions. In experimental systems with these other interactions, we provide direct quantitative evidence that entropic effects of shape also contribute to self-assembly. We use DEFs to draw a distinction between self-assembly and packing behavior. We show that the mechanism that generates directional entropic forces is the maximization of entropy by optimizing local particle packing. Finally, we show that this mechanism occurs in a wide class of systems and we treat, in a unified way, the entropy-driven phase behavior of arbitrary shapes, incorporating the well-known works of Kirkwood, Onsager, and Asakura and Oosawa.

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

    SciTech Connect

    López-Barrón, Carlos R.; Wagner, Norman J.; Porcar, Lionel

    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.

  9. Lateral shearing optical gradient force in coupled nanobeam photonic crystal cavities

    SciTech Connect

    Du, Han; Zhang, Xingwang; Chau, Fook Siong; Zhou, Guangya; Deng, Jie; Zhao, Yunshan

    2016-04-25

    We report the experimental observation of lateral shearing optical gradient forces in nanoelectromechanical systems (NEMS) controlled dual-coupled photonic crystal (PhC) nanobeam cavities. With an on-chip integrated NEMS actuator, the coupled cavities can be mechanically reconfigured in the lateral direction while maintaining a constant coupling gap. Shearing optical gradient forces are generated when the two cavity centers are laterally displaced. In our experiments, positive and negative lateral shearing optical forces of 0.42 nN and 0.29 nN are observed with different pumping modes. This study may broaden the potential applications of the optical gradient force in nanophotonic devices and benefit the future nanooptoelectromechanical systems.

  10. Direct measurement of force between colloidal particles in a nematic liquid crystal

    NASA Astrophysics Data System (ADS)

    Takahashi, Kenji; Ichikawa, Masatoshi; Kimura, Yasuyuki

    2008-02-01

    The interparticle force between two colloidal particles in a nematic liquid crystal is directly measured as a function of the interparticle distance R by two different experimental methods: the free-release method and the optical tweezing method. The obtained force between an elastic 'dipole', which constitutes a colloidal particle and an accompanying hyperbolic hedgehog defect, confirms previous theoretical predictions that the force is attractive and proportional to R-4. We also observe that a repulsive component emerges at short distances to preclude direct contact of the particles. We find that the magnitudes of the forces obtained by the two methods are different. The origin of this discrepancy is discussed by a comparison between the static and the non-static measurements.

  11. Lateral shearing optical gradient force in coupled nanobeam photonic crystal cavities

    NASA Astrophysics Data System (ADS)

    Du, Han; Zhang, Xingwang; Deng, Jie; Zhao, Yunshan; Chau, Fook Siong; Zhou, Guangya

    2016-04-01

    We report the experimental observation of lateral shearing optical gradient forces in nanoelectromechanical systems (NEMS) controlled dual-coupled photonic crystal (PhC) nanobeam cavities. With an on-chip integrated NEMS actuator, the coupled cavities can be mechanically reconfigured in the lateral direction while maintaining a constant coupling gap. Shearing optical gradient forces are generated when the two cavity centers are laterally displaced. In our experiments, positive and negative lateral shearing optical forces of 0.42 nN and 0.29 nN are observed with different pumping modes. This study may broaden the potential applications of the optical gradient force in nanophotonic devices and benefit the future nanooptoelectromechanical systems.

  12. Optical bistability with a repulsive optical force in coupled silicon photonic crystal membranes

    NASA Astrophysics Data System (ADS)

    Hui, Pui-Chuen; Woolf, David; Iwase, Eiji; Sohn, Young-Ik; Ramos, Daniel; Khan, Mughees; Rodriguez, Alejandro W.; Johnson, Steven G.; Capasso, Federico; Loncar, Marko

    2013-07-01

    We demonstrate actuation of a silicon photonic crystal membrane with a repulsive optical gradient force. The extent of the static actuation is extracted by examining the optical bistability as a combination of the optomechanical, thermo-optic, and photo-thermo-mechanical effects using coupled-mode theory. Device behavior is dominated by a repulsive optical force which results in displacements of ≈1 nm/mW. By employing an extended guided resonance which effectively eliminates multi-photon thermal and electronic nonlinearities, our silicon-based device provides a simple, non-intrusive solution to extending the actuation range of micro-electromechanical devices.

  13. Crystal growth of a layered silicate clay mineral as revealed by atomic force microscopy

    SciTech Connect

    Carrado, K.A.; Song, Kang; Zajac, G.W.

    1997-12-31

    Non-contact atomic force microscopy, commonly referred to as {open_quotes}tapping mode{close_quotes} AFM, has been used to scan primarily the morphological features of growing hectorite clay crystallites synthesized in the presence of organo-ammonium cations. The use of such cations allows larger crystals to form in this system, making study by AFM feasible. This is the first time that actual temporal {open_quotes}snapshots{close_quotes} of a clay`s nucleation and crystallization processes have been presented. The observed view does not support the perhaps predicted scene of small crystallites slowly ripening into larger and larger plates. Instead, larger and larger aggregates appear to coalesce from a larger number of small crystallites that are closely associated in globular networks similar in appearance to {open_quotes}strings of pearls{close_quotes} at the initial stages of crystallization.

  14. Effect of mechanical deformations on the growth of crystals (according to atomic force microscopy data)

    NASA Astrophysics Data System (ADS)

    Piskunova, N. N.; Askhabov, A. M.

    2017-05-01

    Nanosized morphological transformations occurring on the surface of a crystal in the area drawn by a probe needle during the growth of a scratch and the growth kinetics of crystals subjected to mechanical impact have been studied by atomic force microscopy (AFM). A series of experiments with mechanical impact on topographically different areas of a growing face (100) of a dioxidine crystal has been performed. It has been shown that even slight local contact between the probe needle and the surface on a nanoscale leads to essential crystallogenetic (morphological and kinetic) consequences, and its effect is perceptible for a long time. Among these consequences are the coarsening of stages, the appearance of great fluctuations in the growth rate of stages, the loss of morphological stability by the surface even at a distance of several tens of micrometers from the contact area, and also the phenomenon of simultaneous growth and dissolution in neighboring areas of stages.

  15. Cofacial Versus Coplanar Arrangement in Centrosymmetric Packing Dimers of Dipolar Small Molecules: Structural Effects on the Crystallization Behaviors and Optoelectronic Characteristics.

    PubMed

    Chou, Shu-Hua; Kang, Hao-Wei; Chang, Shu-Ting; Wu, Kuan-Yi; Bazan, Guillermo C; Wang, Chien-Lung; Lin, Hong-Lin; Chang, Jung-Hao; Lin, Hao-Wu; Huang, Yu-Ching; Tsao, Cheng-Si; Wong, Ken-Tsung

    2016-07-20

    Two D-π-A-A molecules (MIDTP and TIDTP) composed of an electron-rich ditolylamino group (D) and an electron-deficient 5-dicyanovinylenylpyrimidine (A-A) fragment bridged together with indeno[1,2-b]thiophene (IDT) were synthesized. These molecules provide an opportunity to examine in-depth the impact of side-chain variations (methyl vs p-tolyl) on the crystallization behaviors, solid-state morphology, physical properties, and optoelectronic characteristics relevant for practical applications. X-ray analyses on single-crystal structures indicate that methyl-substituted MIDTP forms "coplanar antiparallel dimers" via C-H···S interactions and organizes into an ordered slip-staircase arrays. In contrast, p-tolyl-bearing TIDTP shows "cofacial centrosymmetric dimers" via π-π interactions and packs into a less-ordered layered structures. The X-ray diffraction analyses upon thermal treatment are consistent with a superior crystallinity of MIDTP, as compared to that of TIDTP. This difference indicates a greater propensity to organization by introduction of the smaller methyl group versus the bulkier p-tolyl group. The increased propensity for order by MIDTP facilitates the crystallization of MIDTP in both solution-processed and vacuum-deposited thin films. MIDTP forms solution-processed single-crystal arrays that deliver OFET hole mobility of 6.56 × 10(-4) cm(2) V(-1) s(-1), whereas TIDTP only forms amorhpous films that gave lower hole mobility of 1.34 × 10(-5) cm(2) V(-1) s(-1). MIDTP and TIDTP were utilized to serve as donors together with C70 as acceptor in the fabrication of small-molecule organic solar cells (SMOSCs) with planar heterojunction (PHJ) or planar-mixed heterojunction (PMHJ) device architectures. OPV devices based on higher crystalline MIDTP delivered power conversion efficiencies (PCEs) of 2.5% and 4.3% for PHJ and PMHJ device, respectively, which are higher than those of TIDTP-based cells. The improved PCEs of MIDTP-based devices are attributed to

  16. Force-free state in a superconducting single crystal and angle-dependent vortex helical instability

    NASA Astrophysics Data System (ADS)

    del Valle, J.; Gomez, A.; Gonzalez, E. M.; Manas-Valero, S.; Coronado, E.; Vicent, J. L.

    2017-06-01

    Superconducting 2 H -NbS e2 single crystals show intrinsic low pinning values. Therefore, they are ideal materials with which to explore fundamental properties of vortices. (V , I ) characteristics are the experimental data we have used to investigate the dissipation mechanisms in a rectangular-shaped 2 H -NbS e2 single crystal. Particularly, we have studied dissipation behavior with magnetic fields applied in the plane of the crystal and parallel to the injected currents, i.e., in the force-free state where the vortex helical instability governs the vortex dynamics. In this regime, the data follow the elliptic critical state model and the voltage dissipation shows an exponential dependence, V ∝eα (I -IC ∥ ) , IC ∥ being the critical current in the force-free configuration and α a linear temperature-dependent parameter. Moreover, this exponential dependence can be observed for in-plane applied magnetic fields up to 40° off the current direction, which implies that the vortex helical instability plays a role in dissipation even out of the force-free configuration.

  17. Direct alignment of nematic liquid crystal molecule using atomic force microscope nano-rubbing

    NASA Astrophysics Data System (ADS)

    Nishiyama, Itaru; Yoshida, Norio; Ebisawa, Mizue; Takayanagi, Atsuo; Otani, Yukitoshi; Umeda, Norihiro

    2005-12-01

    The orientation control of liquid crystal (LC) molecular on the polyimide film has been necessary to fabricate LC devices. Nano-rubbing by atomic force microscope (AFM) has been proposed as the one of methods to control it precisely. In the method, a thin polyimide film was rubbed by a sharpened AFM probe-tip with relatively strong load force. However, the method has some drawbacks; the frictional wear of AFM probe-tip and the difficulty of reorientation after rubbing. In this paper, we have proposed the orientation control of LC on the polyimide film and using direct AFM nano-rubbing method with weak load forces. The change of LC alignment was quantitatively observed by a polarization microscope and birefringence-contrast scanning near-field optical microscope. The effect of scanning density was strong for azimuth angle but the effect of the scanning velocity was weak for both retardation and azimuth angle. An optical switching device was developed utilized isotropic-nematic phase change of liquid crystal which was rubbed in the grating pattern with methyl red dying, and the optical device was operated at the frequency of 0.5Hz. As a result, The proposed method had an effective method to fabricate novel liquid crystal optical devices.

  18. Assembling of three-dimensional crystals by optical depletion force induced by a single focused laser beam.

    PubMed

    Deng, Hai-Dong; Li, Guang-Can; Liu, Hai-Ying; Dai, Qiao-Feng; Wu, Li-Jun; Lan, Sheng; Gopal, Achanta Venu; Trofimov, Vyacheslav A; Lysak, Tatiana M

    2012-04-23

    We proposed a method to assemble microspheres into a three-dimensional crystal by utilizing the giant nonequilibrium depletion force produced by nanoparticles. Such assembling was demonstrated in a colloid formed by suitably mixing silica microspheres and magnetic nanoparticles. The giant nonequilibrium depletion force was generated by quickly driving magnetic nanoparticles out of the focusing region of a laser light through both optical force and thermophoresis. The thermophoretic binding of silica beads is so tight that a colloidal photonic crystal can be achieved after complete evaporation of solvent. This technique could be employed for fabrication of colloidal photonic crystals and molecular sieves.

  19. Atomic force microscopy of crystalline insulins: the influence of sequence variation on crystallization and interfacial structure.

    PubMed Central

    Yip, C M; Brader, M L; DeFelippis, M R; Ward, M D

    1998-01-01

    The self-association of proteins is influenced by amino acid sequence, molecular conformation, and the presence of molecular additives. In the presence of phenolic additives, LysB28ProB29 insulin, in which the C-terminal prolyl and lysyl residues of wild-type human insulin have been inverted, can be crystallized into forms resembling those of wild-type insulins in which the protein exists as zinc-complexed hexamers organized into well-defined layers. We describe herein tapping-mode atomic force microscopy (TMAFM) studies of single crystals of rhombohedral (R3) LysB28ProB29 that reveal the influence of sequence variation on hexamer-hexamer association at the surface of actively growing crystals. Molecular scale lattice images of these crystals were acquired in situ under growth conditions, enabling simultaneous identification of the rhombohedral LysB28ProB29 crystal form, its orientation, and its dynamic growth characteristics. The ability to obtain crystallographic parameters on multiple crystal faces with TMAFM confirmed that bovine and porcine insulins grown under these conditions crystallized into the same space group as LysB28ProB29 (R3), enabling direct comparison of crystal growth behavior and the influence of sequence variation. Real-time TMAFM revealed hexamer vacancies on the (001) terraces of LysB28ProB29, and more rounded dislocation noses and larger terrace widths for actively growing screw dislocations compared to wild-type bovine and porcine insulin crystals under identical conditions. This behavior is consistent with weaker interhexamer attachment energies for LysB28ProB29 at active growth sites. Comparison of the single crystal x-ray structures of wild-type insulins and LysB28ProB29 suggests that differences in protein conformation at the hexamer-hexamer interface and accompanying changes in interhexamer bonding are responsible for this behavior. These studies demonstrate that subtle changes in molecular conformation due to a single sequence

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

    NASA Astrophysics Data System (ADS)

    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.

  1. The role of the “Casimir force analogue” at the microscopic processes of crystallization and melting

    SciTech Connect

    Chuvildeev, V.N. Semenycheva, A.V.

    2016-10-15

    Melting (crystallization), a phase transition from a crystalline solid to a liquid state, is a common phenomenon in nature. We suggest a new factor, “the Casimir force analogue”, to describe mechanisms of melting and crystallization. The Casimir force analogue is a force occurring between the surfaces of solid and liquid phases of metals caused by different energy density of phonons of these phases. It explains abrupt changes in geometry and thermodynamic parameters at a melting point. “The Casimir force analogue” helps to estimate latent melting heat and to gain an insight into a solid–liquid transition problem.

  2. Novel Protein Crystal Growth Electrochemical Cell For Applications in X-ray Diffraction and Atomic Force Microscopy

    SciTech Connect

    G Gil-Alvaradejo; R Ruiz-Arellano; C Owen; A Rodriguez-Romero; E Rudino-Pinera; M Antwi; V Stojanoff; A Moreno

    2011-12-31

    A new crystal growth cell based on transparent indium tin oxide (ITO) glass-electrodes for electrochemically assisted protein crystallization allows for reduced nucleation and crystal quality enhancement. The crystallization behavior of lysozyme and ferritin was monitored as a function of the electric current applied to the growth cell. The X-ray diffraction analysis showed that for specific currents, the crystal quality is substantially improved. No conformational changes were observed in the 3D crystallographic structures determined for crystals grown under different electric current regimes. Finally, the strong crystal adhesion on the surface of ITO electrode because of the electroadhesion allows a sufficiently strong fixing of the protein crystals, to undergo atomic force microscopy investigations in a fluid cell.

  3. Assessment of biomolecular force fields for molecular dynamics simulations in a protein crystal.

    PubMed

    Hu, Zhongqiao; Jiang, Jianwen

    2010-01-30

    Different biomolecular force fields (OPLS-AA, AMBER03, and GROMOS96) in conjunction with SPC, SPC/E and TIP3P water models are assessed for molecular dynamics simulations in a tetragonal lysozyme crystal. The root mean square deviations for the C(a) atoms of lysozymes are about 0.1 to 0.2 nm from OPLS-AA and AMBER03, smaller than 0.4 nm from GROMOS96. All force fields exhibit similar pattern in B-factors, whereas OPLS-AA and AMBER03 accurately reproduce experimental measurements. Despite slight variations, the primary secondary structures are well conserved using different force fields. Water diffusion in the crystal is approximately ten-fold slower than in bulk phase. The directional and average water diffusivities from OPLS-AA and AMBER03 along with SPC/E model match fairly well with experimental data. Compared to GROMOS96, OPLS-AA and AMBER03 predict larger hydrophilic solvent-accessible surface area of lysozyme, more hydrogen bonds between lysozyme and water, and higher percentage of water in hydration shell. SPC, SPC/E and TIP3P water models have similar performance in most energetic and structural properties, but SPC/E outperforms in water diffusion. While all force fields overestimate the mobility and electrical conductivity of NaCl, a combination of OPLS-AA for lysozyme and the Kirkwood-Buff model for ions is superior to others. As attributed to the steric restraints and surface interactions, the mobility and conductivity in the crystal are reduced by one to two orders of magnitude from aqueous solution.

  4. Sub-nanometer resolution of an organic semiconductor crystal surface using friction force microscopy in water.

    PubMed

    Pimentel, Carlos; Varghese, Shinto; Yoon, Seong-Jun; Park, Soo Young; Gierschner, Johannes; Gnecco, Enrico; Pina, Carlos M

    2016-04-06

    Organic semiconductors (OSC) are attracting much interest for (opto)electronic applications, such as photovoltaics, LEDs, sensors or solid state lasers. In particular, crystals formed by small π-conjugated molecules have shown to be suitable for constructing OSC devices. However, the (opto)electronic properties are complex since they depend strongly on both the mutual orientation of molecules as well as the perfection of bulk crystal surfaces. Hence, there is an urgent need to control nano-topographic OSC features in real space. Here we show that friction force microscopy in water is a very suitable technique to image the free surface morphology of an OSC single crystal (TDDCS) with sub-nanometer resolution. We demonstrate the power of the method by direct correlation to the structural information extracted from combined single crystal (SC-) and specular (s-) XRD studies, which allows us to identify the pinning centers encountered in the stick-slip motion of the probing tip with the topmost methyl groups on the TDDCS surface.

  5. Atomic force microscopy of AgBr crystals and adsorbed gelatin films

    SciTech Connect

    Haugstad, G.; Gladfelter, W.L.; Keyes, M.P.; Weberg, E.B.

    1993-06-01

    Atomic force microscopy of the (111) surface of macroscopic AgBr crystals revealed steps ranging in height from two atomic layers up to 10 nm, lying predominantly along the (110) and (112) families of crystal directions. Rods of elemental Ag, formed via photoreduction, were observed along the (110) family of directions. Images of adsorbed gelatin films revealed circular pores with diameters of order 10-100 nm, extending to the AgBr surface. The length of deposition time, the pH and concentration of the gelatin solution, and the presence of steps on the AgBr surface were observed to affect the size, number, and location of pores in the gelatin films. 12 refs., 7 figs.

  6. Single-crystal diamond pyramids: synthesis and application for atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Tuyakova, Feruza T.; Obraztsova, Ekaterina A.; Ismagilov, Rinat R.

    2016-03-01

    Here we present the results of investigations aimed at the development and testing of robust, chemically inert single-crystal diamond probes for atomic force microscopy (AFM). The probes were prepared by assembling common silicon probes with micrometer-sized pyramid-shaped single-crystal diamonds (SCD). The SCD were obtained by the selective thermal oxidation of the polycrystalline films grown by chemical vapor deposition. Electrostatic spray of adhesive coating onto silicon probes was used to attach individual SCD. Geometrical parameters of produced AFM SCD probes were revealed with transmission electron microscopy: the apex angle of the pyramidal diamond crystallite was ˜10 deg, and the curvature radius at the apex was ˜2 to 10 nm. The diamond AFM probes were used for surface imaging of deoxyribonucleic acid deposited on graphite substrate. Obtained results demonstrate high efficiency of the diamond AFM probes, allowing improvement of the image quality compared to standard silicon probes.

  7. The structure of an orthorhombic crystal form of a ‘forced reduced’ thiol peroxidase reveals lattice formation aided by the presence of the affinity tag

    PubMed Central

    Beckham, Katherine S. H.; Byron, Olwyn; Roe, Andrew J.; Gabrielsen, Mads

    2012-01-01

    Thiol peroxidase (Tpx) is an atypical 2-Cys peroxiredoxin, which has been suggested to be important for cell survival and virulence in Gram-negative pathogens. The structure of a catalytically inactive version of this protein in an orthorhombic crystal form has been determined by molecular replacement. Structural alignments revealed that Tpx is conserved. Analysis of the crystal packing shows that the linker region of the affinity tag is important for formation of the crystal lattice. PMID:22691780

  8. The structure of an orthorhombic crystal form of a 'forced reduced' thiol peroxidase reveals lattice formation aided by the presence of the affinity tag.

    PubMed

    Beckham, Katherine S H; Byron, Olwyn; Roe, Andrew J; Gabrielsen, Mads

    2012-05-01

    Thiol peroxidase (Tpx) is an atypical 2-Cys peroxiredoxin, which has been suggested to be important for cell survival and virulence in Gram-negative pathogens. The structure of a catalytically inactive version of this protein in an orthorhombic crystal form has been determined by molecular replacement. Structural alignments revealed that Tpx is conserved. Analysis of the crystal packing shows that the linker region of the affinity tag is important for formation of the crystal lattice.

  9. Fabrication of large two-dimensional colloidal crystals via self-assembly in an attractive force gradient.

    PubMed

    Sun, Xiaoyan; Li, Yang; Zhang, Tian Hui; Ma, Yu-qiang; Zhang, Zexin

    2013-06-18

    Colloidal particles in a water-lutidine (WL) binary liquid mixture experience temperature-dependent attraction close to the mixture's demixing temperature. This temperature-tunable interaction can be potentially harnessed to assemble colloids and grow colloidal crystals. In this article, for the first time a novel attractive force gradient method is presented to fabricate high-quality, single-domain colloidal crystals. The well-controlled attractive force gradient here arises from a temperature gradient in the WL mixture. The nucleation of colloidal crystals in such a WL mixture preferably occurs in the high-temperature region because of the stronger attraction there. Crystallization propagates from the high-temperature region to the low-temperature region in a well-controlled way. The growth of the colloidal crystal is characterized in detail by Voronoi construction, the pair correlation function, and the orientational order parameter. It is found that the number of crystal-like particles increases with time, and a single-domain 2D colloidal crystal can be produced. The mechanism of the defect-free crystallization process is discussed on the basis of an analogy to cluster beam deposition methods. This study demonstrates an efficient and robust way to prepare colloidal crystals with little to no defects, being suitable for applications such as colloidal lithography and the fabrication of perfect 3D colloidal crystals.

  10. Method for packing chromatographic beds

    DOEpatents

    Freeman, David H.; Angeles, Rosalie M.; Keller, Suzanne

    1991-01-01

    Column chromatography beds are packed through the application of static force. A slurry of the chromatography bed material and a non-viscous liquid is filled into the column plugged at one end, and allowed to settle. The column is transferred to a centrifuge, and centrifuged for a brief period of time to achieve a predetermined packing level, at a range generally of 100-5,000 gravities. Thereafter, the plug is removed, other fixtures may be secured, and the liquid is allowed to flow out through the bed. This results in an evenly packed bed, with no channeling or preferential flow characteristics.

  11. Valve Packing

    NASA Technical Reports Server (NTRS)

    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.

  12. Disordered spherical bead packs are anisotropic

    NASA Astrophysics Data System (ADS)

    Schröder-Turk, G. E.; Mickel, W.; Schröter, M.; Delaney, G. W.; Saadatfar, M.; Senden, T. J.; Mecke, K.; Aste, T.

    2010-05-01

    Investigating how tightly objects pack space is a long-standing problem, with relevance for many disciplines from discrete mathematics to the theory of glasses. Here we report on the fundamental yet so far overlooked geometric property that disordered mono-disperse spherical bead packs have significant local structural anisotropy manifest in the shape of the free space associated with each bead. Jammed disordered packings from several types of experiments and simulations reveal very similar values of the cell anisotropy, showing a linear decrease with packing fraction. Strong deviations from this trend are observed for unjammed configurations and for partially crystalline packings above 64%. These findings suggest an inherent geometrical reason why, in disordered packings, anisotropic shapes can fill space more efficiently than spheres, and have implications for packing effects in non-spherical liquid crystals, foams and structural glasses.

  13. The study on the nanomachining property and cutting model of single-crystal sapphire by atomic force microscopy.

    PubMed

    Huang, Jen-Ching; Weng, Yung-Jin

    2014-01-01

    This study focused on the nanomachining property and cutting model of single-crystal sapphire during nanomachining. The coated diamond probe is used to as a tool, and the atomic force microscopy (AFM) is as an experimental platform for nanomachining. To understand the effect of normal force on single-crystal sapphire machining, this study tested nano-line machining and nano-rectangular pattern machining at different normal force. In nano-line machining test, the experimental results showed that the normal force increased, the groove depth from nano-line machining also increased. And the trend is logarithmic type. In nano-rectangular pattern machining test, it is found when the normal force increases, the groove depth also increased, but rather the accumulation of small chips. This paper combined the blew by air blower, the cleaning by ultrasonic cleaning machine and using contact mode probe to scan the surface topology after nanomaching, and proposed the "criterion of nanomachining cutting model," in order to determine the cutting model of single-crystal sapphire in the nanomachining is ductile regime cutting model or brittle regime cutting model. After analysis, the single-crystal sapphire substrate is processed in small normal force during nano-linear machining; its cutting modes are ductile regime cutting model. In the nano-rectangular pattern machining, due to the impact of machined zones overlap, the cutting mode is converted into a brittle regime cutting model.

  14. QPlus: atomic force microscopy on single-crystal insulators with small oscillation amplitudes at 5 K.

    PubMed

    Bettac, Andreas; Koeble, Juergen; Winkler, Konrad; Uder, Bernd; Maier, Markus; Feltz, Albrecht

    2009-07-01

    Based on a proven low temperature scanning tunneling microscope (STM) platform, we have integrated a QPlus sensor, which employs a quartz tuning fork for force detection in non-contact atomic force microscopy (AFM). For combined STM operation, this sensor has key advantages over conventional sensors. For quantitative force spectroscopy on insulating thin films or semiconductors, decoupling of the tunneling current and the piezo-electrically induced AFM signal is important. In addition, extremely low signals require the first amplification stage to be very close to the sensor, i.e. to be compatible with low temperatures. We present atomic resolution imaging on single-crystal NaCl(100) with oscillation amplitudes below 100 pm (peak-to-peak) and operation at higher flexural modes in constant frequency shift (df) imaging feedback. We also present atomic resolution measurements on MgO(100) and Au(111), and first evaluation measurements of the QPlus sensor in Kelvin probe microscopy on Si(111) 7 x 7.

  15. Pair correlation function characteristics of nearly jammed disordered and ordered hard-sphere packings

    NASA Astrophysics Data System (ADS)

    Donev, Aleksandar; Torquato, Salvatore; Stillinger, Frank H.

    2005-01-01

    We study the approach to jamming in hard-sphere packings and, in particular, the pair correlation function g2(r) around contact, both theoretically and computationally. Our computational data unambiguously separate the narrowing δ -function contribution to g2 due to emerging interparticle contacts from the background contribution due to near contacts. The data also show with unprecedented accuracy that disordered hard-sphere packings are strictly isostatic: i.e., the number of exact contacts in the jamming limit is exactly equal to the number of degrees of freedom, once rattlers are removed. For such isostatic packings, we derive a theoretical connection between the probability distribution of interparticle forces Pf(f) , which we measure computationally, and the contact contribution to g2 . We verify this relation for computationally generated isostatic packings that are representative of the maximally random jammed state. We clearly observe a maximum in Pf and a nonzero probability of zero force, shedding light on long-standing questions in the granular-media literature. We computationally observe an unusual power-law divergence in the near-contact contribution to g2 , persistent even in the jamming limit, with exponent -0.4 clearly distinguishable from previously proposed inverse-square-root divergence. Additionally, we present high-quality numerical data on the two discontinuities in the split-second peak of g2 and use a shared-neighbor analysis of the graph representing the contact network to study the local particle clusters responsible for the peculiar features. Finally, we present the computational data on the contact contribution to g2 for vacancy-diluted fcc crystal packings and also investigate partially crystallized packings along the transition from maximally disordered to fully ordered packings. We find that the contact network remains isostatic even when ordering is present. Unlike previous studies, we find that ordering has a significant impact on

  16. Valve stem and packing assembly

    DOEpatents

    Wordin, John J.

    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.

  17. Valve stem and packing assembly

    DOEpatents

    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.

  18. Development of a novel liquid crystal based cell traction force transducer system.

    PubMed

    Soon, C F; Youseffi, M; Berends, R F; Blagden, N; Denyer, M C T

    2013-01-15

    Keratinocyte traction forces play a crucial role in wound healing. The aim of this study was to develop a novel cell traction force (CTF) transducer system based on cholesteryl ester liquid crystals (LC). Keratinocytes cultured on LC induced linear and isolated deformation lines in the LC surface. As suggested by the fluorescence staining, the deformation lines appeared to correlate with the forces generated by the contraction of circumferential actin filaments which were transmitted to the LC surface via the focal adhesions. Due to the linear viscoelastic behavior of the LC, Hooke's equation was used to quantify the CTFs by associating Young's modulus of LC to the cell induced stresses and biaxial strain in forming the LC deformation. Young's modulus of the LC was profiled by using spherical indentation and determined at approximately 87.1±17.2kPa. A new technique involving cytochalasin-B treatment was used to disrupt the intracellular force generating actin fibers, and consequently the biaxial strain in the LC induced by the cells was determined. Due to the improved sensitivity and spatial resolution (∼1μm) of the LC based CTF transducer, a wide range of CTFs was determined (10-120nN). These were found to be linearly proportional to the length of the deformations. The linear relationship of CTF-deformations was then applied in a bespoke CTF mapping software to estimate CTFs and to map CTF fields. The generated CTF map highlighted distinct distributions and different magnitude of CTFs were revealed for polarized and non-polarized keratinocytes. Copyright © 2012 Elsevier B.V. All rights reserved.

  19. Sidewall roughness measurement inside photonic crystal holes by atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Strasser, P.; Robin, F.; Carlström, C. F.; Wüest, R.; Kappeler, R.; Jäckel, H.

    2007-10-01

    We present a measurement technique to quantify sidewall roughness inside planar photonic crystal (PhC) holes. Atomic force microscopy is used to scan hole cross-section profiles. By fitting a circle onto each scan line and subtracting this circle from the measurement data, a quantitative value for the deviation from the ideal cylindrical hole shape is extracted. We investigate the sidewall roughness of InP-based PhC holes depending on the nitrogen content of the semiconductor etching plasma. The existence of a trade-off between hole undercut and surface roughness by optimizing the flux of nitrogen during the plasma etching of the PhC holes is confirmed. We further quantify with this technique the influence of the direct-writing of octagons instead of circles by electron-beam lithography on the measured roughness.

  20. Quantitative lateral and vertical piezoresponse force microscopy on a PbTiO3 single crystal

    NASA Astrophysics Data System (ADS)

    Lei, Shiming; Koo, Tae-Yeong; Cao, Wenwu; Eliseev, Eugene A.; Morozovska, Anna N.; Cheong, S.-W.; Gopalan, Venkatraman

    2016-09-01

    Piezoresponse force microscopy (PFM) has emerged as a powerful tool for research in ferroelectric and piezoelectric materials. While the vertical PFM (VPFM) mode is well understood and applied at a quantitative level, the lateral PFM (LPFM) mode is rarely quantified, mainly due to the lack of a practical calibration methodology. Here by PFM imaging on a LiNbO3 180° domain wall, we demonstrate a convenient way to achieve simultaneous VPFM and LPFM calibrations. Using these calibrations, we perform a full quantitative VPFM and LPFM measurement on a (001)-cut PbTiO3 single crystal. The measured effective piezoelectric coefficients d33 e f f and d35 e f f together naturally provide more information on a material's local tensorial electromechanical properties. The proposed approach can be applied to a wide variety of ferroelectric and piezoelectric systems.

  1. The X-Ray Surface Forces Apparatus: Structure of a Thin Smectic Liquid Crystal Film Under Confinement

    NASA Astrophysics Data System (ADS)

    Idziak, Stefan H. J.; Safinya, Cyrus R.; Hill, Robert S.; Kraiser, Keith E.; Ruths, Marina; Warriner, Heidi E.; Steinberg, Suzi; Liang, Keng S.; Israelachvili, Jacob N.

    1994-06-01

    An x-ray surface forces apparatus for simultaneously measuring forces and structures of confined complex fluids under static and flow conditions is described. This apparatus, combined with an intense synchrotron x-ray source, allows investigation of molecular orientations within a thin liquid crystal film confined between two shearing mica surfaces 3900 angstroms apart. The layer-forming smectic liquid crystal 8CB (4-cyano-4'-octylbiphenyl) adopted a series of distinct planar layer orientations, including the bulk flow-forbidden b orientation.

  2. Clean surface processing of rubrene single crystal immersed in ionic liquid by using frequency modulation atomic force microscopy

    SciTech Connect

    Yokota, Yasuyuki; Hara, Hisaya; Morino, Yusuke; Bando, Ken-ichi; Imanishi, Akihito; Fukui, Ken-ichi; Uemura, Takafumi; Takeya, Jun

    2014-06-30

    Surface processing of a rubrene single crystal immersed in ionic liquids is valuable for further development of low voltage transistors operated by an electric double layer. We performed a precise and clean surface processing based on the tip-induced dissolution of rubrene molecules at the ionic liquid/rubrene single crystal interfaces by using frequency modulation atomic force microscopy. Molecular resolution imaging revealed that the tip-induced dissolution proceeded via metastable low density states derived from the anisotropic intermolecular interactions within the crystal structure.

  3. Direct observation of the growth of gibbsite crystals by atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Freij, Sawsan J.; Parkinson, Gordon M.; Reyhani, Manijeh M.

    2004-01-01

    Atomic force microscope (AFM) has been used to investigate the mechanism of gibbsite crystallization on all the morphologically important faces. Growth on single crystal faces has been observed by a series of ex situ experiments, in which the same area was repeatedly located and imaged after growth had occurred in synthetic solution. At the same supersaturation level and temperature, the ex situ experiments have revealed a variety of growth modes: (1) Continuous birth and spread on a flat surface, the nuclei forming as approximately circular features that develop into elongated features, indicating anisotropic growth, followed by restoration of the flatness of the original area after further growth. (2) Step growth followed by rough growth on a surface that contains growth hillocks. (3) Two-dimensional nucleation on a surface that contains a surface defect (tilt boundary). The results are used to establish a clearer picture of the growth mechanism of gibbsite, and the effect of the seed surface structure. On the prismatic faces of gibbsite, steps parallel to the (0 0 1) face and block formation were imaged. Step growth was observed in both the [0 0 1] direction and parallel to the (0 0 1) plane. No nucleation was observed, and no emergent screw dislocations have been resolved.

  4. Crystal lattice imaging of the silica and alumina faces of kaolinite using atomic force microscopy.

    PubMed

    Gupta, Vishal; Hampton, Marc A; Nguyen, Anh V; Miller, Jan D

    2010-12-01

    The crystal lattice images of the two faces of kaolinite (the silica face and the alumina face) have been obtained using contact-mode atomic force microscopy (AFM) under ambient conditions. Lattice resolution images reveal the hexagonal surface lattice of these two faces of kaolinite. Analysis of the silica face of kaolinite showed that the hexagonal surface lattice ring of oxygen atoms had a periodicity of 0.50±0.04nm between neighboring oxygen atoms, which is in good agreement with the surface lattice structure of the mica basal plane. The center of the hexagonal ring of oxygen atoms is vacant. Analysis of the alumina face of kaolinite showed that the hexagonal surface lattice ring of hydroxyls surround a hydroxyl in the center of the ring. The atomic spacing between neighboring hydroxyls was determined as 0.36±0.04nm. Ordering of the kaolinite particles for examination of the silica and alumina surfaces was accomplished using different substrates, a procedure previously established. Crystal lattice imaging supports previous results and independently confirms that the two faces of kaolinite have been properly identified.

  5. Redesigned of T-38 Displacement Gyroscope Pack.

    DTIC Science & Technology

    1984-01-01

    0D-Ai38 847 REDESIGNED OF T-38 DISPLACEMENT GYROSCOPE PACK(U) AIR i/i. - FORCE PflCKAGING EVALUATION AGENCY WRIGHT-PATTERSON AFB OH MATERIALS...Branchv HQ AFLC/DSTZT AUTOVON 787-4519 COMMERCIAL (513) 257-4519 Ci. REDESIGNED OF T-38 DISPLACEMENT GYROSCOPE PACK D T 1 e’ 211984 HQ AFLC/DSTZ AIR FORCE... Air Force Packaging Evaluation Agency redesigned the T-38, 19005 gyroscope displacement pack (TPO-00-077-3218) reducing its cubage by 48% and tare

  6. Three dimensional imaging of soft sphere packings under shear

    NASA Astrophysics Data System (ADS)

    Dijksman, Joshua; Zheng, Hu; Behringer, Robert

    2012-02-01

    The (microscopic) flow of three dimensional disordered athermal granular packings remains poorly understood. However, experimentally studying flow and deformations in a three dimensional packing of grains is challenging due to the opacity of such packings. We use refractive index matched scanning with hydrogel spheres to image such flows. Hydrogel is soft and has low friction, which allows for the study of contact forces via contact deformations. We look at how force networks develop in sheared packings close to the onset of mechanical rigidity.

  7. Packed Bed Reactor Experiment

    NASA Image and Video Library

    The purpose of the Packed Bed Reactor Experiment in low gravity is to determine how a mixture of gas and liquid flows through a packed bed in reduced gravity. A packed bed consists of a metal pipe ...

  8. Quasistatic packings of droplets in flat microfluidic channels

    NASA Astrophysics Data System (ADS)

    Kadivar, Erfan

    2016-02-01

    As observed in recent experiments, monodisperse droplets self-assemble spontaneously in different ordered packings. In this work, we present a numerical study of the droplet packings in the flat rectangular microfluidic channels. Employing the boundary element method, we numerically solve the Stokes equation in two-dimension and investigate the appearance of droplet packing and transition between one and two-row packings of monodisperse emulsion droplets. By calculating packing force applied on the droplet interface, we investigate the effect of flow rate, droplet size, and surface tension on the packing configurations of droplets and transition between different topological packings.

  9. Toward polarizable AMOEBA thermodynamics at fixed charge efficiency using a dual force field approach: application to organic crystals.

    PubMed

    Nessler, Ian J; Litman, Jacob M; Schnieders, Michael J

    2016-11-09

    First principles prediction of the structure, thermodynamics and solubility of organic molecular crystals, which play a central role in chemical, material, pharmaceutical and engineering sciences, challenges both potential energy functions and sampling methodologies. Here we calculate absolute crystal deposition thermodynamics using a novel dual force field approach whose goal is to maintain the accuracy of advanced multipole force fields (e.g. the polarizable AMOEBA model) while performing more than 95% of the sampling in an inexpensive fixed charge (FC) force field (e.g. OPLS-AA). Absolute crystal sublimation/deposition phase transition free energies were determined using an alchemical path that grows the crystalline state from a vapor reference state based on sampling with the OPLS-AA force field, followed by dual force field thermodynamic corrections to change between FC and AMOEBA resolutions at both end states (we denote the three step path as AMOEBA/FC). Importantly, whereas the phase transition requires on the order of 200 ns of sampling per compound, only 5 ns of sampling was needed for the dual force field thermodynamic corrections to reach a mean statistical uncertainty of 0.05 kcal mol(-1). For five organic compounds, the mean unsigned error between direct use of AMOEBA and the AMOEBA/FC dual force field path was only 0.2 kcal mol(-1) and not statistically significant. Compared to experimental deposition thermodynamics, the mean unsigned error for AMOEBA/FC (1.4 kcal mol(-1)) was more than a factor of two smaller than uncorrected OPLS-AA (3.2 kcal mol(-1)). Overall, the dual force field thermodynamic corrections reduced condensed phase sampling in the expensive force field by a factor of 40, and may prove useful for protein stability or binding thermodynamics in the future.

  10. Effect of direction of an external force on crystallization of colloidal particles in a V-shaped groove by sedimentation

    NASA Astrophysics Data System (ADS)

    Sato, Masahide

    2016-09-01

    We carried out Langevin dynamics simulations to study the effect of the direction of a uniform external force on the crystallization of colloidal particles in a V-shaped groove. When the inclination of the side walls of a groove was set to a suitable value and the external force bisected the angle, the face-centered-cubic (fcc) structure grew with a {100} growth interface. When the external force was inclined, the number of solidified particles decreased with increasing inclination, which is different from the growth in an inverted pyramidal container.

  11. Force.

    ERIC Educational Resources Information Center

    Gamble, Reed

    1989-01-01

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

  12. Force.

    ERIC Educational Resources Information Center

    Gamble, Reed

    1989-01-01

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

  13. In situ atomic force microscopy studies of surface morphology, growth kinetics, defect structure and dissolution in macromolecular crystallization

    NASA Astrophysics Data System (ADS)

    Malkin, A. J.; Kuznetsov, Yu. G.; McPherson, A.

    1999-01-01

    Surface morphologies of thaumatin, catalase, lysozyme and xylanase crystals were investigated using in situ atomic force microscopy. For thaumatin, lysozyme and xylanase crystals, growth steps having a height equal to the unit cell parameter were produced both by screw dislocations and two-dimensional nuclei. Growth of catalase crystals proceeded in alternating patterns exclusively by two-dimensional nucleation and the successive deposition of distinctive growth layers, each having a step height equal to half the unit cell parameter. The shapes of islands on successive layers were related by 2-fold rotation axes along the <0 0 1> direction. Experiments revealed that step bunching on crystalline surfaces occurred either due to two- or three-dimensional nucleation on the terraces of vicinal slopes or as a result of uneven step generation by complex dislocation sources. Growth kinetics for thaumatin and catalase crystals were investigated over wide supersaturation ranges. Strong directional kinetic anisotropy in the tangential step growth rates in different directions was seen. From the supersaturation dependencies of tangential step rates and the rates of two-dimensional nucleation, the kinetic coefficients of the steps and the surface free energy of the step edge were calculated. Adsorption of impurities which formed filaments on the surfaces of catalase and thaumatin crystals was recorded. Cessation of growth of xylanase and lysozyme crystals was also observed and appeared to be a consequence of the formation of dense impurity adsorption layers. Crystal growth resumed upon scarring of the impurity adsorption layer and clearing of the crystal surface with the AFM tip. Adsorption of three-dimensional clusters, which consequently developed into either properly aligned multilayer stacks or misaligned microcrystals was recorded. For catalase crystals, incorporation of misoriented microcrystals as large as 50×3×0.1 μm 3 produced elastic deformations in growth layers

  14. Stuffed Derivatives of Close-Packed Structures

    ERIC Educational Resources Information Center

    Douglas, Bodie E.

    2007-01-01

    Decades ago Buerger described and later Palmer reviewed stuffed silica crystal structures widely used by mineralogists. Many publications and books have discussed common crystal structures in terms of close-packing of one set of atoms or ions (P sites) with other atoms or ions in tetrahedral (T) or octahedral (O) sites. Douglas and Ho described…

  15. Stuffed Derivatives of Close-Packed Structures

    ERIC Educational Resources Information Center

    Douglas, Bodie E.

    2007-01-01

    Decades ago Buerger described and later Palmer reviewed stuffed silica crystal structures widely used by mineralogists. Many publications and books have discussed common crystal structures in terms of close-packing of one set of atoms or ions (P sites) with other atoms or ions in tetrahedral (T) or octahedral (O) sites. Douglas and Ho described…

  16. Dense crystalline packings of ellipsoids

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

    An ellipsoid, the simplest nonspherical shape, has been extensively used as a model for elongated building blocks for a wide spectrum of molecular, colloidal, and granular systems. Yet the densest packing of congruent hard ellipsoids, which is intimately related to the high-density phase of many condensed matter systems, is still an open problem. We discover an unusual family of dense crystalline packings of self-dual ellipsoids (ratios of the semiaxes α : √{α }:1 ), containing 24 particles with a quasi-square-triangular (SQ-TR) tiling arrangement in the fundamental cell. The associated packing density ϕ exceeds that of the densest known SM2 crystal [ A. Donev et al., Phys. Rev. Lett. 92, 255506 (2004), 10.1103/PhysRevLett.92.255506] for aspect ratios α in (1.365, 1.5625), attaining a maximal ϕ ≈0.758 06 ... at α = 93 /64 . We show that the SQ-TR phase derived from these dense packings is thermodynamically stable at high densities over the aforementioned α range and report a phase diagram for self-dual ellipsoids. The discovery of the SQ-TR crystal suggests organizing principles for nonspherical particles and self-assembly of colloidal systems.

  17. Toward chaperone-assisted crystallography: Protein engineering enhancement of crystal packing and X-ray phasing capabilities of a camelid single-domain antibody (V[subscript H]H) scaffold

    SciTech Connect

    Tereshko, Valentina; Uysal, Serdar; Koide, Akiko; Margalef, Katrina; Koide, Shohei; Kossiakoff, Anthony A.

    2008-07-28

    A crystallization chaperone is an auxiliary protein that binds to a target of interest, enhances and modulates crystal packing, and provides high-quality phasing information. We critically evaluated the effectiveness of a camelid single-domain antibody (V{sub H}H) as a crystallization chaperone. By using a yeast surface display system for V{sub H}H, we successfully introduced additional Met residues in the core of the V{sub H}H scaffold. We identified a set of SeMet-labeled V{sub H}H variants that collectively produced six new crystal forms as the complex with the model antigen, RNase A. The crystals exhibited monoclinic, orthorhombic, triclinic, and tetragonal symmetry and have one or two complexes in the asymmetric unit, some of which diffracted to an atomic resolution. The phasing power of the Met-enriched V{sub H}H chaperone allowed for auto-building the entire complex using single-anomalous dispersion technique (SAD) without the need for introducing SeMet into the target protein. We show that phases produced by combining SAD and VHH model-based phases are accurate enough to easily solve structures of the size reported here, eliminating the need to collect multiple wavelength multiple-anomalous dispersion (MAD) data. Together with the presence of high-throughput selection systems (e.g., phage display libraries) for V{sub H}H, the enhanced V{sub H}H domain described here will be an excellent scaffold for producing effective crystallization chaperones.

  18. Computational-fluid-dynamics (CFD) modelling of an industrial crystallizer: application to the forced-circulation reactor.

    PubMed

    Essemiani, Karim; de Traversay, Christelle; Gallot, Jean Claude

    2004-12-01

    The CFD (computational fluid dynamics) technique is used to describe the mixing conditions in a pilot-scale FCC (forced-circulation crystallizer) and to study the impact of flow rate and aspect ratio on local flow conditions and RTD (residence-time distribution) in the crystallizer. The analysis adequately predicts the oscillating flow and two-phase (gas-liquid) interaction at the free surface. A comparison has been made between the CFD predictions and models of RTD. The results support the use of CFD methodology as an aid to optimization of commercial-scale FCC design.

  19. Random-close packing limits for monodisperse and polydisperse hard spheres.

    PubMed

    Baranau, Vasili; Tallarek, Ulrich

    2014-06-07

    We investigate how the densities of inherent structures, which we refer to as the closest jammed configurations, are distributed for packings of 10(4) frictionless hard spheres. A computational algorithm is introduced to generate closest jammed configurations and determine corresponding densities. Closest jamming densities for monodisperse packings generated with high compression rates using Lubachevsky-Stillinger and force-biased algorithms are distributed in a narrow density range from φ = 0.634-0.636 to φ≈ 0.64; closest jamming densities for monodisperse packings generated with low compression rates converge to φ≈ 0.65 and grow rapidly when crystallization starts with very low compression rates. We interpret φ≈ 0.64 as the random-close packing (RCP) limit and φ≈ 0.65 as a lower bound of the glass close packing (GCP) limit, whereas φ = 0.634-0.636 is attributed to another characteristic (lowest typical, LT) density φLT. The three characteristic densities φLT, φRCP, and φGCP are determined for polydisperse packings with log-normal sphere radii distributions.

  20. Structural and mechanical features of the order-disorder transition in experimental hard-sphere packings

    NASA Astrophysics Data System (ADS)

    Hanifpour, M.; Francois, N.; Robins, V.; Kingston, A.; Vaez Allaei, S. M.; Saadatfar, M.

    2015-06-01

    Here we present an experimental and numerical investigation on the grain-scale geometrical and mechanical properties of partially crystallized structures made of macroscopic frictional grains. Crystallization is inevitable in arrangements of monosized hard spheres with packing densities exceeding Bernal's limiting density ϕBernal≈0.64 . We study packings of monosized hard spheres whose density spans over a wide range (0.59 <ϕ <0.72 ) . These experiments harness x-ray computed tomography, three-dimensional image analysis, and numerical simulations to access precisely the geometry and the 3D structure of internal forces within the sphere packings. We show that clear geometrical transitions coincide with modifications of the mechanical backbone of the packing both at the grain and global scale. Notably, two transitions are identified at ϕBernal≈0.64 and ϕc≈0.68 . These results provide insights on how geometrical and mechanical features at the grain scale conspire to yield partially crystallized structures that are mechanically stable.

  1. A Phenomenological Model of Bulk Force in a Li-Ion Battery Pack and Its Application to State of Charge Estimation

    SciTech Connect

    Mohan, S; Kim, Y; Siegel, JB; Samad, NA; Stefanopoulou, AG

    2014-09-19

    A phenomenological model of the bulk force exerted by a lithium ion cell during various charge, discharge, and temperature operating conditions is developed. The measured and modeled force resembles the carbon expansion behavior associated with the phase changes during intercalation, as there are ranges of state of charge (SOC) with a gradual force increase and ranges of SOC with very small change in force. The model includes the influence of temperature on the observed force capturing the underlying thermal expansion phenomena. Moreover the model is capable of describing the changes in force during thermal transients, when internal battery heating due to high C-rates or rapid changes in the ambient temperature, which create a mismatch in the temperature of the cell and the holding fixture. It is finally shown that the bulk force model can be very useful for a more accurate and robust SOC estimation based on fusing information from voltage and force (or pressure) measurements. (C) The Author(s) 2014. Published by ECS. This is an open access article distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives 4.0 License (CC BY-NC-ND, http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is not changed in any way and is properly cited. For permission for commercial reuse, please email oa@electrochem.org. All rights reserved.

  2. Liquid-filled photonic-crystal-fiber-based multimodal interferometer for simultaneous measurement of temperature and force.

    PubMed

    Lin, Wei; Song, Binbin; Miao, Yinping; Zhang, Hao; Yan, Donglin; Liu, Bo; Liu, Yange

    2015-02-20

    In this paper, a multimodal interferometer based on the liquid-filled photonic crystal fiber (PCF) has been proposed and experimentally demonstrated for simultaneous measurement of temperature and force. Experimental results show that different spectral minima have distinctive sensitivities to the temperature and force. The proposed interferometer shows the temperature sensitivities of -9.214 nm/°C, -24.757 nm/°C, and -12.543/°C and the force sensitivities of 0 nm/N, 4.978 nm/N, and 0 nm/N, respectively, for the three selected spectral minima. The sensing matrices are thus established and simultaneous measurement of temperature and force has been experimentally demonstrated. The proposed liquid-filled PCF-based multimodal interferometer would find potential applications in multiple-parameter sensing owing to its high sensitivity, compactness, ease of fabrication, and low cost.

  3. Surface-Induced Optimal Packing of Two-Dimensional Molecular Networks

    NASA Astrophysics Data System (ADS)

    Copie, Guillaume; Cleri, Fabrizio; Makoudi, Younes; Krzeminski, Christophe; Berthe, Maxime; Cherioux, Frédéric; Palmino, Frank; Grandidier, Bruno

    2015-02-01

    High-density packing in organic crystals is usually associated with an increase of the coordination between molecules. Such a concept is not necessarily extended to two-dimensional molecular networks self-assembled on a solid surface, for which we demonstrate the key role of the surface in inducing the optimal packing. By a combination of scanning tunneling microscopy experiments and multiscale computer simulations, we study the phase transition between two polymorphs. We find that, contrary to intuition, the structure with the lowest packing fraction corresponds to the highest molecular coordination number, due to the competition between surface and intermolecular forces. Having the lowest free energy, this structure spreads out as the most stable polymorph over a wide range of molecular concentrations.

  4. Shock wave compression of hexagonal-close-packed metal single crystals: Time-dependent, anisotropic elastic-plastic response of beryllium

    SciTech Connect

    Winey, J. M.; Gupta, Y. M.

    2014-07-21

    Understanding and modeling the response of hcp metals to high stress impulsive loading is challenging because the lower crystal symmetry, compared to cubic metals, results in a significantly more complex material response. To gain insight into the inelastic deformation of hcp metals subjected to high dynamic stresses, shock wave compression of single crystals provides a useful approach because different inelastic deformation mechanisms can be examined selectively by shock compression along different crystal orientations. As a representative example, we report, here, on wave propagation simulations for beryllium (Be) single crystals shocked along the c-axis, a-axis, and several low-symmetry directions to peak stresses reaching 7 GPa. The simulations utilized a time-dependent, anisotropic material model that incorporated dislocation dynamics, deformation twinning, and shear cracking based descriptions of inelastic deformation. The simulation results showed good overall agreement with measured wave profiles for all the different crystal orientations examined [Pope and Johnson, J. Appl. Phys. 46, 720 (1975)], including features arising from wave mode coupling due to the highly anisotropic inelastic response of Be. This good agreement demonstrates that the measured profiles can be understood in terms of dislocation slip along basal, prismatic, and pyramidal planes, together with deformation twinning along (101{sup ¯}2) planes. Our results show that the response of shocked Be single crystals involves the simultaneous operation of multiple, distinct inelastic deformation mechanisms for all orientations except the c-axis. For shocked c-axis Be, the measured wave profiles do not provide good discrimination between pyramidal slip and other inelastic deformation mechanisms, such as shear cracking. The findings presented here provide insight into the complex inelastic deformation response of shocked Be single crystals and are expected to be useful for other hcp crystals

  5. Simultaneous measurement of temperature and force with high sensitivities based on filling different index liquids into photonic crystal fiber.

    PubMed

    Liang, Hu; Zhang, Weigang; Geng, Pengcheng; Liu, Yange; Wang, Zhi; Guo, Junqi; Gao, Shecheng; Yan, Suyuan

    2013-04-01

    A double-filled photonic crystal fiber (PCF) was fabricated by filling liquids of different indexes into two air holes in the cladding. The core mode coupled to the local cladding modes LP(01) and LP(11) in the 1310 and 1550 nm wavebands, respectively. Due to the unique characteristics of the mode coupling, the resonant peaks in different resonance areas shifted to the opposite directions with the variations of the temperature or the force. The double-filled PCFs achieved in this work showed useful applications in the simultaneous measurement of both the temperature and the force.

  6. Polarizable protein packing.

    PubMed

    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.

  7. Simulations of a protein crystal with a high resolution X-ray structure: Evaluation of force fields and water models

    PubMed Central

    Cerutti, David S.; Freddolino, Peter L.; Duke, Robert E.; Case, David A.

    2010-01-01

    We use classical molecular dynamics and sixteen combinations of force fields and water models to simulate a protein crystal observed by room-temperature X-ray diffraction. The high resolution of the diffraction data (0.96Å) and the simplicity of the crystallization solution (nearly pure water) makes it possible to attribute any inconsistencies between the crystal structure and our simulations to artifacts of the models rather than inadequate representation of the crystal environment or uncertainty in the experiment. All simulations were extended for 100ns of production dynamics, permitting some long-timescale artifacts of each model to emerge. The most noticeable effect of these artifacts is a model-dependent drift in the unit cell dimensions, which can become as large as 5% in certain force fields; the underlying cause is the replacement of native crystallographic contacts with non-native ones, which can occur with heterogeneity (loss of crystallographic symmetry) in simulations with some force fields. We find that the AMBER FF99SB force field maintains a lattice structure nearest that seen in the X-ray data, and produces the most realistic atomic fluctuations (by comparison to crystallographic B-factors) of all the models tested. We find that the choice of water model has a minor effect in comparison to the choice of protein model. We also identify a number of artifacts that occur throughout all of the simulations: excessive formation of hydrogen bonds or salt bridges between polar groups and loss of hydrophobic interactions. This study is intended as a foundation for future work that will identify individual parameters in each molecular model that can be modified to improve their representations of protein structure and thermodynamics. PMID:20860388

  8. Simulations of a protein crystal with a high resolution X-ray structure: evaluation of force fields and water models.

    PubMed

    Cerutti, David S; Freddolino, Peter L; Duke, Robert E; Case, David A

    2010-10-14

    We use classical molecular dynamics and 16 combinations of force fields and water models to simulate a protein crystal observed by room-temperature X-ray diffraction. The high resolution of the diffraction data (0.96 Å) and the simplicity of the crystallization solution (nearly pure water) make it possible to attribute any inconsistencies between the crystal structure and our simulations to artifacts of the models rather than inadequate representation of the crystal environment or uncertainty in the experiment. All simulations were extended for 100 ns of production dynamics, permitting some long-time scale artifacts of each model to emerge. The most noticeable effect of these artifacts is a model-dependent drift in the unit cell dimensions, which can become as large as 5% in certain force fields; the underlying cause is the replacement of native crystallographic contacts with non-native ones, which can occur with heterogeneity (loss of crystallographic symmetry) in simulations with some force fields. We find that the AMBER FF99SB force field maintains a lattice structure nearest that seen in the X-ray data, and produces the most realistic atomic fluctuations (by comparison to crystallographic B-factors) of all the models tested. We find that the choice of water model has a minor effect in comparison to the choice of protein model. We also identify a number of artifacts that occur throughout all of the simulations: excessive formation of hydrogen bonds or salt bridges between polar groups and loss of hydrophobic interactions. This study is intended as a foundation for future work that will identify individual parameters in each molecular model that can be modified to improve their representations of protein structure and thermodynamics.

  9. Influence of force constant on surface phonon polariton properties of cubic ZnS1-xSex crystals

    NASA Astrophysics Data System (ADS)

    Yew, P.; Lee, S. C.; Ng, S. S.; Yoon, T. L.; Hassan, H. Abu.

    2015-04-01

    In this paper, our attention is focused on the influence of force constant on surface phonon polariton (SPhP) properties of cubic ZnS1-xSex mixed crystals. Two different force constants were used, i.e., one considers only the first nearest neighbour interactions and another considers up to the second nearest neighbour interactions. For the theoretical modelling, modified random element iso-displacement (MREI) model was used. The results revealed that the second nearest neighbour interactions assumption gives significant impact on composition dependence of optical phonon spectra in which it can produce theoretical results closer to experimental data. Because of the dependence of SPhP on optical phonon modes, it is expected that the SPhP properties are also sensitive to the force constant. The SPhP dispersion curves are calculated for both of the end member binary crystals (x = 0 and 1) and mixed crystal with composition x = 0.3, 0.5, and 0.8. Finally, implication of the theoretical results on relevant experiment is discussed.

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

    PubMed

    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.

  11. Study of polymeric additive effect on calcium oxalate dihydrate crystal growth using real-time atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Jung, Taesung; Kim, Jong-Nam; Kim, Woo-Sik; Kyun Choi, Chang

    2011-07-01

    Microscopic events associated with crystal growth and characterization of the growth hillocks on the (1 0 0) and (1 0 1) faces of COD were examined by atomic force microscopy. The (1 0 0) and (1 0 1) faces of COD developed elliptical and triangular hillocks and pits, respectively. Each face exhibited hillocks with step sites that can be assigned to specific crystal planes, enabling direct determination of the growth rates along specific crystallographic directions. The addition of macromolecules with anionic side chains, poly- L-aspartate, poly- L-glutamate, and polyacrylate resulted in inhibition of growth on the hillock step planes. The magnitude of their effect depended on the macromolecule structures and identity of the step site. The isotropic shape of the COD hillocks mimicked the shape of the resulting macroscopic COD crystals based on step-specific binding of the macromolecules to the COD crystal, with stronger step pinning along the [0 1 0] direction than in the [0 0 1] direction. Electrostatic matching between the crystal faces and additives according to the ionic array of calcium oxalate in the COD structure was found to be responsible for the preferential binding of the macromolecules to terraces.

  12. Moisture-induced surface crystallization of spray-dried amorphous lactose particles studied by atomic force microscopy.

    PubMed

    Mahlin, Denny; Berggren, Jonas; Alderborn, Göran; Engström, Sven

    2004-01-01

    The aim of this study was to show that atomic force microscopy (AFM) can be used to obtain mechanistic and kinetic information about the process of moisture-induced surface crystallization of single particles of amorphous lactose. Completely amorphous lactose particles were prepared by spray-drying a solution of alpha-lactose monohydrate, and moisture-induced crystallization was monitored for a bed of particles by microcalorimetry and for single particles by AFM. From the AFM images it was found that crystallization of the surface of single particles can be described in terms of a sequence of three events: an initial smoothening of the surface, formation of crystalline nanostructures dispersed in amorphous material, and growth of these structures to a complete crystalline surface. The surface roughness parameter rugosity was used to estimate the fraction crystalline surface, and the growth kinetics were found to obey the JMAK equation. The fraction crystalline surface at different times could also be estimated by determining the growth rate of individual crystals. It was concluded that AFM offers a unique means of visualizing the process of moisture-induced surface crystallization of amorphous particles and enables mechanistic and kinetic information about the process to be extracted. Copyright 2004 Wiley-Liss, Inc.

  13. Modified corrections for London forces in solid-state density functional theory calculations of structure and lattice dynamics of molecular crystals.

    PubMed

    King, Matthew D; Korter, Timothy M

    2012-06-28

    Dispersion forces are critical for defining the crystal structures and vibrational potentials of molecular crystals. It is, therefore, important to include corrections for these forces in periodic density functional theory (DFT) calculations of lattice vibrational frequencies. In this study, DFT was augmented with a correction term for London-type dispersion forces in the simulations of the structures and terahertz (THz) vibrational spectra of the dispersion-bound solids naphthalene and durene. The parameters of the correction term were modified to best reproduce the experimental crystal structures and THz spectra. It was found that the accurate reproduction of the lattice dimensions by adjusting the magnitude of the applied dispersion forces resulted in the highest-quality fit of the calculated vibrational modes with the observed THz absorptions. The method presented for the modification of the dispersion corrections provides a practical approach to accurately simulating the THz spectra of molecular crystals, accounting for inherent systematic errors imposed by computational and experimental factors.

  14. Importance of C-H-donor and C-H-anion contact interactions for the crystal packing, the lattice softness and the superconducting transition temperatures of organic conducting salts

    SciTech Connect

    Whangbo, M.-H.; Novoa, J.J.; Jung, D. . Dept. of Chemistry); Williams, J.M.; Kinj, A.M.; Wang, H.H.; Geiser, U.; Beno, M.A.; Carlson, K.D. )

    1990-01-01

    The organic donor molecule BEDT-TTF and its analogs 2--4 have yielded a number of ambient-pressure superconducting salts. What structural and electronic factors govern the magnitudes of their superconducting transition temperature {Tc} has been a topic of intense studies. Examination of the band electronic structures of closely related superconducting salts shows, that the magnitudes of their {Tc}'s are primarily determined by the softness of their crystal lattices. The crystal packing and the lattice softness of organic donor salts are strongly influenced by the donor{hor ellipsis}donor and donor{hor ellipsis}anion contact interactions involving the donor-molecule C-H bonds. In the present work, we briefly review the electronic structures of some representative organic salt superconductors and discuss the softness of their crytsal lattices on the basis of the interaction energies calculated for the C-H{hor ellipsis}donor and C-H{hor ellipsis}anion contact interactions. 34 refs., 14 figs., 8 tabs.

  15. Transferable force field for crystal structure predictions, investigation of performance and exploration of different rescoring strategies using DFT-D methods.

    PubMed

    Broo, Anders; Nilsson Lill, Sten O

    2016-08-01

    A new force field, here called AZ-FF, aimed at being used for crystal structure predictions, has been developed. The force field is transferable to a new type of chemistry without additional training or modifications. This makes the force field very useful in the prediction of crystal structures of new drug molecules since the time-consuming step of developing a new force field for each new molecule is circumvented. The accuracy of the force field was tested on a set of 40 drug-like molecules and found to be very good where observed crystal structures are found at the top of the ranked list of tentative crystal structures. Re-ranking with dispersion-corrected density functional theory (DFT-D) methods further improves the scoring. After DFT-D geometry optimization the observed crystal structure is found at the leading top of the ranking list. DFT-D methods and force field methods have been evaluated for use in predicting properties such as phase transitions upon heating, mechanical properties or intrinsic crystalline solubility. The utility of using crystal structure predictions and the associated material properties in risk assessment in connection with form selection in the drug development process is discussed.

  16. Enzymatic degradation processes of poly[(R)-3-hydroxybutyric acid] and poly[(R)-3-hydroxybutyric acid-co-(R)-3-hydroxyvaleric acid] single crystals revealed by atomic force microscopy: effects of molecular weight and second-monomer composition on erosion rates.

    PubMed

    Numata, Keiji; Kikkawa, Yoshihiro; Tsuge, Takeharu; Iwata, Tadahisa; Doi, Yoshiharu; Abe, Hideki

    2005-01-01

    Enzymatic degradation processes of poly[(R)-3-hydroxybutyric acid] (P(3HB)) and poly[(R)-3-hydroxybutyric acid-co-(R)-3-hydroxyvaleric acid] (P(3HB-co-3HV)) single crystals in the presence of PHB depolymerase from Ralstonia pickettii T1 were studied by real-time and static atomic force microscopy (AFM) observations. Fibril-like crystals were generated along the long axis of single crystals during the enzymatic degradation, and then the dimensions of fibril-like crystals were analyzed quantitatively. The morphologies and sizes of fibril-like crystals were dependent on the molecular weight and copolymer composition of polymers. For all samples, the crystalline thickness gradually decreased toward a tip from the root of a fibril-like crystal after enzymatic degradation for 1 h. The thinning of fibril-like crystals may be attributed to the destruction of chain-packing structure toward crystallographic c axis by the adsorption of enzyme. From the real-time AFM images, it was found that at the initial stage of degradation the enzymatic erosion started from the disordered chain-packing region in single crystals to form the grooves along the a axis. The generated fibril-like crystals deformed at a constant rate along the a axis with a constant rate after the induction time. The erosion rate at the grooves along the a axis increased with a decrease of molecular weight and with an increase of copolymer composition. On the other hand, the erosion rate along the a axis, at the tip of the fibril-like crystal, was dependent on only the copolymer composition, and the value increased with an increase in the copolymer composition. The morphologies and sizes of fibril-like crystals were governed by both the erosion rates along the a axis at the grooves and tip of fibril-like crystals. In addition, we were able to estimated the overall enzymatic erosion rate of single crystals by PHB depolymerase from the volumetric analysis.

  17. 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

    PubMed Central

    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

  18. 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.

    PubMed

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

    2013-06-01

    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.

  19. Vertical Magnetic Levitation Force Measurement on Single Crystal YBaCuO Bulk at Different Temperatures

    NASA Astrophysics Data System (ADS)

    Celik, Sukru; Guner, Sait Baris; Ozturk, Kemal; Ozturk, Ozgur

    Magnetic levitation force measurements of HTS samples are performed with the use of liquid nitrogen. It is both convenient and cheap. However, the temperature of the sample cannot be changed (77 K) and there is problem of frost. So, it is necessary to build another type of system to measure the levitation force high Tc superconductor at different temperatures. In this study, we fabricated YBaCuO superconducting by top-seeding-melting-growth (TSMG) technique and measured vertical forces of them at FC (Field Cooling) and ZFC (Zero Field Cooling) regimes by using our new designed magnetic levitation force measurement system. It was used to investigate the three-dimensional levitation force and lateral force in the levitation system consisting of a cylindrical magnet and a permanent cylindrical superconductor at different temperatures (37, 47, 57, 67 and 77 K).

  20. Layered solids based on second-sphere coordination interactions: synthesis, spectroscopic characterization, crystal structure and packing of two copper(II) naphthalene-2-sulfonates

    NASA Astrophysics Data System (ADS)

    Sharma, Raj Pal; Sharma, Rajni; Bala, Ritu; Rychlewska, Urszula; Warżajtis, Beata

    2005-03-01

    [Cu(H 2O) 6](C 10H 7SO 3) 21 was obtained from reaction of CuCO 3·Cu(OH) 2 and naphthalene-2-sulphonic acid in aqueous medium in 1:4 molar ratio. It crystallizes in the monoclinic space group P2 1/ n with a=7.0582(3) Å, b=6.2666(3) Å, and c=27.1420(10) Å, β=92.678(4)°, Z=2. The structure was determined from 1986 observed reflections and refined to R=0.033. When ethylenediamine was added to hexaaquacopper(II) naphthalene-2-sulfonate dissolved in water, [Cu(en) 2(H 2O) 2](C 10H 7SO 3) 22 was obtained which crystallizes in the triclinic space group P1¯ with a=7.1491(5) Å, b=7.1949(5) Å, and c=14.6500(10) Å, α=99.025(6)°, β=98.976(6)°, and γ=104.262(6)°, Z=1. The structure was determined from 2296 observed reflections and refined to R=0.0313. X-ray structure determination of 1 revealed an ionic structure consisting of [Cu(H 2O) 6] +2 and two naphthalene-2-sulfonate anions while that of 2 contains [Cu(en) 2(H 2O) 2] 2+ cation and two naphthalene-2-sulfonate anions. Characteristic for the studied crystals is the alternated-layer arrangement of complex cations and naphthalene-2-sulfonate anions, linked together via hydrogen bonding, and the presence of a particularly robust R22(8) hydrogen-bonding motif that joins the complex cation with two oxygen atoms of the same sulfonate group. Elemental analyses, IR, UV/vis spectroscopic studies are consistent with the structures revealed by X-ray structure determination.

  1. Te inclusion-induced electrical field perturbation in CdZnTe single crystals revealed by Kelvin probe force microscopy.

    PubMed

    Gu, Yaxu; Jie, Wanqi; Li, Linglong; Xu, Yadong; Yang, Yaodong; Ren, Jie; Zha, Gangqiang; Wang, Tao; Xu, Lingyan; He, Yihui; Xi, Shouzhi

    2016-09-01

    To understand the effects of tellurium (Te) inclusions on the device performance of CdZnTe radiation detectors, the perturbation of the electrical field in and around Te inclusions was studied in CdZnTe single crystals via Kelvin probe force microscopy (KPFM). Te inclusions were proved to act as lower potential centers with respect to surrounding CdZnTe matrix. Based on the KPFM results, the energy band diagram at the Te/CdZnTe interface was established, and the bias-dependent effects of Te inclusion on carrier transportation is discussed.

  2. Blocking force of a piezoelectric stack actuator made of single crystal layers (PMN-29PT)

    NASA Astrophysics Data System (ADS)

    Tran, K. S.; Phan, H. V.; Lee, H. Y.; Kim, Yongdae; Park, H. C.

    2016-09-01

    In this study, we fabricated and characterized a stack actuator made of forty layers of 1 mm thick PMN-29PT with a cross-sectional area of 10 × 10 mm2. From the measurement of actuation displacement, we confirmed that the piezoelectric strain constant in the direction of thickness of the material is 2000 pm V-1, as suggested by the manufacturer. The blocking forces of the actuator are measured to be 230 N, 369 N, and 478 N for 100 V, 200 V, and 300 V, respectively. The measured blocking forces showed large discrepancies from the estimated blocking forces calculated using linear models, especially for a high voltage application. An empirical equation acquired by fitting the measured blocking forces indicates that the blocking force has a nonlinear relationship with the applied voltage. The measured hysteresis showed a slight nonlinear voltage-stroke relationship and small energy loss.

  3. Electronically configured battery pack

    SciTech Connect

    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.

  4. Modified technique of anterior nasal packing: a comparative study report.

    PubMed

    Dutta, Sirshak; Mukherjee, Ankur; Saha, Jayanta; Biswas, Goutam; Haldar, Dibakar; Sen, Indranil; Sinha, Ramanuj

    2012-12-01

    Anterior nasal packing, which is a common procedure in otorhinolaryngology practice, has different complications. Pain during introduction and removal of pack, bleeding after removal due to mucosal damage and synechia formation are common among them. A continuous effort is going on worldwide to combat those by modifying the nature of pack material or inventing new materials for nasal packing. In the present study an effort was made to compare a new modification of conventional gauze pack by using aluminum foil prepared from the cover of suture materials as septal splint (to reduce the mucosal damage) with conventional gauze pack and another costly material, nasal tampon (merocel). Comparisons were done in terms of cost, efficacy and complications. Prospective hospital based interventional study. Patients were distributed into three groups according to the material used for anterior nasal packing. Comparisons were made in terms of cost of the material used, pain during introduction of pack, rise of systolic blood pressure, incidences of bleeding while pack in situ, incidences of bleeding after removal of pack that required repacking and incidences of synechia formation after pack removal. The episodes of bleeding while pack in situ, within first 48 h and forced for repacking was observed to be significantly more prevalent among nasal tampon groups (12.5%) of patients but only 2.1 and 2.4% with use of conventional gauze pack and our modification respectively. Regarding bleeding after removal of pack, 10.6% patients experienced bleeding with conventional gauze pack, whereas with our modification it was only 2.4%. Synechia formation was found to be highest among the cases with conventional gauze pack (14.9%), but with our modification it is only 2.4%. In this study it is found that use of aluminum foil prepared from the cover of suture materials can be very useful and cost effective method to reduce some of the complications of anterior nasal packing.

  5. Charge transfer of single laser crystallized intrinsic and phosphorus-doped Si-nanocrystals visualized by Kelvin probe force microscopy

    SciTech Connect

    Xu, Jie; Xu, Jun Lu, Peng; Shan, Dan; Li, Wei; Chen, Kunji

    2014-10-07

    Isolated intrinsic and phosphorus doped (P-doped) Si-nanocrystals (Si-NCs) on n- and p-Si substrates are fabricated by excimer laser crystallization techniques. The formation of Si-NCs is confirmed by atomic force microscopy (AFM) and conductive AFM measurements. Kelvin probe force microscopy (KPFM) is then carried out to visualize the trapped charges in a single Si-NC dot which derives from the charge transfer between Si-NCs and Si substrates due to their different Fermi levels. The laser crystallized P-doped Si-NCs have a similar Fermi level around the mid-gap to the intrinsic counterparts, which might be caused by the inactivated impurity atoms or the surface states-related Fermi level pinning. A clear rise of the Fermi level in P-doped Si-NCs is observed after a short time thermal annealing treatment, indicating the activation of dopants in Si-NCs. Moreover, the surface charge quantity can be estimated using a simple parallel plate capacitor model for a quantitative understanding of the KPFM results at the nanoscale.

  6. Nuclear magnetic resonance force microscopy of (NH_4)_2SO4 crystal and PMMA thin film

    NASA Astrophysics Data System (ADS)

    Choi, Jae-Hyuk; Miller, Casey W.; Guchhait, Samaresh; Chabot, Michelle D.; Markert, John T.

    2004-03-01

    In preparation for scanning dynamical studies, we performed room temperature 1-D and 2-D nuclear magnetic resonance force microscopy (NMRFM) measurements on a (NH_4)_2SO4 (ammonium sulfate) single crystal and on PMMA thin films using `magnet-on-oscillator' scanning mode. A cantilever-frequency modulation of the ˜ 350-MHz rf field induced cyclic adiabatic inversion of a resonant slice of ^1H nuclear spins. 1-D scans through the surface of the ammonium sulfate crystal with a resonant-slice thickness (z resolution) as small as 150 nm were achieved using a permalloy thin-film magnet, 4.0 μm in diameter and 0.18 μm thick. For the 2D scans, ˜1 μm-thick PMMA films were patterned to provide a 2-D array of 5.0 μm-diameter polymer islands. Oscillator-detected NMR-induced forces around 1× 10-15 N were typical. These NMRFM imaging studies employed mechanical oscillators with sping constants k ≈ 2× 10-4 N/m, resonant frequencies near 4 kHz, and quality factors in the range Q = 1--6× 10^3.

  7. An atomic force microscopic investigation of surface degradation of potassium hydrogen phthalate (KAP) crystals caused by removal from solution

    NASA Astrophysics Data System (ADS)

    Ester, G. R.; Price, R.; Halfpenny, P. J.

    1997-12-01

    Atomic force microscopy (AFM) has been used to examine the nature and extent of surface degradation of the {0 1 0} faces of potassium hydrogen phthalate (KAP) crystals removed from aqueous solution. Crystals separated from their growth solutions by passage through a layer of n-hexane or using a jet of n-hexane exhibited clearly preserved growth spirals. The step terraces, however, were found to be extensively pitted, typically to a depth of approximately 1.4 nm which corresponds to one lattice spacing in the b-direction. In addition to such nanoscale pitting, larger pits several microns in lateral dimensions were also observed. These were frequently hexagonal in shape usually with a shallow mound within or adjacent to the pit. More rapid removal of solution from crystal surfaces was effected using a pulse of compressed air or argon. Under optimised conditions this approach yielded much better surface protection with step terraces in this case being essentially smooth. Step heights on the spirals shown were found to be 1.4 ± 0.2 nm and thus of single unit cell height. The occurrence of pits on the terraces is attributed to deposition of KAP by two dimensional nucleation on the terraces, producing partial coverage and thus the apparently pitted surface.

  8. Internal packing of helical membrane proteins

    PubMed Central

    Eilers, Markus; Shekar, Srinivasan C.; Shieh, Ted; Smith, Steven O.; Fleming, Patrick J.

    2000-01-01

    Helix packing is important in the folding, stability, and association of membrane proteins. Packing analysis of the helical portions of 7 integral membrane proteins and 37 soluble proteins show that the helices in membrane proteins have higher packing values (0.431) than in soluble proteins (0.405). The highest packing values in integral membrane proteins originate from small hydrophobic (G and A) and small hydroxyl-containing (S and T) amino acids, whereas in soluble proteins large hydrophobic and aromatic residues have the highest packing values. The highest packing values for membrane proteins are found in the transmembrane helix–helix interfaces. Glycine and alanine have the highest occurrence among the buried amino acids in membrane proteins, whereas leucine and alanine are the most common buried residue in soluble proteins. These observations are consistent with a shorter axial separation between helices in membrane proteins. The tight helix packing revealed in this analysis contributes to membrane protein stability and likely compensates for the lack of the hydrophobic effect as a driving force for helix–helix association in membranes. PMID:10823938

  9. Traceable atomic force microscopy of high-quality solvent-free crystals of [6,6]-phenyl-C{sub 61}-butyric acid methyl ester

    SciTech Connect

    Lazzerini, Giovanni Mattia; Yacoot, Andrew; Paternò, Giuseppe Maria; Tregnago, Giulia; Cacialli, Franco; Treat, Neil; Stingelin, Natalie

    2016-02-01

    We report high-resolution, traceable atomic force microscopy measurements of high-quality, solvent-free single crystals of [6,6]-phenyl-C61-butyric acid methyl ester (PCBM). These were grown by drop-casting PCBM solutions onto the spectrosil substrates and by removing the residual solvent in a vacuum. A home-built atomic force microscope featuring a plane mirror differential optical interferometer, fiber-fed from a frequency-stabilized laser (emitting at 632.8 nm), was used to measure the crystals' height. The optical interferometer together with the stabilized laser provides traceability (via the laser wavelength) of the vertical measurements made with the atomic force microscope. We find that the crystals can conform to the surface topography, thanks to their height being significantly smaller compared to their lateral dimensions (namely, heights between about 50 nm and 140 nm, for the crystals analysed, vs. several tens of microns lateral dimensions). The vast majority of the crystals are flat, but an isolated, non-flat crystal provides insights into the growth mechanism and allows identification of “molecular terraces” whose height corresponds to one of the lattice constants of the single PCBM crystal (1.4 nm) as measured with X-ray diffraction.

  10. Pattern of Hydroxyapatite Crystal Growth on Bleached Enamel Following the Application of Two Antioxidants: An Atomic Force Microscope Study.

    PubMed

    Bhusari, Chitra P; Sharma, Divya S

    This study observed the topographical pattern of hydroxyapatite deposition and growth (D&G) on bleached enamel following application of two antioxidants (sodium ascorbate and catalase) using atomic force microscope. Twenty enamel specimens (4×3×2mm), prepared from extracted impacted third molars, were mounted in self-cure acrylic and randomly grouped as: Group I-untreated; Group II- 35%H2O2; Group III- 35%H2O2 + artificial saliva; Group IV- 35%H2O2 + catalase+ artificial saliva; Group V- 35%H2O2 + sodium ascorbate+ artificial saliva. Groups I and II were observed immediately after treatment. Groups III-V were observed after 72 hrs. Roughness average was also calculated and analyzed with non-parametric Kruskall-Wallis ANOVA and Mann-Whitney tests. H2O2 dissolved matrix, exposed hydroxyapatite crystals (HACs), causing dissolution on the sides of and within HACs and opening up of nano-spaces. Artificial saliva showed growth of dissoluted crystals. Antioxidants+saliva showed potentiated remineralization by D&G on dissoluted HACs of bleached enamel. Catalase potentiated blockshaped, while sodium ascorbate the needle-shaped crystals with stair-pattern of crystallization. Evidence of oxygen bubbles was a new finding with catalase. Maximum roughness average was in group V followed by group II > group IV > group III > group I. Post-bleaching application of catalase and sodium ascorbate potentiated remineralization by saliva, but in different patterns. None of the tested antioxidant could return the original topography of enamel.

  11. Crystal structure of a trapped catalytic intermediate suggests that forced atomic proximity drives the catalysis of mIPS.

    PubMed

    Neelon, Kelly; Roberts, Mary F; Stec, Boguslaw

    2011-12-07

    1-L-myo-inositol-phosphate synthase (mIPS) catalyzes the first step of the unique, de novo pathway of inositol biosynthesis. However, details about the complex mIPS catalytic mechanism, which requires oxidation, enolization, intramolecular aldol cyclization, and reduction, are not fully known. To gain further insight into this mechanism, we determined the crystal structure of the wild-type mIPS from Archaeoglobus fulgidus at 1.7 Å, as well as the crystal structures of three active-site mutants. Additionally, we obtained the structure of mIPS with a trapped 5-keto-glucose-6-phosphate intermediate at 2 Å resolution by a novel (to our knowledge) process of activating the crystal at high temperature. A comparison of all of the crystal structures of mIPS described in this work suggests a novel type of catalytic mechanism that relies on the forced atomic proximity of functional groups. The lysine cluster is contained in a small volume in the active site, where random motions of these side chains are responsible for the progress of the complex multistep reaction as well as for the low rate of catalysis. The mechanism requires that functional groups of Lys-274, Lys-278, Lys-306, and Lys-367 assume differential roles in the protonation/deprotonation steps that must occur during the mIPS reaction. This mechanism is supported by the complete loss of activity of the enzyme caused by the Leu-257 mutation to Ala that releases the lysine containment.

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

    ERIC Educational Resources Information Center

    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)

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

    ERIC Educational Resources Information Center

    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)

  14. A Validation Study of the General Amber Force Field Applied to Energetic Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Bergh, Magnus; Caleman, Carl

    2016-01-01

    Molecula dynamics is a well-established tool to computationally study molecules. However, to reach predictive capability at the level required for applied research and design, extensive validation of the available force fields is pertinent. Here we present a study of density, isothermal compressibility and coefficients of thermal expansion of four energetic materials (FOX-7, RDX, CL-20 and HMX) based on molecular dynamics simulations with the General Amber Force Field (GAFF), and compare the results to experimental measurements from the literature. Furthermore, we quantify the accuracy of the calculated properties through hydrocode simulation of a typical impact scenario. We find that molecular dynamics simulations with generic and computationally efficient force fields may be used to understand and estimate important physical properties of nitramine-like energetic materials.

  15. Flat Pack Toy Design

    ERIC Educational Resources Information Center

    Hutcheson, Brian

    2007-01-01

    In this article, the author introduces the concept of flat pack toys. Flat pack toys are designed using a template on a single sheet of letter-sized card stock paper. Before being cut out and built into a three-dimensional toy, they are scanned into the computer and uploaded to a website. With the template accessible from the website, anyone with…

  16. TLC Pack Unpacked

    ERIC Educational Resources Information Center

    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. Forced diffusion via electrically induced crystallization for fabricating ZnO–Ti–Si structures

    SciTech Connect

    Chen, Yen-Ting; Hung, Fei-Yi

    2014-11-15

    Highlights: • ZnO–Ti–Si system is very important for the structural design. • The electrically induced crystallization method is useful to diffusion process. • Intermetallic compound characteristics have been presented using electrically induced crystallization. • Interface mechanism about diffusion of TZO–TiSi{sub x}–Si structure is presented. - Abstract: Electrically induced crystallization (EIC) is a recently developed process for material modification. This study is applied to EIC to fabricate ZnO–Ti–Si multi-layer structures of various thicknesses to dope Ti into ZnO thin film and to form TiSi{sub x} intermetallic compound (IMC) in a single step. The IMC layer was confirmed using transmission electron microscopy images. The Ti layer thickness was more than 40 nm, which enhanced electron transmission and decreased the total electrical resistance in the structure. Finally, the diffusion mechanisms of EIC and the annealing process were investigated. This study shows that the EIC process has potential for industrial applications.

  18. Theory of random packings

    NASA Astrophysics Data System (ADS)

    Makse, Hernan; Song, Chaoming; Wang, Ping

    2009-03-01

    We present a theory of random packings to describe the statistical mechanics of jammed matter with the aim of shedding light to the long-standing problem of characterizing the random close packing (RCP) and random loose packing (RLP) of particles. We describe the jammed system with equations of state relating observables such as entropy, coordination number, volume fraction, and compactivity as well as the probability distributions of volume and contacts. We follow a systematic route to classify packings into a phase diagram of jamming, from frictionless to frictional particles, from hard to deformable particles, from monodisperse to polydisperse systems, from spherical particles to nonspherical convex particles, in an attempt to understand the packing problem from a unifying perspective. The studies of RCP and RLP includes 2d, nd, and the mean field limit of infinite dimension.

  19. Structural Evolution of a Granular Pack under Manual Tapping

    NASA Astrophysics Data System (ADS)

    Iikawa, Naoki; Bandi, Mahesh M.; Katsuragi, Hiroaki

    2015-09-01

    We experimentally study a two-dimensional (2D) granular pack of photoelastic disks subject to vertical manual tapping. Using bright- and dark-field images, we employ gradient-based image analysis methods to analyze various structural quantities. These include the packing fraction (ϕ), force per disk (Fd), and force chain segment length (l) as functions of the tapping number (τ). The increase in the packing fraction with the tapping number is found to exponentially approach an asymptotic value. An exponential distribution is observed for the cumulative numbers of both the force per disk Fd:Ncum(Fd) = AFexp ( - Fd/F0), and the force chain segment length l:Ncum(l) = Alexp ( - l/l0). Whereas the coefficient AF varies with τ for Fd, l shows no dependence on τ. The τ dependences of Fd and ϕ allow us to posit a linear relationship between the total force of the granular pack Ftot*(τ ) and ϕ(τ).

  20. Entropy of hard spheres in the close-packing limit

    NASA Astrophysics Data System (ADS)

    Noya, Eva G.; Almarza, Noé G.

    2015-05-01

    The Helmholtz free energies of the face-centred cubic (FCC) and hexagonal close packed (HCP) hard-sphere solids in the close-packing limit have been evaluated using two different approaches based on the Einstein crystal method. Different system sizes and orientations of the crystal with respect to the simulation box have been investigated, both methods giving free energies that are consistent within statistical uncertainty. Our results show that for a given orientation of the crystal and system size, the FCC crystal is always slightly more stable than the HCP, the free-energy difference remaining practically constant with the number of particles up to the thermodynamic limit. In agreement with previous calculations, it is found that the free-energy difference between the HCP and FCC crystals at close packing in the thermodynamic limit is 0.001 164(8) NkBT.

  1. Packing in protein cores

    NASA Astrophysics Data System (ADS)

    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.

  2. Graphitic packing removal tool

    SciTech Connect

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

    1997-11-11

    Graphitic packing removal tools for removal of the seal rings in one piece are disclosed. 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. 5 figs.

  3. Graphitic packing removal tool

    SciTech Connect

    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.

  4. Graphitic packing removal tool

    DOEpatents

    Meyers, Kurt Edward; Kolsun, George J.

    1997-01-01

    Graphitic packing removal tools for removal of the seal rings in one piece. he 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.

  5. Graphitic packing removal tool

    DOEpatents

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

    1997-11-11

    Graphitic packing removal tools for removal of the seal rings in one piece are disclosed. 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. 5 figs.

  6. Liquid crystal visualization and computer modeling of enhanced heat transfer on a flat plate in forced convection

    SciTech Connect

    Voegler, G.R.; Anderson, A.M.

    1996-12-31

    This paper presents the results of an experimental and computational study of heat transfer enhancement found in the vicinity of a three dimensional block placed on a constant heat flux plate in turbulent forced convection. The experiments used thermochromic liquid crystals to visualize temperature on the surface. Photographs were taken to establish temperature contour lines at a range of velocities and a variety of block sizes and configurations. The results show heat transfer enhancement exists upstream and downstream of the blocks. The enhancement is caused by a horse shoe vortex which stagnates on the front surface of the block and then wraps around the sides. Thin blocks (narrow in the flow direction) show the best enhancement. The computer simulations used the {kappa}-epsilon turbulence model and had reasonable qualitative agreement with the experiments.

  7. Domain reversal and relaxation in LiNbO3 single crystals studied by piezoresponse force microscope

    NASA Astrophysics Data System (ADS)

    Kan, Yi; Lu, Xiaomei; Wu, Xiumei; Zhu, Jinsong

    2006-12-01

    The LiNbO3 crystal was polarized and characterized by the piezoresponse force mode of scanning probe microscope. By using the Kolmogorov-Avrami-Ishibashi [Izv. Akad. Nauk, USSR: Ser. Math. 3, 355 (1937); J. Chem. Phys. 8, 212 (1940); J. Phys. Soc. Jpn. 63, 1031 (1994); 63, 1601 (1994)] theory to analyze the relaxation process after domain switching, it was found that (1) the percent of final switched domains after poling increased with the enhancing poling voltage, (2) the nucleation time was a constant to a certain sample, (3) the dimension of domain growth decreased with the enhancing poling voltage, and (4) the relaxation time had a maximum at a medial voltage. The corresponding mechanism for domain switching was discussed, which is hopefully useful for domain engineering.

  8. Chitinase activity on amorphous chitin thin films: a quartz crystal microbalance with dissipation monitoring and atomic force microscopy study.

    PubMed

    Wang, Chao; Kittle, Joshua D; Qian, Chen; Roman, Maren; Esker, Alan R

    2013-08-12

    Chitinases are widely distributed in nature and have wide-ranging pharmaceutical and biotechnological applications. This work highlights a real-time and label-free method to assay Chitinase activity via a quartz crystal microbalance with dissipation monitoring (QCM-D) and atomic force microscopy (AFM). The chitin substrate was prepared by spincoating a trimethylsilyl chitin solution onto a silica substrate, followed by regeneration to amorphous chitin (RChi). The QCM-D and AFM results clearly showed that the hydrolysis rate of RChi films increased as Chitinase (from Streptomyces griseus) concentrations increased, and the optimal temperature and pH for Chitinase activity were around 37 °C and 6-8, respectively. The Chitinase showed greater activity on chitin substrates, having a high degree of acetylation, than on chitosan substrates, having a low degree of acetylation.

  9. Quantitative Atomic Force Microscopy Characterization and Crystal Plasticity Finite Element Modeling of Heterogeneous Deformation in Commercial Purity Titanium

    NASA Astrophysics Data System (ADS)

    Yang, Y.; Wang, L.; Bieler, T. R.; Eisenlohr, P.; Crimp, M. A.

    2011-03-01

    Using a four-point bend sample of commercial purity titanium deformed to a surface strain around 1.5 pct, the active dislocation slip and twin systems in a microstructural patch of about 15 grains were quantitatively analyzed by a technique combining atomic force microscopy (AFM), backscattered electron (BSE) imaging, and electron backscattered diffraction (EBSD). Local shear distribution maps derived from z-displacement data measured by AFM were directly compared to results of a crystal plasticity finite element (CPFE) simulation that incorporates a phenomenological model of the deformation processes to evaluate the ability of the CPFE model to match the experimental observations. The CPFE model successfully predicted most types of active dislocation slip systems within the grains at correct magnitudes, but the spatial distribution of strains within grains differed between the measurements and the simulation.

  10. Optimization of the GAFF force field to describe liquid crystal molecules: the path to a dramatic improvement in transition temperature predictions.

    PubMed

    Boyd, Nicola Jane; Wilson, Mark R

    2015-10-14

    The physical properties and phase transitions of thermotropic liquid crystals are highly sensitive to small changes in chemical structure. However, these changes are challenging to model, as both the phase diagram and mesophase properties obtained from fully atomistic simulations are strongly dependent on the force field model employed, and the current generation of chemical force fields has not proved accurate enough to provide reliable predictions of transition temperatures for many liquid crystals. This paper presents a strategy for improving the nematic clearing point, TNI, in atomistic simulations, by systematic optimization of the General Amber Force Field (GAFF) for key mesogenic fragments. We show that with careful optimization of the parameters describing a series of liquid crystal fragment molecules, it is possible to transfer these parameters to larger liquid crystal molecules and make accurate predictions for nematic mesophase formation. This new force field, GAFF-LCFF, is used to predict the nematic-isotropic clearing point to within 5 °C for the nematogen 1,3-benzenedicarboxylic acid,1,3-bis(4-butylphenyl)ester, an improvement of 60 °C over the standard GAFF force field.

  11. A methodology to determine boundary conditions from forced convection experiments using liquid crystal thermography

    NASA Astrophysics Data System (ADS)

    Jakkareddy, Pradeep S.; Balaji, C.

    2016-05-01

    This paper reports the results of an experimental study to estimate the heat flux and convective heat transfer coefficient using liquid crystal thermography and Bayesian inference in a heat generating sphere, enclosed in a cubical Teflon block. The geometry considered for the experiments comprises a heater inserted in a hollow hemispherical aluminium ball, resulting in a volumetric heat generation source that is placed at the center of the Teflon block. Calibrated thermochromic liquid crystal sheets are used to capture the temperature distribution at the front face of the Teflon block. The forward model is the three dimensional conduction equation which is solved within the Teflon block to obtain steady state temperatures, using COMSOL. Match up experiments are carried out for various velocities by minimizing the residual between TLC and simulated temperatures for every assumed loss coefficient, to obtain a correlation of average Nusselt number against Reynolds number. This is used for prescribing the boundary condition for the solution to the forward model. A surrogate model obtained by artificial neural network built upon the data from COMSOL simulations is used to drive a Markov Chain Monte Carlo based Metropolis Hastings algorithm to generate the samples. Bayesian inference is adopted to solve the inverse problem for determination of heat flux and heat transfer coefficient from the measured temperature field. Point estimates of the posterior like the mean, maximum a posteriori and standard deviation of the retrieved heat flux and convective heat transfer coefficient are reported. Additionally the effect of number of samples on the performance of the estimation process has been investigated.

  12. A methodology to determine boundary conditions from forced convection experiments using liquid crystal thermography

    NASA Astrophysics Data System (ADS)

    Jakkareddy, Pradeep S.; Balaji, C.

    2017-02-01

    This paper reports the results of an experimental study to estimate the heat flux and convective heat transfer coefficient using liquid crystal thermography and Bayesian inference in a heat generating sphere, enclosed in a cubical Teflon block. The geometry considered for the experiments comprises a heater inserted in a hollow hemispherical aluminium ball, resulting in a volumetric heat generation source that is placed at the center of the Teflon block. Calibrated thermochromic liquid crystal sheets are used to capture the temperature distribution at the front face of the Teflon block. The forward model is the three dimensional conduction equation which is solved within the Teflon block to obtain steady state temperatures, using COMSOL. Match up experiments are carried out for various velocities by minimizing the residual between TLC and simulated temperatures for every assumed loss coefficient, to obtain a correlation of average Nusselt number against Reynolds number. This is used for prescribing the boundary condition for the solution to the forward model. A surrogate model obtained by artificial neural network built upon the data from COMSOL simulations is used to drive a Markov Chain Monte Carlo based Metropolis Hastings algorithm to generate the samples. Bayesian inference is adopted to solve the inverse problem for determination of heat flux and heat transfer coefficient from the measured temperature field. Point estimates of the posterior like the mean, maximum a posteriori and standard deviation of the retrieved heat flux and convective heat transfer coefficient are reported. Additionally the effect of number of samples on the performance of the estimation process has been investigated.

  13. Dense packings of polyhedra: Platonic and Archimedean solids.

    PubMed

    Torquato, S; Jiao, Y

    2009-10-01

    regarded to be the analog of Kepler's sphere conjecture for these solids.The truncated tetrahedron is the only nonchiral Archimedean solid that is not centrally symmetric [corrected], the densest known packing of which is a non-lattice packing with density at least as high as 23/24=0.958 333... . We discuss the validity of our conjecture to packings of superballs, prisms, and antiprisms as well as to high-dimensional analogs of the Platonic solids. In addition, we conjecture that the optimal packing of any convex, congruent polyhedron without central symmetry generally is not a lattice packing. Finally, we discuss the possible applications and generalizations of the ASC scheme in predicting the crystal structures of polyhedral nanoparticles and the study of random packings of hard polyhedra.

  14. Lubricant Supply from Crystal Boundaries of Perpendicular Magnetic Disk Evaluated by Lateral Modulation Friction Force Microscopy

    NASA Astrophysics Data System (ADS)

    Miyake, Shojiro; Takahashi, Yuuzi; Wang, Mei; Saitoh, Tadashi; Matsunuma, Satoshi

    2004-11-01

    The tribological behavior of perfluoropolyether (PFPE) films attached to perpendicular recording magnetic disks coated with diamondlike carbon (DLC) was studied in lateral vibration wear tests using lateral modulus friction force microscopy (LM-FFM). The viscoelastic and frictional properties of these PFPE films without heat cure were improved due to the lubricant supply by tip sliding. However, the PFPE films were easily removed with increasing load and lateral vibration amplitude following heat treatment since the free lubricants on the films solidified resulting in the lost of fluidity.

  15. Nasal packing and stenting

    PubMed Central

    Weber, Rainer K.

    2011-01-01

    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. PMID:22073095

  16. Packing of elastic wires in flexible shells

    NASA Astrophysics Data System (ADS)

    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.

  17. Interactions of hyaluronan grafted on protein surfaces studied using a quartz crystal microbalance and a surface force balance.

    PubMed

    Jiang, Lei; Han, Juan; Yang, Limin; Ma, Hongchao; Huang, Bo

    2015-10-07

    Vocal folds are complex and multilayer-structured where the main layer is widely composed of hyaluronan (HA). The viscoelasticity of HA is key to voice production in the vocal fold as it affects the initiation and maintenance of phonation. In this study a simple layer-structured surface model was set up to mimic the structure of the vocal folds. The interactions between two opposing surfaces bearing HA were measured and characterised to analyse HA's response to the normal and shear compression at a stress level similar to that in the vocal fold. From the measurements of the quartz crystal microbalance, atomic force microscopy and the surface force balance, the osmotic pressure, normal interactions, elasticity change, volume fraction, refractive index and friction of both HA and the supporting protein layer were obtained. These findings may shed light on the physical mechanism of HA function in the vocal fold and the specific role of HA as an important component in the effective treatment of the vocal fold disease.

  18. Evaluation of the OPLS-AA force field for the study of structural and energetic aspects of molecular organic crystals.

    PubMed

    Bernardes, Carlos E S; Joseph, Abhinav

    2015-03-26

    Motivated by the need for reliable experimental data for the assessment of theoretical predictions, this work proposes a data set of enthalpies of sublimation determined for specific crystalline structures, for the validation of molecular force fields (FF). The selected data were used to explore the ability of the OPLS-AA parametrization to investigate the properties of solid materials in molecular dynamics simulations. Furthermore, several approaches to improve this parametrization were also considered. These modifications consisted in replacing the original FF atomic point charges (APC), by values calculated using quantum chemical methods, and by the implementation of a polarizable FF. The obtained results indicated that, in general, the best agreement between theoretical and experimental data is found when the OPLS-AA force field is used with the original APC or when these are replaced by ChelpG charges, computed at the MP2/aug-cc-pVDZ level of theory, for isolated molecules in the gaseous phase. If a good description of the energetic relations between the polymorphs of a compound is required then either the use of polarizable FF or the use of charges determined taking into account the vicinity of the molecules in the crystal (combining the ChelpG and MP2/cc-pVDZ methods) is recommended. Finally, it was concluded that density functional theory methods, like B3LYP or B3PW91, are not advisable for the evaluation of APC of organic compounds for molecular dynamic simulations. Instead, the MP2 method should be considered.

  19. First principles crystal engineering of nonlinear optical materials. I. Prototypical case of urea.

    PubMed

    Masunov, Artëm E; Tannu, Arman; Dyakov, Alexander A; Matveeva, Anastasia D; Freidzon, Alexandra Ya; Odinokov, Alexey V; Bagaturyants, Alexander A

    2017-06-28

    The crystalline materials with nonlinear optical (NLO) properties are critically important for several technological applications, including nanophotonic and second harmonic generation devices. Urea is often considered to be a standard NLO material, due to the combination of non-centrosymmetric crystal packing and capacity for intramolecular charge transfer. Various approaches to crystal engineering of non-centrosymmetric molecular materials were reported in the literature. Here we propose using global lattice energy minimization to predict the crystal packing from the first principles. We developed a methodology that includes the following: (1) parameter derivation for polarizable force field AMOEBA; (2) local minimizations of crystal structures with these parameters, combined with the evolutionary algorithm for a global minimum search, implemented in program USPEX; (3) filtering out duplicate polymorphs produced; (4) reoptimization and final ranking based on density functional theory (DFT) with many-body dispersion (MBD) correction; and (5) prediction of the second-order susceptibility tensor by finite field approach. This methodology was applied to predict virtual urea polymorphs. After filtering based on packing similarity, only two distinct packing modes were predicted: one experimental and one hypothetical. DFT + MBD ranking established non-centrosymmetric crystal packing as the global minimum, in agreement with the experiment. Finite field approach was used to predict nonlinear susceptibility, and H-bonding was found to account for a 2.5-fold increase in molecular hyperpolarizability to the bulk value.

  20. First principles crystal engineering of nonlinear optical materials. I. Prototypical case of urea

    NASA Astrophysics Data System (ADS)

    Masunov, Artëm E.; Tannu, Arman; Dyakov, Alexander A.; Matveeva, Anastasia D.; Freidzon, Alexandra Ya.; Odinokov, Alexey V.; Bagaturyants, Alexander A.

    2017-06-01

    The crystalline materials with nonlinear optical (NLO) properties are critically important for several technological applications, including nanophotonic and second harmonic generation devices. Urea is often considered to be a standard NLO material, due to the combination of non-centrosymmetric crystal packing and capacity for intramolecular charge transfer. Various approaches to crystal engineering of non-centrosymmetric molecular materials were reported in the literature. Here we propose using global lattice energy minimization to predict the crystal packing from the first principles. We developed a methodology that includes the following: (1) parameter derivation for polarizable force field AMOEBA; (2) local minimizations of crystal structures with these parameters, combined with the evolutionary algorithm for a global minimum search, implemented in program USPEX; (3) filtering out duplicate polymorphs produced; (4) reoptimization and final ranking based on density functional theory (DFT) with many-body dispersion (MBD) correction; and (5) prediction of the second-order susceptibility tensor by finite field approach. This methodology was applied to predict virtual urea polymorphs. After filtering based on packing similarity, only two distinct packing modes were predicted: one experimental and one hypothetical. DFT + MBD ranking established non-centrosymmetric crystal packing as the global minimum, in agreement with the experiment. Finite field approach was used to predict nonlinear susceptibility, and H-bonding was found to account for a 2.5-fold increase in molecular hyperpolarizability to the bulk value.

  1. Microstructural characterization of random packings of cubic particles

    PubMed Central

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

    2016-01-01

    Understanding the properties of random packings of solid objects is of critical importance to a wide variety of fundamental scientific and practical problems. The great majority of the previous works focused, however, on packings of spherical and sphere-like particles. We report the first detailed simulation and characterization of packings of non-overlapping cubic particles. Such packings arise in a variety of problems, ranging from biological materials, to colloids and fabrication of porous scaffolds using salt powders. In addition, packing of cubic salt crystals arise in various problems involving preservation of pavements, paintings, and historical monuments, mineral-fluid interactions, CO2 sequestration in rock, and intrusion of groundwater aquifers by saline water. Not much is known, however, about the structure and statistical descriptors of such packings. We have developed a version of the random sequential addition algorithm to generate such packings, and have computed a variety of microstructural descriptors, including the radial distribution function, two-point probability function, orientational correlation function, specific surface, and mean chord length, and have studied the effect of finite system size and porosity on such characteristics. The results indicate the existence of both spatial and orientational long-range order in the packing, which is more distinctive for higher packing densities. The maximum packing fraction is about 0.57. PMID:27725736

  2. Microstructural characterization of random packings of cubic particles

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

    Understanding the properties of random packings of solid objects is of critical importance to a wide variety of fundamental scientific and practical problems. The great majority of the previous works focused, however, on packings of spherical and sphere-like particles. We report the first detailed simulation and characterization of packings of non-overlapping cubic particles. Such packings arise in a variety of problems, ranging from biological materials, to colloids and fabrication of porous scaffolds using salt powders. In addition, packing of cubic salt crystals arise in various problems involving preservation of pavements, paintings, and historical monuments, mineral-fluid interactions, CO2 sequestration in rock, and intrusion of groundwater aquifers by saline water. Not much is known, however, about the structure and statistical descriptors of such packings. We have developed a version of the random sequential addition algorithm to generate such packings, and have computed a variety of microstructural descriptors, including the radial distribution function, two-point probability function, orientational correlation function, specific surface, and mean chord length, and have studied the effect of finite system size and porosity on such characteristics. The results indicate the existence of both spatial and orientational long-range order in the packing, which is more distinctive for higher packing densities. The maximum packing fraction is about 0.57.

  3. α-amylase crystal growth investigated by in situ atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Astier, J. P.; Bokern, D.; Lapena, L.; Veesler, S.

    2001-06-01

    The growth behavior of porcine pancreatic α-amylase at defined supersaturation has been investigated by means of temperature controlled in situ atomic force microscopy (AFM). The step velocities measured by AFM were in overall agreement with the normal growth rates of an individual face measured by optical microscopy. In addition, highly local growth dynamics could be visualized. Imaging in tapping mode revealed crystalline amylase aggregates attached to the basal face and their subsequent incorporation into growing terraces producing a macrodefect. At high supersaturation ( β=1.6) 2-D nucleation was found to be the dominating growth mechanism, whereas at lower supersaturation ( β=1.3) the growth process appears to be defect controlled (spiral growth). The analysis of step heights on 2-D nucleation islands (monomolecular protein layers) and growth steps (two molecules in height) in combination with results from light scattering experiments suggest that a single protein molecule is the basic growth unit.

  4. Solidification (crystal growth) in the presence of gravitational forces. [indium antimonide melts at reduced gravity

    NASA Technical Reports Server (NTRS)

    Gatos, H. C.; Witt, A. F.

    1978-01-01

    The surface tension behavior of doped and undoped InSb melts was investigated as well as their temperature and composition dependence. Surface tension in InSb melts was determined using the sessile-drop technique covering the temperature range from 530 C to 880 C. A linear regression of the data obtained shows that the temperature dependence of sigma is 392- (T-530) x (7000) plus or minus 10 dyne/cm. The d sigma/d Tau for intrinsics InSb is less than that previously reported. On the basis of the surface tension data obtained, it is concluded that surface tension induced convective flow velocities in InSb under reduced gravity conditions range from zero to at most 1 cm/sec. Accordingly, no interference with dopant segregation can be expected during growth in space because the momentum boundary layer (at the crystal melt interface) associated with any Marangoni-type convective flows would, at the given growth rate, be significantly larger than the predicted diffusion boundary layer thickness.

  5. 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.

    PubMed

    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.

  6. Random close packing in protein cores

    NASA Astrophysics Data System (ADS)

    Gaines, Jennifer C.; Smith, W. Wendell; Regan, Lynne; O'Hern, Corey S.

    2016-03-01

    Shortly after the determination of the first protein x-ray crystal structures, researchers analyzed their cores and reported packing fractions ϕ ≈0.75 , a value that is similar to close packing of equal-sized spheres. A limitation of these analyses was the use of extended atom models, rather than the more physically accurate explicit hydrogen model. The validity of the explicit hydrogen model was proved in our previous studies by its ability to predict the side chain dihedral angle distributions observed in proteins. In contrast, the extended atom model is not able to recapitulate the side chain dihedral angle distributions, and gives rise to large atomic clashes at side chain dihedral angle combinations that are highly probable in protein crystal structures. Here, we employ the explicit hydrogen model to calculate the packing fraction of the cores of over 200 high-resolution protein structures. We find that these protein cores have ϕ ≈0.56 , which is similar to results obtained from simulations of random packings of individual amino acids. This result provides a deeper understanding of the physical basis of protein structure that will enable predictions of the effects of amino acid mutations to protein cores and interfaces of known structure.

  7. Enzymatic degradation processes of lamellar crystals in thin films for poly[(R)-3-hydroxybutyric acid] and its copolymers revealed by real-time atomic force microscopy.

    PubMed

    Numata, Keiji; Hirota, Takuya; Kikkawa, Yoshihiro; Tsuge, Takeharu; Iwata, Tadahisa; Abe, Hideki; Doi, Yoshiharu

    2004-01-01

    Enzymatic degradation processes of flat-on lamellar crystals in melt-crystallized thin films of poly[(R)-3-hydroxybutyric acid] (P(3HB)) and its copolymers were characterized by real-time atomic force microscopy (AFM) in a phosphate buffer solution containing PHB depolymerase from Ralstonia pickettii T1. Fiberlike crystals with regular intervals were generated along the crystallographic a axis at the end of lamellar crystals during the enzymatic degradation. The morphologies and sizes of the fiberlike crystals were markedly dependent on the compositions of comonomer units in the polyesters. Length, width, interval, and thickness of the fiberlike crystals after the enzymatic degradation for 2 h were measured by AFM, and the dimensions were related to the solid-state structures of P(3HB) and its copolymers. The width and thickness decreased at the tip of fiberlike crystals, indicating that the enzymatic degradation of crystals takes place not only along the a axis but also along the b and c axes. These results from AFM measurement were compared with the data on crystal size by wide-angle X-ray diffraction, and on lamellar thickness and long period by small-angle X-ray scattering. In addition, the enzymatic erosion rate of flat-on lamellar crystals along the a axis was measured from real-time AFM height images. A schematic glacier model for the enzymatic degradation of flat-on lamellar crystals of P(3HB) by PHB depolymerase has been proposed on the basis of the AFM observations.

  8. Mechanics of DNA Packing in Viruses

    NASA Astrophysics Data System (ADS)

    Phillips, Rob

    2004-03-01

    Viruses are amongst the most beautiful and fascinating of self-assembled structures. Recently, as a result of the confluence of techniques ranging from structural biology to single molecule biophysics, it has become possible to obtain quantitative insights into the physical processes that attend the viral life cycle. In particular, the forces that build up as a result of the DNA packing process have been measured in optical tweezers experiments. The aim of this talk is to describe such experiments on the mechanics of viral DNA packing and ejection and to show how these experiments can be greeted with simple, yet predictive models.

  9. Protein Crystal Growth Under Forced Solution Flow: Experimental Setup and General Response of Lysozyme

    NASA Technical Reports Server (NTRS)

    Vekilov, P. G.; Rosenberger, F.

    1998-01-01

    We have experimentally studied the effects of solution flow on the growth kinetics of the protein lysozyme. To this end, we have expanded our interferometry setup by a novel crystallization cell and solution recirculation system. This combination permits monitoring of interface morphology and kinetics with a depth resolution of 200 A at bulk flow rates of up to 2000 micron/s. Particular attention was paid to the prevention of protein denaturation that is often associated with the pumping of protein solutions. We found that at bulk flow rates it less than 250 microns/s the average growth rate and step velocity, R(sub avg) and upsilon(sub avg) increase with increasing it. This can be quantitatively understood in terms of the enhanced, convective solute supply to the interface. With high-purity solutions, it u greater than 250 microns/s lead to growth deceleration, and, at low supersaturations sigma, to growth cessation. When solutions containing approx. 1% of other protein impurities were used, growth deceleration occurred at any u greater than 0 and cessation in the low sigma experiments was reached at about half the it causing cessation with pure solution. The flow-induced changes in R(sub avg) and upsilon(sub avg) including growth cessation, were reversible and reproducible, independent of the direction of the u-changes and solution purity. Hence, we attribute the deceleration to the convection-enhanced supply of impurities to the interface, which at higher flow rates overpowers the effects of enhanced interfacial solute concentration. Most importantly, we found that convective transport leads to a significant reduction in kinetics fluctuations, in agreement with our earlier expectations for the lysozyme system. This supports our hypothesis that these long-term fluctuations represent an intrinsic response feature of the coupled bulk transport-interfacial kinetics system in the mixed growth control regime.

  10. Protein Crystal Growth Under Forced Solution Flow: Experimental Setup and General Response of Lysozyme

    NASA Technical Reports Server (NTRS)

    Vekilov, P. G.; Rosenberger, F.

    1998-01-01

    We have experimentally studied the effects of solution flow on the growth kinetics of the protein lysozyme. To this end, we have expanded our interferometry setup by a novel crystallization cell and solution recirculation system. This combination permits monitoring of interface morphology and kinetics with a depth resolution of 200 A at bulk flow rates of up to 2000 micron/s. Particular attention was paid to the prevention of protein denaturation that is often associated with the pumping of protein solutions. We found that at bulk flow rates it less than 250 microns/s the average growth rate and step velocity, R(sub avg) and upsilon(sub avg) increase with increasing it. This can be quantitatively understood in terms of the enhanced, convective solute supply to the interface. With high-purity solutions, it u greater than 250 microns/s lead to growth deceleration, and, at low supersaturations sigma, to growth cessation. When solutions containing approx. 1% of other protein impurities were used, growth deceleration occurred at any u greater than 0 and cessation in the low sigma experiments was reached at about half the it causing cessation with pure solution. The flow-induced changes in R(sub avg) and upsilon(sub avg) including growth cessation, were reversible and reproducible, independent of the direction of the u-changes and solution purity. Hence, we attribute the deceleration to the convection-enhanced supply of impurities to the interface, which at higher flow rates overpowers the effects of enhanced interfacial solute concentration. Most importantly, we found that convective transport leads to a significant reduction in kinetics fluctuations, in agreement with our earlier expectations for the lysozyme system. This supports our hypothesis that these long-term fluctuations represent an intrinsic response feature of the coupled bulk transport-interfacial kinetics system in the mixed growth control regime.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    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.

  13. Morphology Change of C60 Islands on Organic Crystals Observed by Atomic Force Microscopy.

    PubMed

    Freund, Sara; Hinaut, Antoine; Pawlak, Rémy; Liu, Shi-Xia; Decurtins, Silvio; Meyer, Ernst; Glatzel, Thilo

    2016-06-28

    Organic-organic heterojunctions are nowadays highly regarded materials for light-emitting diodes, field-effect transistors, and photovoltaic cells with the prospect of designing low-cost, flexible, and efficient electronic devices.1-3 However, the key parameter of optimized heterojunctions relies on the choice of the molecular compounds as well as on the morphology of the organic-organic interface,4 which thus requires fundamental studies. In this work, we investigated the deposition of C60 molecules at room temperature on an organic layer compound, the salt bis(benzylammonium)bis(oxalato)cupurate(II), by means of noncontact atomic force microscopy. Three-dimensional molecular islands of C60 having either triangular or hexagonal shapes are formed on the substrate following a "Volmer-Weber" type of growth. We demonstrate the dynamical reshaping of those C60 nanostructures under the local action of the AFM tip at room temperature. The dissipated energy is about 75 meV and can be interpreted as the activation energy required for this migration process.

  14. Battery Pack Thermal Design

    SciTech Connect

    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.

  15. The packing of particles

    SciTech Connect

    Cumberland, D.J.; Crawford, R.J.

    1987-01-01

    The wide range of information currently available on the packing of particles is brought together in this monograph. The authors' interest in the subject was initially aroused by the question of whether there is an optimum particle size distribution which would maximise the packing density of particles - a question which has attracted the interest of scientists and engineers for centuries. The densification of a powder mass is of relevance in a great many industries, among them the pharmaceutical, ceramic, powder metallurgy and civil engineering industries. In addition, the packing of regular - or irregular - shaped particles is also of relevance to a surprisingly large number of other industries and subject areas, i.e. the foundry industry, nuclear engineering, chemical engineering, crystallography, geology, biology, telecommunications, and so on. Accordingly, this book is written for a wide audience.

  16. Spiral disk packings

    NASA Astrophysics Data System (ADS)

    Yamagishi, Yoshikazu; Sushida, Takamichi

    2017-04-01

    It is shown that van Iterson's metric for disk packings, proposed in 1907 in the study of a centric model of spiral phyllotaxis, defines a bounded distance function in the plane. This metric is also related to the bifurcation of Voronoi tilings for logarithmic spiral lattices, through the continued fraction expansion of the divergence angle. The phase diagrams of disk packings and Voronoi tilings for logarithmic spirals are dual graphs to each other. This gives a rigorous proof that van Iterson's diagram in the centric model is connected and simply connected. It is a nonlinear analog of the duality between the phase diagrams for disk packings and Voronoi tilings on the linear lattices, having the modular group symmetry.

  17. In situ atomic force microscopy investigation of the growth of secondary nuclei produced by contact of different growth faces of potash alum crystals under supersaturated solutions

    NASA Astrophysics Data System (ADS)

    Reyhani, Manijeh M.; Freij, Sawsan; Parkinson, Gordon M.

    1999-03-01

    Contact of a potash alum crystal in a supersaturated solution with a solid surface may easily produce many secondary nuclei of the same orientation and crystal structure as the parent crystal contact faces. Previous studies have shown that, if this contact is sufficiently gentle, secondary nuclei may be produced by the transfer of ordered solute molecules without the need for microabrasion of the parent solid. In this investigation, crystal faces of the {1 0 0}, {1 1 0}, and {1 1 1} families were identified in a parent crystal, and gentle contact between these and a solid surface (glass slide) in a slightly supersaturated solution of potash alum produced many secondary nuclei, the external symmetry of which reflected that of the parent face. In situ atomic force microscopy (AFM) measurements were carried out to study the early stages of the growth of these new nuclei. A strong correlation was found between the symmetry of the nuclei produced and that of the parent crystal face. The topographies of the in situ growth of the (1 1 1) face of the parent crystal and those of the very small new nuclei produced were compared.

  18. Microstructural characterization of random packings of cubic particles

    DOE PAGES

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

    2016-10-11

    Understanding the properties of random packings of solid objects is of critical importance to a wide variety of fundamental scientific and practical problems. The great majority of the previous works focused, however, on packings of spherical and sphere-like particles. We report the first detailed simulation and characterization of packings of non-overlapping cubic particles. Such packings arise in a variety of problems, ranging from biological materials, to colloids and fabrication of porous scaffolds using salt powders. In addition, packing of cubic salt crystals arise in various problems involving preservation of pavements, paintings, and historical monuments, mineral-fluid interactions, CO2 sequestration in rock,more » and intrusion of groundwater aquifers by saline water. Not much is known, however, about the structure and statistical descriptors of such packings. We have developed a version of the random sequential addition algorithm to generate such packings, and have computed a variety of microstructural descriptors, including the radial distribution function, two-point probability function, orientational correlation function, specific surface, and mean chord length, and have studied the effect of finite system size and porosity on such characteristics. Here, the results indicate the existence of both spatial and orientational long-range order in the packing, which is more distinctive for higher packing densities.« less

  19. Microstructural characterization of random packings of cubic particles

    SciTech Connect

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

    2016-10-11

    Understanding the properties of random packings of solid objects is of critical importance to a wide variety of fundamental scientific and practical problems. The great majority of the previous works focused, however, on packings of spherical and sphere-like particles. We report the first detailed simulation and characterization of packings of non-overlapping cubic particles. Such packings arise in a variety of problems, ranging from biological materials, to colloids and fabrication of porous scaffolds using salt powders. In addition, packing of cubic salt crystals arise in various problems involving preservation of pavements, paintings, and historical monuments, mineral-fluid interactions, CO2 sequestration in rock, and intrusion of groundwater aquifers by saline water. Not much is known, however, about the structure and statistical descriptors of such packings. We have developed a version of the random sequential addition algorithm to generate such packings, and have computed a variety of microstructural descriptors, including the radial distribution function, two-point probability function, orientational correlation function, specific surface, and mean chord length, and have studied the effect of finite system size and porosity on such characteristics. Here, the results indicate the existence of both spatial and orientational long-range order in the packing, which is more distinctive for higher packing densities.

  20. Surface-initiated dehydrogenative polymerization of monolignols: a quartz crystal microbalance with dissipation monitoring and atomic force microscopy study.

    PubMed

    Wang, Chao; Qian, Chen; Roman, Maren; Glasser, Wolfgang G; Esker, Alan R

    2013-11-11

    This work highlights a real-time and label-free method to monitor the dehydrogenative polymerization of monolignols initiated by horseradish peroxidase (HRP) physically immobilized on surfaces using a quartz crystal microbalance with dissipation monitoring (QCM-D). The dehydrogenative polymer (DHP) films are expected to provide good model substrates for studying ligninolytic enzymes. The HRP was adsorbed onto gold or silica surfaces or onto and within porous desulfated nanocrystalline cellulose films from an aqueous solution. Surface-immobilized HRP retained its activity and selectivity for monolignols as coniferyl and p-coumaryl alcohol underwent dehydrogenative polymerization in the presence of hydrogen peroxide, whereas sinapyl alcohol polymerization required the addition of a nucleophile. The morphologies of the DHP layers on the surfaces were investigated via atomic force microscopy (AFM). Data from QCM-D and AFM showed that the surface-immobilized HRP-initiated dehydrogenative polymerization of monolignols was greatly affected by the support surface, monolignol concentration, hydrogen peroxide concentration, and temperature.

  1. Fully ordered to disordered granular sphere packings with random deposition

    NASA Astrophysics Data System (ADS)

    Kudrolli, Arshad; Panaitescu, Andreea

    2013-03-01

    Granular packings are typically obtained by pouring grains into a container in a gravitational field as when sugar is poured into a jar, or grains into a silo. We deconstruct this method and study the impact on packing by simply varying the pour rate and energy of particles dropped randomly but spatially uniformly in a large container whose substrate can act as a template. We find that fully disordered packings are observed when large number of particles are added all at once but an ordered fcc crystal is observed when particles are added sequentially at random locations and allowed to come to rest before adding the next layer. By scanning the packings obtained by 3D X-ray tomography, we identify the positions of all the particles and the growth of order and defects. We present an analysis of the structures formed and compare and contrast it with packings obtained using other protocols including by cyclic shear.

  2. Electromechanics of packed granular beds

    SciTech Connect

    Robinson, K.S.

    1982-01-01

    Strong, electrical, interparticle forces are induced by applied electric fields within packed beds of dielectric particles. Proposed applications utilizing electropacked beds (EPBs) or electrofluidized beds (EFBs) include air filtration and gas clean-up, fine particle separation, commercial drying and coating processes, heat and mass transfer, and bulk bed control. A new distributed circuit model of the electrical interparticle force is presented that identifies the role of surface roughness as determining the interparticle spacing. The dc steady state force is predicted to increase nearly linearly with the applied electric field and is theoretically independent of particle surface conductivity. The electric stress is found to vary nearly linearly with the applied electric field. Data are generally consistent with the theoretical contention that increased surface roughness decreases electromechanical effects. Surface conductivity variations of three to four times have no measurable effect on the dc steady state electric stress. The electric stress is insensitive to the dielectric properties of the interstitial gas eliminating Townsend discharge as a candidate for the nonlinear charge transport process thought to occur near interparticle contacts. The theoretical upper bound of the electric stress calculated using the distributed circuit model falls within the scatter of the data if a limit on the electric field in the interparticle gap which models nonlinear charge transport is in the range of 1 to 6 x 10/sup 7/ V/m. Estimates of the charge relaxation time using transient angle of repose experiments are somewhat smaller but comparable with theoretical values calculated by ignoring nonlinear charge transport.

  3. Economics Action Pack.

    ERIC Educational Resources Information Center

    McDonald's Corp., Oak Brook, IL.

    One of five McDonald's Action Packs, this learning package introduces intermediate grade students to basic economic concepts. The fourteen activities include the topics of consumption (4 activities), production (5), the market system (3), a pretest, and a posttest. Specific titles under consumption include The Wonderful Treasure Tree (introduction…

  4. DIY Fraction Pack.

    ERIC Educational Resources Information Center

    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)

  5. Nutrition Action Pack.

    ERIC Educational Resources Information Center

    Sockut, Joanne; Stumpe, Stephanie

    One of five McDonald's Action Packs, these instructional materials integrate elementary school-level nutrition education into other disciplines--biology, sociology, physiology, mathematics, and art. Contents include four units consisting of twelve activities. Unit 1, Why You Need Food, is a self-examination of what is needed for growth, health,…

  6. Economics Action Pack.

    ERIC Educational Resources Information Center

    McDonald's Corp., Oak Brook, IL.

    One of five McDonald's Action Packs, this learning package introduces intermediate grade students to basic economic concepts. The fourteen activities include the topics of consumption (4 activities), production (5), the market system (3), a pretest, and a posttest. Specific titles under consumption include The Wonderful Treasure Tree (introduction…

  7. Sun Packs Double Punch

    NASA Image and Video Library

    On August 3, the sun packed a double punch, emitting a M6.0-class flare at 9:43 am EDT. This video is of the second, slightly stronger M9.3-class flare at 11:41 pm EDT. Both flares had significant ...

  8. DIY Fraction Pack.

    ERIC Educational Resources Information Center

    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)

  9. Nutrition Action Pack.

    ERIC Educational Resources Information Center

    Sockut, Joanne; Stumpe, Stephanie

    One of five McDonald's Action Packs, these instructional materials integrate elementary school-level nutrition education into other disciplines--biology, sociology, physiology, mathematics, and art. Contents include four units consisting of twelve activities. Unit 1, Why You Need Food, is a self-examination of what is needed for growth, health,…

  10. Softening of stressed granular packings with resonant sound waves.

    PubMed

    Reichhardt, C J Olson; Lopatina, L M; Jia, X; Johnson, P A

    2015-08-01

    We perform numerical simulations of a two-dimensional bidisperse granular packing subjected to both a static confining pressure and a sinusoidal dynamic forcing applied by a wall on one edge of the packing. We measure the response experienced by a wall on the opposite edge of the packing and obtain the resonant frequency of the packing as the static or dynamic pressures are varied. Under increasing static pressure, the resonant frequency increases, indicating a velocity increase of elastic waves propagating through the packing. In contrast, when the dynamic amplitude is increased for fixed static pressure, the resonant frequency decreases, indicating a decrease in the wave velocity. This occurs both for compressional and for shear dynamic forcing and is in agreement with experimental results. We find that the average contact number Zc at the resonant frequency decreases with increasing dynamic amplitude, indicating that the elastic softening of the packing is associated with a reduced number of grain-grain contacts through which the elastic waves can travel. We image the excitations created in the packing and show that there are localized disturbances or soft spots that become more prevalent with increasing dynamic amplitude. Our results are in agreement with experiments on glass bead packings and earth materials such as sandstone and granite and may be relevant to the decrease in elastic wave velocities that has been observed to occur near fault zones after strong earthquakes, in surficial sediments during strong ground motion, and in structures during earthquake excitation.

  11. Two-dimensional folded chain crystals composed of a single isotactic poly(methyl methacrylate) chain observed by atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Kumaki, Jiro; Anzai, Takahiro

    2014-03-01

    We successfully visualized crystallization behavior of a single isolated polymer chain at a molecular level by atomic force microscopy (AFM). Previously, we found that isotactic poly(methyl methacrylate) (it-PMMA) formed two-dimensional folded chain crystals upon compression of its Langmuir monolayer on a water surface, and the molecular images of the crystals deposited on mica were clearly visualized by AFM (Kumaki, et al. JACS 2005, 127, 5788; J. Phys. Chem. B 2013, 117, 5594). In the present study, a high-molecular-weight it-PMMA was diluted in a monolayer of an it-PMMA oligomer which cannot crystallize due to the low molecular weight. At a low surface pressure, isolated amorphous chains of the high-molecular-weight it-PMMA solubilized in the oligomer monolayer were observed. On compression, the isolated chains converted to crystals composed of a single chain. Detailed AFM observations of the crystals indicated that the crystalline nuclei preferably formed at the ends of the chains, and the size of the nuclei was almost independent on the molecular weight of the it-PMMA in a wide range.

  12. The relationship between crystal growth and defect structure: a study of potassium hydrogen phthalate using x-ray topography and atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Ester, G. R.; Price, R.; Halfpenny, P. J.

    1999-05-01

    An investigation of the defect structure of crystals of potassium hydrogen phthalate (KAP) and its relationship to the crystallization behaviour has been carried out using x-ray diffraction topography and atomic force microscopy (AFM). Crystals of KAP grown from aqueous solution were found to exhibit very low defect densities in the range 5 to 15 cm-2 and remarkably low levels of strain. The character and distribution of the dominant growth dislocation types were determined using x-ray topography. The most significant features of the dislocation structure were a tendency for certain dislocation types to nucleate in pairs and at growth sector boundaries. X-ray topography revealed sectorial variations in solvent inclusions and the complementary use of AFM has shown the relationship of this to growth spiral anisotropy on the (010) face of KAP crystals. Changes in KAP crystal morphology have been observed which result from extreme variations in dislocation density, leading to either spiral growth or, in the case of dislocation-free growth sectors, a two-dimensional nucleation mechanism. The bending of dislocations from one growth sector to another and the tendency of dislocations in this material to nucleate in pairs are discussed in the context of size-dependent crystal growth rates.

  13. Effect of packing method on the randomness of disc packings

    NASA Astrophysics Data System (ADS)

    Zhang, Z. P.; Yu, A. B.; Oakeshott, R. B. S.

    1996-06-01

    The randomness of disc packings, generated by random sequential adsorption (RSA), random packing under gravity (RPG) and Mason packing (MP) which gives a packing density close to that of the RSA packing, has been analysed, based on the Delaunay tessellation, and is evaluated at two levels, i.e. the randomness at individual subunit level which relates to the construction of a triangle from a given edge length distribution and the randomness at network level which relates to the connection between triangles from a given triangle frequency distribution. The Delaunay tessellation itself is also analysed and its almost perfect randomness at the two levels is demonstrated, which verifies the proposed approach and provides a random reference system for the present analysis. It is found that (i) the construction of a triangle subunit is not random for the RSA, MP and RPG packings, with the degree of randomness decreasing from the RSA to MP and then to RPG packing; (ii) the connection of triangular subunits in the network is almost perfectly random for the RSA packing, acceptable for the MP packing and not good for the RPG packing. Packing method is an important factor governing the randomness of disc packings.

  14. Thermodynamic and kinetic aspects of fat crystallization.

    PubMed

    Himawan, C; Starov, V M; Stapley, A G F

    2006-09-25

    Naturally occurring fats are multi-component mixtures of triacylglycerols (TAGs), which are triesters of fatty acids with glycerol, and of which there are many chemically distinct compounds. Due to the importance of fats to the food and consumer products industries, fat crystallization has been studied for many years and many intricate features of TAG interactions, complicated by polymorphism, have been identified. The melting and crystallization properties of triacylglycerols are very sensitive to even small differences in fatty acid composition and position within the TAG molecule which cause steric hindrance. Differences of fatty acid chain length within a TAG lead to packing imperfections, and differences in chain lengths between different TAG molecules lead to a loss of intersolubility in the solid phase. The degree of saturation is hugely important as the presence of a double bond in a fatty acid chain causes rigid kinks in the fatty acid chains that produce huge disruption to packing structures with the result that TAGs containing double bonds have much lower melting points than completely saturated TAGs. All of these effects are more pronounced in the most stable polymorphic forms, which require the most efficient molecular packing. The crystallization of fats is complicated not just by polymorphism, but also because it usually occurs from a multi-component melt rather than from a solvent which is more common in other industrial crystallizations. This renders the conventional treatment of crystallization as a result of supersaturation somewhat meaningless. Most studies in the literature consequently quantify crystallization driving forces using the concept of supercooling below a distinct melting point. However whilst this is theoretically valid for a single component system, it can only at best represent a rough approximation for natural fat systems, which display a range of melting points. This paper reviews the latest attempts to describe the sometimes

  15. Influence of different packing methods on the hydrodynamic stability of chromatography columns.

    PubMed

    Dorn, M; Eschbach, F; Hekmat, D; Weuster-Botz, D

    2017-09-22

    It is well known that packing non-uniformity may cause peak asymmetry and limit the performance of packed-bed chromatographic columns. However, understanding of the reasons leading to packing non-uniformity is still limited. Therefore, the effect of different column packing methods, i.e. dynamic axial compression (DAC), flow packing, and combinations of both on the hydrodynamic packing heterogeneity and stability of packings composed of polymer-based compressible porous resins with a mean diameter of 90μm was investigated experimentally as well as in-silico. Deterministic Euler-Lagrange modeling of a small chromatographic column with a diameter of 9.6mm and a bed height of 30mm was applied by coupling Computational Fluid Dynamics (CFD) and the Discrete Element Method (DEM). Interparticle micromechanics as well as the fluid-particle and particle-wall interactions were taken into account. Experiments and simulations revealed substantial non-uniformity of compression force transmission and axial packing density distribution during both dynamic axial compression and flow packing which was related to wall support and interparticle friction. By combining both packing methods sequentially (dynamic axial compression followed by flow packing or vice versa), the compression forces were more homogeneous resulting in improved packing procedures. Repeated alternating application of flow packing and DAC (the so-called hybrid packing method) resulted in the most homogeneous packing density distribution and the highest packing stability which was kept nearly constant during long-term operation with cyclic hydrodynamic load. The hydrodynamic stability of the chromatographic column was evaluated by calculating the integral porosity deviation and packing induced flow velocity dispersion. The hybrid packing method gave the best results for both parameters. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. CT appearance of omental packs

    SciTech Connect

    Sefczek, R.J.; Lupetin, A.R.; Beckman, I.; Dash, N.

    1985-08-01

    Liver lacerations may be surgically treated by using the omentum as packing. A radiologist can differentiate potential postoperative complications, such as abscess, hematoma, and biloma, from these packs on computed tomographic scans by noting attenuation values.

  17. Random close packing in protein cores

    NASA Astrophysics Data System (ADS)

    Ohern, Corey

    Shortly after the determination of the first protein x-ray crystal structures, researchers analyzed their cores and reported packing fractions ϕ ~ 0 . 75 , a value that is similar to close packing equal-sized spheres. A limitation of these analyses was the use of `extended atom' models, rather than the more physically accurate `explicit hydrogen' model. The validity of using the explicit hydrogen model is proved by its ability to predict the side chain dihedral angle distributions observed in proteins. We employ the explicit hydrogen model to calculate the packing fraction of the cores of over 200 high resolution protein structures. We find that these protein cores have ϕ ~ 0 . 55 , which is comparable to random close-packing of non-spherical particles. This result provides a deeper understanding of the physical basis of protein structure that will enable predictions of the effects of amino acid mutations and design of new functional proteins. We gratefully acknowledge the support of the Raymond and Beverly Sackler Institute for Biological, Physical, and Engineering Sciences, National Library of Medicine training grant T15LM00705628 (J.C.G.), and National Science Foundation DMR-1307712 (L.R.).

  18. Forced convection by Inclined Rotary Bridgman method for growth of CoSb3 and FeSb2 single crystals from Sb-rich solutions

    NASA Astrophysics Data System (ADS)

    Pillaca, Mirtha; Harder, Oliver; Miller, Wolfram; Gille, Peter

    2017-10-01

    Sb-based compounds such as CoSb3 and FeSb2 are interesting materials for thermoelectric applications. Their single crystal growth can be achieved from high-temperature solutions that are strongly enriched in Sb. In Bridgman growth using closed ampoules, effective mixing of the solution is an important prerequisite in order to minimize the high risk of liquid inclusion formation. We have successfully grown inclusion-free single crystal of CoSb3 and FeSb2 by rotating the ampoule in a Bridgman-type crystal growth set-up being inclined by 75° with respect to the vector of gravity. Numerical modelling as well as experimental growth studies have demonstrated the strong influence of forced convection that is achieved by this modified directional solidification technique called Inclined Rotary Bridgman method.

  19. Hydrophobic core packing and backbone flexibility in coiled coils

    NASA Astrophysics Data System (ADS)

    Plecs, Joseph John

    1999-11-01

    An understanding of the structure and function of protein molecules requires an understanding of how their hydrophobic cores are assembled, including how the peptide backbone can adjust to accommodate different packing arrangements. Using coiled-coil molecules as a model of protein structures, we studied several cases in which the arrangement of packing groups in the hydrophobic core controls the structure of a folded molecule. First, we consider an example of a prosthetic packing group, where the addition of a hydrophobic ligand permits a new packing arrangement that incorporates the ligand, leading to a new overall structure. Second, the crystal structures of two peptides designed to adopt a novel fold, the right-handed coiled coils, reveal how a small change in core packing can discriminate between two different folds. And last, the design of heterodimers based on core-packing complementarity establishes that core packing can convey specificity of association between different molecules, as well as determining the molecular structure. The heterodimer designs also demonstrate the importance of a combination of backbone freedom and restriction in predicting the energetics of folded molecules. In this case, a parametrized coiled- coil backbone with appropriate parameters and restrictions was required to predict stabilities. We conclude that core packing can exert a great deal of control over the structure of proteins, and that many of its effects can be accurately predicted by modeling the molecular interactions in the context of a flexible overall structure.

  20. Prepacking perforations improves gravel packs

    SciTech Connect

    Hall, B.E.; Pace, J.R. )

    1990-05-21

    Productivity can be increased by prepacking perforations with gravel before a major gravel pack is pumped. The main gravel-pack treatment follows immediately after the prepack. This procedure can increase perforation permeability due to a more complete gravel fill of the perforation. The gravel pack prevents perforations from collapsing or filling with formation sand.

  1. Crystallization process

    DOEpatents

    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.

  2. Method for gravel packing wells

    SciTech Connect

    Jones, L.G.

    1990-08-07

    This patent describes a method for gravel packing a well that penetrates an unconsolidated or poorly consolidated subterranean oil or gas reservoir. It comprises: providing a borehole casing through the reservoir; perforating the casing at preselected intervals therealong to form at least one set of longitudinal, perforation tunnels adjacent a substantial portion of the reservoir; locating a sand screen inside the casing and in juxtaposition with the perforation tunnels, an annulus being formed between the sand screen and the casing; positioning a conduit in juxtaposition with the sand screen extending substantially the length of the sand screen and having its upper extremity open to fluids; injecting a fluid slurry containing gravel down through the annulus and conduit whereby the fluid portion of the slurry is forced out of the annulus through the perforation tunnels into the reservoir and the gravel portion of the slurry deposited in the annulus and forced into the perforation tunnels into the formation; sizing the cross-sectional area of the conduit and the annulus so that if gravel forms a bridge in a portion of the annulus thereby blocking the flow of fluid slurry through the the annulus, fluid slurry containing gravel will continue to flow through the conduit and into the annulus around the gravel bridge; and terminating the injection of the slurry.

  3. An Economic Analysis of Alternative Tray Pack Sizes

    DTIC Science & Technology

    1990-08-01

    I"IC FILE COPY TECHNICAL REPORT AD NATICK/TR-90/048 AN ECONOMIC ANALYSIS OF ALTERNATIVE TRAY PACK SIZES BY NMARK M. DAVIS BENTLEY COLLEGE, WALTHAM...AUGUST 199 FINAL REPORT APR 89 TO SEP 89 4. TITLE AND SUBTITLE 5. FUNDING NUMBERS AN ECONOMIC ANALYSIS OF ALTERNATIVE PE 62 786 TRAY PACK SIZES PR AH99...the current tray pack container to a 6/9 and to an 8/12 portion tray padr container. Force structures for field feeding were derived from data

  4. Condensation in Nanoporous Packed Beds.

    PubMed

    Ally, Javed; Molla, Shahnawaz; Mostowfi, Farshid

    2016-05-10

    In materials with tiny, nanometer-scale pores, liquid condensation is shifted from the bulk saturation pressure observed at larger scales. This effect is called capillary condensation and can block pores, which has major consequences in hydrocarbon production, as well as in fuel cells, catalysis, and powder adhesion. In this study, high pressure nanofluidic condensation studies are performed using propane and carbon dioxide in a colloidal crystal packed bed. Direct visualization allows the extent of condensation to be observed, as well as inference of the pore geometry from Bragg diffraction. We show experimentally that capillary condensation depends on pore geometry and wettability because these factors determine the shape of the menisci that coalesce when pore filling occurs, contrary to the typical assumption that all pore structures can be modeled as cylindrical and perfectly wetting. We also observe capillary condensation at higher pressures than has been done previously, which is important because many applications involving this phenomenon occur well above atmospheric pressure, and there is little, if any, experimental validation of capillary condensation at such pressures, particularly with direct visualization.

  5. A sphere packing slideshow

    NASA Astrophysics Data System (ADS)

    Holmes-Cerfon, Miranda; Gortler, Steven; Brenner, Michael

    2014-03-01

    We have enumerated all the ways to arrange n <= 13+ spheres as a cluster that is nonlinearly rigid. We have discovered many packings that are hypostatic, namely they have fewer than the 3n-6 contacts required to be linearly rigid. Simple scaling arguments explain why these are thermodynamically important when the spheres are colloids interacting with a short-range potential. We discuss these clusters, as well as other surprises that came up along the way. (''+'' means we have enumerated only a particular kind of cluster for n=14, 15, and beyond.)

  6. Marginal rigidity and history dependence in packings of attractive athermal emulsions

    NASA Astrophysics Data System (ADS)

    Bargteil, Dylan; Pontani, Lea-Laetitia; Brujic, Jasna

    2014-03-01

    The geometry and stress through particulate packings depends on the method of preparation and the interaction potential between the particles. Previously, we discovered that creaming frictionless, athermal emulsions with a short-range depletion attraction leads to an initial increase in the packing density above random close packing, followed by a monotonic decrease in density (Jorjadze et al, PNAS, 2011). This decrease is because the attractive force stabilizes loose voids, thus reducing the average coordination number, , of the packing. In order to understand the mechanism of packing creation, we investigate whether the final density is influenced by the polydispersity or the initial volume fraction of droplets, as it is in frictional packings. Finally, we compress the attractive packings by centrifugation to probe the scaling laws of pressure versus density and and compare them with those found in repulsive packings (Jorjadze et al, PRL, 2013).

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

    NASA Astrophysics Data System (ADS)

    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.

  8. ExactPack Documentation

    SciTech Connect

    Singleton, Jr., Robert; Israel, Daniel M.; Doebling, Scott William; Woods, Charles Nathan; Kaul, Ann; Walter, Jr., John William; Rogers, Michael Lloyd

    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.

  9. Consolidatable gravel pack method

    SciTech Connect

    Friedman, R.H.; Surles, B.W.

    1989-01-31

    A method is described for forming a consolidated gravel pack in a washed-out cavity adjacent to a producing well penetrating a subterranean oil formation comprising the steps of: (a) forming a quantity of resin coated gravel comprising granular mineral particles including gravel, the gravel particles being coated with a resin fluid containing a polymerizable oligomer of furfuryl alcohol resin, a catalyst comprising an oil soluble, very slightly water soluble organic acid and an ester of a weak organic acid to consume water produced by the polymerization of resin, the polymer coated gravel comprising a sticky solid material; (b) preparing an aqueous saline carrier fluid comprising water which is from 70 to 100% saturated with sodium chloride; (c) suspending the resin-coated gravel in the carrier fluid, forming a fluid mixture of resin-coated gravel and carrier fluid; (d) introducing the fluid mixture comprising the resin coated gravel particles suspended in the aqueous saline carrier fluid into the washed-out cavity of the formation adjacent to the producing well and shutting in the well for sufficient period of time to allow polymerization of the resin, forming the permeable gravel pack in the washed-out cavity of the formation.

  10. Effect of crystal anisotropy and adhesive forces on laser induced deformation patterns in covalently bonded thin films

    NASA Astrophysics Data System (ADS)

    Walgraef, D.; Ghoniem, N. M.

    2002-04-01

    The effect of crystal structure on laser induced deformation patterns in thin films and surfaces is analyzed within the framework of a dynamical model for the coupled evolution of defect densities and deformation fields. In crystals with covalent bonding, such as Si and SiC, preferential bond breaking may occur, as a result of the relative orientation of the laser electric field and crystallographic axes. We extend here our theoretical framework to incorporate the effects of anisotropic defect diffusion, and the influence of film-substrate adhesion on deformation pattern selection and stability of thin films subjected to laser beams. We also compare theoretical predictions to experimental observations on single crystal silicon wafer surfaces. Furthermore, it is predicted that the laser induced damage threshold for SiC single crystals can be in excess of 200 J/cm2.

  11. Numerical simulation of gravel packing

    SciTech Connect

    Winterfeld, P.H.; Schroeder, D.E. Jr. )

    1992-08-01

    To obtain maximum productivity from unconsolidated formations where sand control is required, it is important to understand the mechanics of gravel packing. This paper describes a finite-element, numerical simulator that can predict gravel placement in the perforations and annulus of a wellbore. The equations for the simulator include mass and momentum conservation. Wellbore geometry, physical properties, and fluid and gravel-pack properties are simulator input. Experiments in a 100-ft full-scale wellbore model for three gravel-packing configurations have been successfully simulated. These configurations are a circulating pack with a washpipe, a squeeze pack, and a circulating/squeeze pack with a washpipe and a lower telltale screen. The low cost, speed, and extrapolation capabilities of the numerical simulator will greatly enhance our ability to predict gravel placement in a wellbore.

  12. Hexatic-to-disorder transition in colloidal crystals near electrodes: rapid annealing of polycrystalline domains.

    PubMed

    Dutcher, C S; Woehl, T J; Talken, N H; Ristenpart, W D

    2013-09-20

    Colloids are known to form planar, hexagonal closed packed (hcp) crystals near electrodes in response to electrohydrodynamic (EHD) flow. Previous work has established that the EHD velocity increases as the applied ac frequency decreases. Here we report the existence of an order-to-disorder transition at sufficiently low frequencies, despite the increase in the attractive EHD driving force. At large frequencies (~500 Hz), spherical micron-scale particles form hcp crystals; as the frequency is decreased below ~250 Hz, however, the crystalline structure transitions to randomly closed packed (rcp). The transition is reversible and second order with respect to frequency, and independent measurements of the EHD aggregation rate confirm that the EHD driving force is indeed higher at the lower frequencies. We present evidence that the transition is instead caused by an increased particle diffusivity due to increased particle height over the electrode at lower frequencies, and we demonstrate that the hcp-rcp transition facilitates rapid annealing of polycrystalline domains.

  13. Granular Packings and Fault Zones

    NASA Astrophysics Data System (ADS)

    Åström, J. A.; Herrmann, H. J.; Timonen, J.

    2000-01-01

    The failure of a two-dimensional packing of elastic grains is analyzed using a numerical model. The packing fails through formation of shear bands or faults. During failure there is a separation of the system into two grain-packing states. In a shear band, local ``rotating bearings'' are spontaneously formed. The bearing state is favored in a shear band because it has a low stiffness against shearing. The ``seismic activity'' distribution in the packing has the same characteristics as that of the earthquake distribution in tectonic faults. The directions of the principal stresses in a bearing are reminiscent of those found at the San Andreas Fault.

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

    NASA Astrophysics Data System (ADS)

    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.

  15. Understanding Force Chains in Dense Granular Materials

    NASA Astrophysics Data System (ADS)

    Sun, Qicheng; Jin, Feng; Liu, Jianguo; Zhang, Guohua

    When a load is applied to a dense granular material, the stress is largely transmitted by relatively rigid, heavily stressed chains of particles forming a sparse network of larger contact forces. Force chains act as the key determinant of mechanical properties such as stability, elasticity and flowability. To understand the structure and evolution of force chains, related physical processes and three corresponding characteristic time scales are analyzed in this study. We also propose three dimensionless numbers for the measurement of the relative importance of force chains. To solely study the effect of particle surface friction on force chains, uniaxial compression tests of 11,000 equal-sized particles in 2D were numerically simulated using the discrete element method. By proposing three conditions to define a force chain, the chain length distribution is found in the form of a power law. The exponent of 1.744 is independent of the surface friction. Although these results were obtained from partially crystallized jammed packings, they provide new insight into the physical processes and the structure of force chains, and thus will be helpful in the interpretation of force chains in other dense granular systems.

  16. Unraveling Interactions in Molecular Crystals Using Dispersion Corrected Density Functional Theory: The Case of the Epoxydihydroarsanthrene Molecules.

    PubMed

    Otero-de-la-Roza, A; Luaña, Víctor; Tiekink, Edward R T; Zukerman-Schpector, Julio

    2014-11-11

    Noncovalent interactions are prevalent in crystal packing and supramolecular chemistry. Directional noncovalent interactions such as donor-acceptor bonds (e.g., hydrogen, chalcogen, and pnictogen bonds) as well as nondirectional forces (such as dispersion) come together to stabilize supramolecular assemblies by striking a delicate energetic balance. Typically, a two-pronged approach employing experimental X-ray structures and gas phase quantum chemical modeling has been used to understand and design supramolecular architectures. Drawing from recent advances in molecular crystal modeling with dispersion corrected density functional theory (DFT), we propose in this article a combination of qualitative noncovalent index (NCI) analysis and periodic and gas phase DFT calculations on substitutional crystal analogues to unravel the dominant interactions in a particular crystal packing. We illustrate the possibilities of this approach by studying three crystal packings of epoxydihydroarsanthrene analogues that present a complex combination of donor-acceptor interactions including pnictogen-pnictogen, pnictogen-π, and pnictogen-chalcogen. We show that, in these crystals, the chalcogen-pnictogen interaction dominates over the pnictogen-pnictogen and pnictogen-π. In the latter, the role of donor and acceptor is reversed depending on the interacting moieties. Multiple chalcogen-pnictogen interactions necessitate larger donor atoms, such as sulfur. These observations explain and rationalize the experimentally observed crystal structures.

  17. Langevin Dynamics Simulations of Genome Packing in Bacteriophage

    PubMed Central

    Forrey, Christopher; Muthukumar, M.

    2006-01-01

    We use Langevin dynamics simulations to study the process by which a coarse-grained DNA chain is packaged within an icosahedral container. We focus our inquiry on three areas of interest in viral packing: the evolving structure of the packaged DNA condensate; the packing velocity; and the internal buildup of energy and resultant forces. Each of these areas has been studied experimentally, and we find that we can qualitatively reproduce experimental results. However, our findings also suggest that the phage genome packing process is fundamentally different than that suggested by the inverse spool model. We suggest that packing in general does not proceed in the deterministic fashion of the inverse-spool model, but rather is stochastic in character. As the chain configuration becomes compressed within the capsid, the structure, energy, and packing velocity all become dependent upon polymer dynamics. That many observed features of the packing process are rooted in condensed-phase polymer dynamics suggests that statistical mechanics, rather than mechanics, should serve as the proper theoretical basis for genome packing. Finally we suggest that, as a result of an internal protein unique to bacteriophage T7, the T7 genome may be significantly more ordered than is true for bacteriophage in general. PMID:16617089

  18. Effect of homolog doping on surface morphology and mass-loss rates from PETN crystals. Studies using atomic force microscope and thermo-gravimetric analysis

    DOE PAGES

    Bhattacharya, S. K.; Maiti, A; Gee, R. H.; ...

    2012-08-28

    Pentaerythritol tetranitrate (PETN) is an important energetic material and its performance as a secondary explosive depends strongly on the density as well as flow porosity of powdered material, which in turn is governed by the size and surface properties of the PETN crystallite particles. Historically there has been evidence that the surface properties of PETN particles can be strongly influenced by the presence of homolog impurities of PETN, in particular, dipentaerythritol hexanitrate (diPEHN) and tripentaerythritol octanitrate (triPEON), although not many systematic studies characterizing such influence exist. In this work we employ thermogravimetric analysis (TGA) to measure mass-loss rates at elevatedmore » temperatures and show that doping with a small amount of diPEHN and triPEON can reduce the mass-loss rate from PETN single-crystal surfaces by as much as 35 % as compared to undoped crystals. Arrhenius plots of mass-loss rates as a function of temperature suggest that the reduction in evaporation is not due to the change in activation barrier of the molecular evaporation process, but perhaps due to the impedance to the receding motion of the steps by the immobile impurities on the surface. Removal of surface impurities through gentle washing with ethanol leads to enhanced mass-loss rate relative to pure PETN suggesting a roughened surface morphology. Some surface roughening in doped crystals is supported by Atomic force microscopy (AFM) images of growth layers that show evidences of growth layer stacking and rough edges. Furthermore, we find that a larger amount of impurity added to the original solution does not necessarily lead to a more highly doped crystal, which could perhaps be interpreted as PETN crystals being able to accommodate only up to a certain weight percent of homolog impurities.« less

  19. Effect of homolog doping on surface morphology and mass-loss rates from PETN crystals. Studies using atomic force microscope and thermo-gravimetric analysis

    SciTech Connect

    Bhattacharya, S. K.; Maiti, A; Gee, R. H.; Nunley, J.; Weeks, B. L.

    2012-08-28

    Pentaerythritol tetranitrate (PETN) is an important energetic material and its performance as a secondary explosive depends strongly on the density as well as flow porosity of powdered material, which in turn is governed by the size and surface properties of the PETN crystallite particles. Historically there has been evidence that the surface properties of PETN particles can be strongly influenced by the presence of homolog impurities of PETN, in particular, dipentaerythritol hexanitrate (diPEHN) and tripentaerythritol octanitrate (triPEON), although not many systematic studies characterizing such influence exist. In this work we employ thermogravimetric analysis (TGA) to measure mass-loss rates at elevated temperatures and show that doping with a small amount of diPEHN and triPEON can reduce the mass-loss rate from PETN single-crystal surfaces by as much as 35 % as compared to undoped crystals. Arrhenius plots of mass-loss rates as a function of temperature suggest that the reduction in evaporation is not due to the change in activation barrier of the molecular evaporation process, but perhaps due to the impedance to the receding motion of the steps by the immobile impurities on the surface. Removal of surface impurities through gentle washing with ethanol leads to enhanced mass-loss rate relative to pure PETN suggesting a roughened surface morphology. Some surface roughening in doped crystals is supported by Atomic force microscopy (AFM) images of growth layers that show evidences of growth layer stacking and rough edges. Furthermore, we find that a larger amount of impurity added to the original solution does not necessarily lead to a more highly doped crystal, which could perhaps be interpreted as PETN crystals being able to accommodate only up to a certain weight percent of homolog impurities.

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

    NASA Astrophysics Data System (ADS)

    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.

  1. Packing Products: Polystyrene vs. Cornstarch

    ERIC Educational Resources Information Center

    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…

  2. Packing Products: Polystyrene vs. Cornstarch

    ERIC Educational Resources Information Center

    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…

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

    NASA Astrophysics Data System (ADS)

    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.

  4. Calcium carbonate crystal growth beneath Langmuir monolayers of acidic β-hairpin peptides.

    PubMed

    Gong, Haofei; Yang, Yi; Pluntke, Manuela; Marti, Othmar; Majer, Zsuzsa; Sewald, Norbert; Volkmer, Dirk

    2014-11-28

    Four amphiphilic peptides with designed hairpin structure were synthesized and their monolayers were employed as model systems to study biologically inspired calcium carbonate crystallization. Langmuir monolayers of hairpin peptides were investigated by surface pressure area isotherms, surface potential isotherms, Brewster angle microscopy (BAM), atomic force microscopy (AFM) and Fourier transform infrared (FTIR) spectroscopy. A β-hairpin conformation was found for all peptides at the air-water interface although their packing arrangements seem to be different. Crystallization of calcium carbonate under these peptide monolayers was investigated at different surface pressures and growth times both by in situ optical microscopy, BAM and ex situ investigations such as scanning electron microscopy (SEM) and transmission electron microscopy (TEM). An amorphous calcium carbonate precursor was found at the initial crystallization stage. The crystallization process occurred in three stages. It starts from the nucleation of amorphous particles being a kinetically controlled process. Crystal nuclei subsequently aggregate to large particles and vaterite crystals start to form inside the amorphous layer, with the monolayer fluidity exerting an important role. The third process includes the re-crystallization of vaterite to calcite, which is thermodynamically controlled by monolayer structural factors including the monolayer flexibility and packing arrangement of the polar headgroups. Thus, the kinetic factors, monolayer fluidity and flexibility as well as structure factors govern the crystal morphology and polymorph distribution simultaneously and synergistically.

  5. 7 CFR 51.310 - Packing requirements.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... STANDARDS) United States Standards for Grades of Apples Packing Requirements § 51.310 Packing requirements. (a) Apples tray packed or cell packed in cartons shall be arranged according to approved and... that apples are of the proper size for molds or cell compartments in which they are packed, and that...

  6. 7 CFR 51.310 - Packing requirements.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... STANDARDS) United States Standards for Grades of Apples Packing Requirements § 51.310 Packing requirements. (a) Apples tray packed or cell packed in cartons shall be arranged according to approved and... that apples are of the proper size for molds or cell compartments in which they are packed, and that...

  7. 7 CFR 51.310 - Packing requirements.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... STANDARDS) United States Standards for Grades of Apples Packing Requirements § 51.310 Packing requirements. (a) Apples tray packed or cell packed in cartons shall be arranged according to approved and... that apples are of the proper size for molds or cell compartments in which they are packed, and that...

  8. Packed Planetary Systems

    NASA Astrophysics Data System (ADS)

    Barnes, R.; Greenberg, R.

    2005-08-01

    Planetary systems display a wide range of appearances, with apparently arbitrary values of semi-major axis, eccentricity, etc. We reduce the complexity of orbital configurations to a single value, δ , which is a measure of how close, over secular timescales ( ˜10,000 orbits), two consecutive planets come to each other. We measure this distance relative to the sum of the radii of their Hill spheres, sometimes referred to as mutual Hill radii (MHR). We determine the closest approach distance by numerically integrating the entire system on coplanar orbits, using minimum masses. For non-resonant systems, close approach occurs during apsidal alignment, either parallel or anti-parallel. For resonant pairs the distance at conjunction determines the closest approach distance. Previous analytic work found that planets on circular orbits were assuredly unstable if they came within 3.5 MHR (i.e. Gladman 1993; Chambers, Wetherill & Boss 1996). We find that most known pairs of jovian planets (including those in our solar system) come within 3.5 -- 7 MHR of each other. We also find that several systems are unstable (their closest approach distance is less than 3.5 MHR). These systems, if they are real, probably exist in an observationally permitted location somewhat different from the current best fit. In these cases, the planets' closest approach distance will most likely also be slightly larger than 3.5 MHR. Most pairs beyond 7 MHR probably experienced post-formation migration (i.e. tidal circularization, inward scattering of small bodies) which moved them further apart. This result is even more remarkable since we have used the minimum masses; most likely the systems are inclined to the line of sight, making the Hill spheres larger, and shrinking δ . This dense packing may reflect a tendency for planets to form as close together as they can without being dynamically unstable. This result further implies there may be a large number of smaller, currently undetectable

  9. Probe with integrated heater and thermocouple pack

    DOEpatents

    McCulloch, Reginald W.; Dial, Ralph E.; Finnell, Wilber K. R.

    1988-01-01

    A probe for measuring heat includes an elongate rod fitted within a sheath, and a plurality of annular recesses are formed on the surface of the rod in a spaced-apart relationship to form annular chambers that are resistant to heat flow. A longitudinal bore extends axially into the rod and within the cylinders defined by the annular chambers, and an integrated heater and thermocouple pack is dimensioned to fit within the bore. In construction, the integrated pack includes a plurality of wires disposed in electrical insulation within a sheath and a heater cable. These wires include one common wire and a plurality of thermocouple wires. The common wire is constructed of one type of conductive material while the thermocouple wires are each constructed of two types of materials so that at least one thermocouple junction is formed therein. All of the wires extend the length of the integrated pack and are connected together at their ends. The thermocouple wires are constructed to form thermocouple junctions proximate to each annular chamber for producing electromotive forces corresponding to the temperature of the rod within the annular chambers relative to outside the chambers. In the preferred embodiment, each thermocouple wire forms two thermocouple junctions, one junction being disposed within an annular chamber and the second junction being disposed outside of, but proximate to, the same annular chamber. In one embodiment two thermocouple wires are configured to double the sensitivity of the probe in one region.

  10. Probe with integrated heater and thermocouple pack

    DOEpatents

    McCulloch, Reg W.; Dial, Ralph E.; Finnell, Wilber K. R.

    1990-01-01

    A probe for measuring heat includes an elongate rod fitted within a sheath, and a plurality of annular recesses are formed on the surface of the rod in a spaced-apart relationship to form annular chambers that are resistant to heat flow. A longitudinal bore extends axially into the rod and within the cylinders defined by the annular chambers, and an integrated heater and thermocouple pack is dimensioned to fit within the bore. In construction, the integrated pack includes a plurality of wires disposed in electrical insulation within a sheath and a heater cable. These wires include one common wire and a plurality of thermocuple wires. The common wire is constructed of one type of conductive material while the thermocouple wires are each constructed of two types of materials so that at least one thermocouple junction is formed therein. All of the wires extend the length of the integrated pack and are connected together at their ends. The thermocouple wires are constructed to form thermocouple junctions proximate to each annular chamber for producing electromotive forces corresponding to the temperature of the rod within the annular chambers relative to outside the chambers. In the preferred embodiment, each thermocouple wire forms two thermocouple junctions, one junction being disposed within an annular chamber and the second junction being disposed outside of, but proximate to, the same annular chamber. In one embodiment two thermocouple wires are configured to double the sensitivity of the probe in one region.

  11. Advanced Protein Crystallization Facility (APCF)

    NASA Technical Reports Server (NTRS)

    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

  12. [Evaluation of capillary chromatographic columns packed by electrokinetic packing method].

    PubMed

    Li, Z; You, H; Hu, S; Wei, W; Luo, G

    1997-01-01

    In this paper, a method for electrokinetic packing capillary columns is reported. A higher column effeciency was obtained by performing electrochromatography on electrokinetic packing columns. The highest column efficiency in number of theoretical plate per meter was more than 200000, corresponding to reduced plate height less than 2. The reproducibilities of the same column in different intervals and different columns prepared from the same or different batches were compared. The relative standard deviations of the number of theoretical plate and retention time were less than 10% and 8%, respectively. The results indicated that high column efficiency and good reproducibility can be obtained on these new capillary packed columns.

  13. Observation of two-dimensional nucleation on the {0 1 0} face of potassium hydrogen phthalate (KAP) crystals using ex situ atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Ester, G. R.; Halfpenny, P. J.

    1998-04-01

    The surface topology of microcrystals of potassium hydrogen phthalate (KAP) grown at a relative supersaturation of approximately 26% has been investigated using ex situ atomic force microscopy (AFM). Two distinctly different plate-like habits were observed. The thicker of the two habits resulted from growth by a spiral mechanism on the {0 1 0} faces while a thinner, less common, plate-like morphology occurred due to growth by two-dimensional nucleation on this face. The nuclei, being both asymmetric and partially polygonised, are essentially identical in shape to that of the spirals observed on the thicker crystals. They range in size from about 1200 to 400 nm with the smallest of the nuclei being substantially larger than the estimated radius of the critical two-dimensional nucleus at this supersaturation. This is attributed to continued growth of the nuclei, during separation from the growth solution. The nuclei are distributed non uniformly across the surface of the crystals, being greatest in number at the edges and corners of the {0 1 0} face. This distribution reflects the expected variation in surface supersaturation across the crystal face.

  14. DHS Internship Summary-Crystal Assembly at Different Length Scales

    SciTech Connect

    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.

  15. Nasal packing after septoplasty: a randomized comparison of packing versus no packing in 88 patients.

    PubMed

    Awan, Mohammad Sohail; Iqbal, Moghira

    2008-11-01

    The once-common practice of packing the nose after septoplasty was based on a desire to prevent postoperative complications such as bleeding, septal hematoma, and adhesion formation. However, it was since found that not only is nasal packing ineffective in this regard, it can actually cause these complications. Although the consensus in the world literature is that packing should be avoided, to the best of our knowledge, no truly randomized study has been undertaken in Southwest Asia upon which to justify this recommendation here. Therefore, we conducted a prospective randomized comparison of the incidence of a variety of postoperative signs and symptoms in 88 patients, 15 years of age and older, who did (n = 44) and did not (n = 44) undergo nasal packing following septoplasty. We found that the patients who underwent packing experienced significantly more postoperative pain, headache, epiphora, dysphagia, and sleep disturbance on the night of surgery. Oral and nasal examinations 7 days postoperatively revealed no significant difference between the two groups in the incidence of bleeding, septal hematoma, adhesion formation, and local infection. Finally, the packing group reported a moderate to high level of pain during removal of the packing. Our findings confirm that nasal packing after septoplasty is not only unnecessary, it is actually a source of patient discomfort and other signs and symptoms.

  16. Co-operation of π⋯π, Cu(II)⋯π, carbonyl⋯π and hydrogen-bonding forces leading to the formation of water cluster mimics observed in the reassessed crystal structure of [Cu(mal)(phen)(H 2O)]2·3H 2O (H 2mal = malonic acid, phen = 1,10-phenanthroline)

    NASA Astrophysics Data System (ADS)

    Choudhury, Somnath Ray; Lee, Hon Man; Hsiao, Tsun-Hung; Colacio, Enrique; Jana, Atish Dipankar; Mukhopadhyay, Subrata

    2010-04-01

    A copper(II) malonate complex with formula [Cu(mal)(phen)(H 2O)] 2·3H 2O ( 1) [H 2mal = malonic acid, phen = 1,10-phenanthroline] has been synthesized and its crystal structure has been re-determined with an improved R value (the compound 1 was originally synthesized and crystallographically characterized by Kwik et al. with R = 0.047, see: J. Chem. Soc. Dalton Trans. (1986) 2529) with the water hydrogen atom positions located. This has led to the revelation that the water molecules organize around the carboxylate group of the malonate ligand forming tetramer, hexamer and octameric water cluster mimics. These cooperative hydrogen-bonding forces and various π-forces (π⋯π, Cu(II)⋯π, carbonyl⋯π) involving 1,10-phenanthroline aromatic rings determine the overall packing of the molecular units in the unit cell. There exists two identical monomers in the asymmetric unit with Z// = 2. TG measurements reveal the loss of water molecules that are all released at 120 °C. The water sorption/desorption process is reversible as supported by FTIR spectroscopic and XRPD studies.

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

    PubMed Central

    Jin, Weiwei; Lu, Peng; Li, Shuixiang

    2015-01-01

    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). PMID:26490670

  18. Dog pack attack: hunting humans.

    PubMed

    Avis, S P

    1999-09-01

    Dog bite-related fatalities, although unusual, accounted for 304 deaths in the United States between 1979 and 1996 and 6 fatalities in Canada between 1994 and 1996. Fatal dog pack attacks and attacks involving human predation are less common. The following describes a dog pack attack on a family of four involving 2 fatalities with predation of the victims. Factors previously identified that contribute to pack attacks and predation, including prior group hunting, social feeding, territorial defense, lack of human interaction, and prey stimuli, are discussed.

  19. Aspiration of Nasopore nasal packing.

    PubMed

    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.

  20. 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

    NASA Astrophysics Data System (ADS)

    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.

  1. Hyperstaticity and loops in frictional granular packings

    NASA Astrophysics Data System (ADS)

    Tordesillas, Antoinette; Lam, Edward; Metzger, Philip T.

    2009-06-01

    The hyperstatic nature of granular packings of perfectly rigid disks is analyzed algebraically and through numerical simulation. The elementary loops of grains emerge as a fundamental element in addressing hyperstaticity. Loops consisting of an odd number of grains behave differently than those with an even number. For odd loops, the latent stresses are exterior and are characterized by the sum of frictional forces around each loop. For even loops, the latent stresses are interior and are characterized by the alternating sum of frictional forces around each loop. The statistics of these two types of loop sums are found to be Gibbsian with a "temperature" that is linear with the friction coefficient μ when μ<1.

  2. Significant melting point depression of two-dimensional folded-chain crystals of isotactic poly(methyl methacrylate)s observed by high-resolution in situ atomic force microscopy.

    PubMed

    Takanashi, Yuma; Kumaki, Jiro

    2013-05-09

    The properties of polymer ultrathin films are a subject of intense study from both practical and academic viewpoints. Previously, we found that upon compression, an isotactic poly(methyl methacrylate) (it-PMMA) Langmuir monolayer crystallized to form a two-dimensional (2D) folded-chain crystal, and the molecular image of the crystal with chain folding and tie chains was clearly visualized by atomic force microscopy (AFM). In the present study, the melting behaviors of the it-PMMA 2D crystals were successfully observed in situ by high-temperature AFM at the molecular lever for the first time. The chain-chain distances (~1.2 nm) of the crystals were clearly resolved even at temperatures close to the melting temperatures (Tm) of the 2D crystals. We found that the Tm of the 2D crystals was at most 90 °C lower than the bulk crystals. The Tm depression strongly depended on the molecular weight, while the molecular weight dependence of the bulk Tm was negligible in the molecular weight regime studied. The Tm depression also depended on the substrates, a slightly larger depression being observed on a sapphire substrate compared to that on a mica. The large Tm depressions of the 2D crystals could not be explained by a simple Thomson-Gibbs argument, theoretical developments are necessary to understand the melting of the 2D crystals.

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

    SciTech Connect

    Cinacchi, Giorgio; Torquato, Salvatore

    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.

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

    NASA Astrophysics Data System (ADS)

    Cinacchi, Giorgio; Torquato, Salvatore

    2015-12-01

    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.

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

    PubMed

    Cinacchi, Giorgio; Torquato, Salvatore

    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.

  6. Response of Jammed Ellipsoid Packings

    NASA Astrophysics Data System (ADS)

    Zeravcic, Zorana; Liu, Andrea; Nagel, Sidney

    2011-03-01

    We investigate the nature of the jamming transition for packings of spheroids by examining the elastic moduli as a function of the aspect ratio of the particles ɛ and the compression. Irrespective of the particle aspect ratio, both shear modulus G and bulk modulus B show the same scaling as a function of compression as is found for packings of spheres. Moreover, for any value of ɛ , G is proportional to the excess of the coordination number above that found at the jamming threshold; this recovers the result for frictionless spheres at ɛ = 1 . Our results imply a new diverging length scale associated with the loss of rigidity of these spheroid packings. The critical behavior of ellipsoid packings is an extension of that found for spheres.

  7. Storing Chemicals in Packed Spheres

    NASA Technical Reports Server (NTRS)

    Wang, T. G.; Elleman, D. D.

    1986-01-01

    Reactants released by crushing or puncturing. Agglomerated gas-filled spheres hexagonally close packed and sintered or glued together into rods strung together at ends. Rods fed into crushing machine to release material in spheres as needed.

  8. Vacuum skin pack of beef--a consumer friendly alternative.

    PubMed

    Lagerstedt, Åsa; Ahnström, Maria L; Lundström, Kerstin

    2011-07-01

    The aim of this study was to assess how beef quality traits are affected by skin packaging compared with vacuum and high-oxygen modified atmosphere packaging (MAP; 80% O(2) and 20% CO(2)). Both M. longissimus dorsi from 6 young bulls were cut and aged in vacuum for 7 days and then cut into 3.5-cm steaks, thereafter either frozen directly day 7 or stored in skin pack, vacuum pack or MAP for an additional 7 or 14 days and then frozen. Warner-Bratzler shear force, loss and colour were measured and sensory analysis was performed. The results showed no differences in shear force, sensory analysis and total loss between steaks packed in skin pack or vacuum, but skin packed steaks had lower purge loss. MAP steaks had lower sensory scores than the other treatments at days 14 and 21. Raw MAP-steaks were bright red, but showed signs of premature browning when cooked. Copyright © 2011 Elsevier Ltd. All rights reserved.

  9. Pattern formations and optimal packing.

    PubMed

    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.

  10. Fluidization of a vertically vibrated two-dimensional hard sphere packing: a granular meltdown.

    PubMed

    Götzendorfer, Andreas; Tai, Chi-Hwang; Kruelle, Christof A; Rehberg, Ingo; Hsiau, Shu-San

    2006-07-01

    We report measurements of the fluidization process in vertically vibrated two-dimensional granular packings. An initially close packed granular bed is exposed to sinusoidal container oscillations with gradually increasing amplitude. At first the particles close to the free surface become mobile. When a critical value of the forcing strength is reached the remaining crystal suddenly breaks up and the bed fluidizes completely. This transition leads to discontinuous changes in the density distribution and in the root mean square displacement of the individual particles. Likewise the vertical center of mass coordinate increases by leaps and bounds at the transition. It turns out that the maximum container velocity v0 is the crucial driving parameter determining the state of a fully fluidized system. For particles of various sizes the transition to full fluidization occurs at the same value of v 2 0/gd, where d is the particle diameter and g is the gravitational acceleration. A discontinuous fluidization transition is only observed when the particles are highly elastic.

  11. Jammed lattice sphere packings

    NASA Astrophysics Data System (ADS)

    Kallus, Yoav; Marcotte, Étienne; Torquato, Salvatore

    2013-12-01

    We generate and study an ensemble of isostatic jammed hard-sphere lattices. These lattices are obtained by compression of a periodic system with an adaptive unit cell containing a single sphere until the point of mechanical stability. We present detailed numerical data about the densities, pair correlations, force distributions, and structure factors of such lattices. We show that this model retains many of the crucial structural features of the classical hard-sphere model and propose it as a model for the jamming and glass transitions that enables exploration of much higher dimensions than are usually accessible.

  12. Crystal structures and properties of nylon polymers from theory

    SciTech Connect

    Dasgupta, S.; Goddard, W.A. III; Hammond, W.B.

    1996-12-11

    A complete force field (MSXX) for simulation of all nylon polymers is derived from ab initio quantum calculations. Special emphasis is given to the accuracy of the hydrogen bond potential for the amide unit and the torsional potential between the peptide and alkane fragments. The MSXX force field was used to predict the structures, moduli, and detailed geometries of all nine nylons for which there are experimental crystal data plus one other. For nylon-(2n) with 2n = 6, the {alpha} crystal structure (with all-trans CH{sub 2} chains nearly coplanar with the hydrogen bonding plane) is more stable, while for 2n > 6, {gamma} (with the alkane plane twisted by 70{degree}) is more stable. This change results from the increased importance of methylene packing interactions over H bonds for larger 2n. We find the highest Young`s modulus for nylon-7. 51 refs., 6 figs., 7 tabs.

  13. Geometric Ginzburg-Landau theory for faceted crystals in one dimension: From coarsening to chaos through a driving force.

    PubMed

    Hausser, Frank; Voigt, Axel

    2009-01-01

    We consider the dynamic behavior in driven phase transitions dominated either by attachment-detachment or by surface diffusion mass transport mechanisms. As the driving force increases, we numerically demonstrate for both cases that the spatiotemporal faceted structure of the surface undergoes a sequential transition from slow coarsening turning to accelerated coarsening followed by fixed length scale structures before finally becoming spatiotemporally chaotic. For the attachment-detachment dominated phase transition problem we compare in the accelerated coarsening regime the simulation results with an intrinsic dynamical system governing the leading-order piecewise-affine dynamic surface (PADS), which can be obtained through a matched asymptotic analysis. The PADS predicts the numerically observed coarsening law for the growth in time of the characteristic morphological length scale L_{M} . In particular we determine the prefactor of the scaling law which allows for quantitative predictions necessary for any use of the theory in preparing patterned surfaces through modifications of the driving force.

  14. Visualizing water molecule distribution by atomic force microscopy.

    PubMed

    Kimura, Kenjiro; Ido, Shinichiro; Oyabu, Noriaki; Kobayashi, Kei; Hirata, Yoshiki; Imai, Takashi; Yamada, Hirofumi

    2010-05-21

    Hydration structures at biomolecular surfaces are essential for understanding the mechanisms of the various biofunctions and stability of biomolecules. Here, we demonstrate the measurement of local hydration structures using an atomic force microscopy system equipped with a low-noise deflection sensor. We applied this method to the analysis of the muscovite mica/water interface and succeeded in visualizing a hydration structure that is site-specific on a crystal. Furthermore, at the biomolecule/buffer solution interface, we found surface hydration layers that are more packed than those at the muscovite mica/water interface.

  15. A new approach to pH of point of zero charge measurement: crystal-face specificity by scanning force microscopy (SFM)

    NASA Astrophysics Data System (ADS)

    Eggleston, Carrick M.; Jordan, Guntram

    1998-06-01

    The pH of point of zero charge (pH pzc) is a fundamentally important property used in modeling the interaction of solid surfaces with aqueous solutions and solutes. The pH pzc is normally measured by acid-base titration of solid suspensions. Here, a scanning force microscope (SFM) is used to measure forces of repulsion or attraction between chemically tailored tips and quartz (101) and hematite (001) surfaces, as a function of tip-surface separation and pH. The force at contact (FAC) is at a minimum near the expected point of pH pzc for a chemically similar tip and sample. The results are compared to predicted interaction forces from a simple DLVO model, which shows that the SFM technique for pH pzc measurement is most promising for surfaces (such as iron oxides) that have not-too-widely spaced pK a1 and pK a2 values for surface site deprotonation. However, improvements in precision will be necessary to fully utilize the technique. The SFM approach to pH pzc measurement may in future allow the measurement of crystal-face-specific pH pzc, rather than a weighted average of all exposed surface sites, and thus allow us to ask better-defined structure-reactivity questions for mineral surfaces. The approach can in theory be extended to the single-site scale in order to probe the properties (e.g., potential and charge) of individual terrace, step, or kink sites.

  16. 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.

    PubMed

    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.

  17. Crystallization of a Two-Dimensional Hydrogen-Bonded Molecular Assembly: Evolution of the Local Structure Resolved by Atomic Force Microscopy.

    PubMed

    Patera, Laerte L; Liu, Xunshan; Mosso, Nico; Decurtins, Silvio; Liu, Shi-Xia; Repp, Jascha

    2017-08-28

    Structures of the aromatic N-heterocyclic hexaazatriphenylene (HAT) molecular synthon obtained by surface-assisted self-assembly were analyzed with sub-Å resolution by means of noncontact atomic force microscopy (nc-AFM), both in the kinetically trapped amorphous state and in the thermodynamically stable crystalline phase. These results reveal how the crystallization governs the length scale of the network order for non-flexible molecular species without affecting the local bonding schemes. The capability of nc-AFM to accurately resolve structural relaxations will be highly relevant for the characterization of vitreous two-dimensional supramolecular materials. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Real-time atomic-resolution imaging of crystal growth process in water by phase modulation atomic force microscopy at one frame per second

    SciTech Connect

    Miyata, Kazuki; Asakawa, Hitoshi; Fukuma, Takeshi

    2013-11-11

    Recent advancement in dynamic-mode atomic force microscopy (AFM) has enabled its operation in liquid with atomic-scale resolution. However, its imaging speed has often been too slow to visualize atomic-scale dynamic processes. Here, we propose a method for making a significant improvement in the operation speed of dynamic-mode AFM. In this method, we use a wideband and low-latency phase detector with an improved algorithm for the signal complexification. We demonstrate atomic-scale imaging of a calcite crystal growth process in water at one frame per second. The significant improvement in the imaging speed should enable various studies on unexplored atomic-scale interfacial processes.

  19. Electrochemically assisted localized etching of ZnO single crystals in water using a catalytically active Pt-coated atomic force microscopy probe

    NASA Astrophysics Data System (ADS)

    Shibata, Takayuki; Yamamoto, Kota; Sasano, Junji; Nagai, Moeto

    2017-09-01

    This paper presents a nanofabrication technique based on the electrochemically assisted chemical dissolution of zinc oxide (ZnO) single crystals in water at room temperature using a catalytically active Pt-coated atomic force microscopy (AFM) probe. Fabricated grooves featured depths and widths of several tens and several hundreds of nanometers, respectively. The material removal rate of ZnO was dramatically improved by controlling the formation of hydrogen ions (H+) on the surface of the catalytic Pt-coated probe via oxidation of H2O molecules; this reaction can be enhanced by applying a cathodic potential to an additional Pt-wire working electrode in a three-electrode configuration. Consequently, ZnO can be dissolved chemically in water as a soluble Zn2+ species via a reaction with H+ species present in high concentrations in the immediate vicinity of the AFM tip apex.

  20. Optical dipole forces: Working together

    NASA Astrophysics Data System (ADS)

    Aiello, Clarice D.

    2016-12-01

    Strength lies in numbers and in teamwork: tens of thousands of artificial atoms tightly packed in a nanodiamond act cooperatively, enhancing the optical trapping forces beyond the expected classical bulk polarizability contribution.

  1. Optical dipole forces: Working together

    NASA Astrophysics Data System (ADS)

    Aiello, Clarice D.

    2017-03-01

    Strength lies in numbers and in teamwork: tens of thousands of artificial atoms tightly packed in a nanodiamond act cooperatively, enhancing the optical trapping forces beyond the expected classical bulk polarizability contribution.

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

    PubMed

    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.

  3. Molecular View of Protein Crystal Growth: Molecular Interactions, Surface Reconstruction and Growth Mechanism

    NASA Technical Reports Server (NTRS)

    Nadarajah, Arunan; Li, Huayu; Konnert, John H.; Pusey, Marc L.

    2000-01-01

    Studies of the growth and molecular packing of tetragonal lysozyme crystals suggest that there is an underlying molecular growth mechanism, in addition to the classical one involving screw dislocation/2D) nucleation growth. These crystals are constructed by strongly bonded molecular chains forming helices about the 43 axes. The helices are connected to each other by weaker bonds. Crystal growth proceeds by the formation of these 4(sub 3) helices, which would explain some unexpected observations by earlier investigators, such as bimolecular growth steps on the (110) face. Another consequence of these molecular considerations is that only one of two possible packing arrangements could occur on the crystal faces and that their growth unit was at least a tetramer corresponding to the 4(sub 3) helix. Two new high resolution atomic force microscopy (AFM) techniques were developed to directly confirm these predictions on tetragonal lysozyme crystals. Most earlier investigations of protein crystal growth with AFM were in the low resolution mode which is adequate to investigate the classical growth mechanisms, but cannot resolve molecular features and mechanisms. Employing the first of the newly developed techniques, high resolution AFM images of the (110) face were compared with the theoretically constructed images for the two possible packing arrangements on this face. The prediction that the molecular packing arrangement of these faces corresponded to that for complete 4(sub 3) helices was confirmed in this manner. This investigation also showed the occurrence of surface reconstruction on protein crystals. The molecules on the surface of the (110) face were found to pack closer along the 4(sub 3) axes than those in the interior. The second new AFM technique was used to follow the growth process by measuring the dimensions of individual growth units on the (110) face. Linescans across a growth step, performed near the saturation limit of the crystals, allowed the growth

  4. Molecular View of Protein Crystal Growth: Molecular Interactions, Surface Reconstruction and Growth Mechanism

    NASA Technical Reports Server (NTRS)

    Nadarajah, Arunan; Li, Huayu; Konnert, John H.; Pusey, Marc L.

    2000-01-01

    Studies of the growth and molecular packing of tetragonal lysozyme crystals suggest that there is an underlying molecular growth mechanism, in addition to the classical one involving screw dislocation/2D) nucleation growth. These crystals are constructed by strongly bonded molecular chains forming helices about the 43 axes. The helices are connected to each other by weaker bonds. Crystal growth proceeds by the formation of these 4(sub 3) helices, which would explain some unexpected observations by earlier investigators, such as bimolecular growth steps on the (110) face. Another consequence of these molecular considerations is that only one of two possible packing arrangements could occur on the crystal faces and that their growth unit was at least a tetramer corresponding to the 4(sub 3) helix. Two new high resolution atomic force microscopy (AFM) techniques were developed to directly confirm these predictions on tetragonal lysozyme crystals. Most earlier investigations of protein crystal growth with AFM were in the low resolution mode which is adequate to investigate the classical growth mechanisms, but cannot resolve molecular features and mechanisms. Employing the first of the newly developed techniques, high resolution AFM images of the (110) face were compared with the theoretically constructed images for the two possible packing arrangements on this face. The prediction that the molecular packing arrangement of these faces corresponded to that for complete 4(sub 3) helices was confirmed in this manner. This investigation also showed the occurrence of surface reconstruction on protein crystals. The molecules on the surface of the (110) face were found to pack closer along the 4(sub 3) axes than those in the interior. The second new AFM technique was used to follow the growth process by measuring the dimensions of individual growth units on the (110) face. Linescans across a growth step, performed near the saturation limit of the crystals, allowed the growth

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

    PubMed

    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.

  6. Controlled graphene oxide assembly on silver nanocube monolayers for SERS detection: dependence on nanocube packing procedure

    PubMed Central

    Banchelli, Martina; Tiribilli, Bruno; Pini, Roberto; Dei, Luigi

    2016-01-01

    Summary Hybrid graphene oxide/silver nanocubes (GO/AgNCs) arrays for surface-enhanced Raman spectroscopy (SERS) applications were prepared by means of two procedures differing for the method used in the assembly of the silver nanocubes onto the surface: Langmuir–Blodgett (LB) transfer and direct sequential physisorption of silver nanocubes (AgNCs). Adsorption of graphene oxide (GO) flakes on the AgNC assemblies obtained with both procedures was monitored by quartz crystal microbalance (QCM) technique as a function of GO bulk concentration. The experiment provided values of the adsorbed GO mass on the AgNC array and the GO saturation limit as well as the thickness and the viscoelastic properties of the GO film. Atomic force microscopy (AFM) measurements of the resulting samples revealed that a similar surface coverage was achieved with both procedures but with a different distribution of silver nanoparticles. In the GO covered LB film, the AgNC distribution is characterized by densely packed regions alternating with empty surface areas. On the other hand, AgNCs are more homogeneously dispersed over the entire sensor surface when the nanocubes spontaneously adsorb from solution. In this case, the assembly results in less-packed silver nanostructures with higher inter-cube distance. For the two assembled substrates, AFM of silver nanocubes layers fully covered with GO revealed the presence of a homogeneous, flexible and smooth GO sheet folding over the silver nanocubes and extending onto the bare surface. Preliminary SERS experiments on adenine showed a higher SERS enhancement factor for GO on Langmuir–Blodgett films of AgNCs with respect to bare AgNC systems. Conversely, poor SERS enhancement for adenine resulted for GO-covered AgNCs obtained by spontaneous adsorption. This indicated that the assembly and packing of AgNCs obtained in this way, although more homogeneous over the substrate surface, is not as effective for SERS analysis. PMID:26925348

  7. Controlled graphene oxide assembly on silver nanocube monolayers for SERS detection: dependence on nanocube packing procedure.

    PubMed

    Banchelli, Martina; Tiribilli, Bruno; Pini, Roberto; Dei, Luigi; Matteini, Paolo; Caminati, Gabriella

    2016-01-01

    Hybrid graphene oxide/silver nanocubes (GO/AgNCs) arrays for surface-enhanced Raman spectroscopy (SERS) applications were prepared by means of two procedures differing for the method used in the assembly of the silver nanocubes onto the surface: Langmuir-Blodgett (LB) transfer and direct sequential physisorption of silver nanocubes (AgNCs). Adsorption of graphene oxide (GO) flakes on the AgNC assemblies obtained with both procedures was monitored by quartz crystal microbalance (QCM) technique as a function of GO bulk concentration. The experiment provided values of the adsorbed GO mass on the AgNC array and the GO saturation limit as well as the thickness and the viscoelastic properties of the GO film. Atomic force microscopy (AFM) measurements of the resulting samples revealed that a similar surface coverage was achieved with both procedures but with a different distribution of silver nanoparticles. In the GO covered LB film, the AgNC distribution is characterized by densely packed regions alternating with empty surface areas. On the other hand, AgNCs are more homogeneously dispersed over the entire sensor surface when the nanocubes spontaneously adsorb from solution. In this case, the assembly results in less-packed silver nanostructures with higher inter-cube distance. For the two assembled substrates, AFM of silver nanocubes layers fully covered with GO revealed the presence of a homogeneous, flexible and smooth GO sheet folding over the silver nanocubes and extending onto the bare surface. Preliminary SERS experiments on adenine showed a higher SERS enhancement factor for GO on Langmuir-Blodgett films of AgNCs with respect to bare AgNC systems. Conversely, poor SERS enhancement for adenine resulted for GO-covered AgNCs obtained by spontaneous adsorption. This indicated that the assembly and packing of AgNCs obtained in this way, although more homogeneous over the substrate surface, is not as effective for SERS analysis.

  8. COLLOIDS. Colloidal matter: Packing, geometry, and entropy.

    PubMed

    Manoharan, Vinothan N

    2015-08-28

    Colloidal particles with well-controlled shapes and interactions are an ideal experimental system for exploring how matter organizes itself. Like atoms and molecules, these particles form bulk phases such as liquids and crystals. But they are more than just crude analogs of atoms; they are a form of matter in their own right, with complex and interesting collective behavior not seen at the atomic scale. Their behavior is affected by geometrical or topological constraints, such as curved surfaces or the shapes of the particles. Because the interactions between the particles are often short-ranged, we can understand the effects of these constraints using geometrical concepts such as packing. The geometrical viewpoint gives us a window into how entropy affects not only the structure of matter, but also the dynamics of how it forms.

  9. Pseudo-fivefold diffraction symmetries in tetrahedral packing.

    PubMed

    Lee, Stephen; Henderson, Ryan; Kaminsky, Corey; Nelson, Zachary; Nguyen, Jeffers; Settje, Nick F; Schmidt, Joshua Teal; Feng, Ji

    2013-07-29

    We review the way in which atomic tetrahedra composed of metallic elements pack naturally into fused icosahedra. Orthorhombic, hexagonal, and cubic intermetallic crystals based on this packing are all shown to be united in having pseudo-fivefold rotational diffraction symmetry. A unified geometric model involving the 600-cell is presented: the model accounts for the observed pseudo-fivefold symmetries among the different Bravais lattice types. The model accounts for vertex-, edge-, polygon-, and cell-centered fused-icosahedral clusters. Vertex-centered and edge-centered types correspond to the well-known pseudo-fivefold symmetries in Ih and D5h quasicrystalline approximants. The concept of a tetrahedrally-packed reciprocal space cluster is introduced, the vectors between sites in this cluster corresponding to the principal diffraction peaks of fused-icosahedrally-packed crystals. This reciprocal-space cluster is a direct result of the pseudosymmetry and, just as the real-space clusters, can be rationalized by the 600-cell. The reciprocal space cluster provides insights for the Jones model of metal stability. For tetrahedrally-packed crystals, Jones zone faces prove to be pseudosymmetric with one another. Lower and upper electron per atom bounds calculated for this pseudosymmetry-based Jones model are shown to accord with the observed electron counts for a variety of Group 10-12 tetrahedrally-packed structures, among which are the four known Cu/Cd intermetallic compounds: CdCu2, Cd3Cu4, Cu5Cd8, and Cu3Cd10. The rationale behind the Jones lower and upper bounds is reviewed. The crystal structure of Zn11Au15Cd23, an example of a 1:1 MacKay cubic quasicrystalline approximant based solely on Groups 10-12 elements is presented. This compound crystallizes in Im3 (space group no. 204) with a = 13.842(2) Å. The structure was solved with R1 = 3.53 %, I > 2σ; = 5.33 %, all data with 1282/0/38 data/restraints/parameters. Copyright © 2013 WILEY-VCH Verlag GmbH & Co

  10. 7 CFR 51.1527 - Standard pack.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 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 size of those in the remainder of the package. (3) “Well filled” means that the plums or prunes packed...

  11. 7 CFR 51.1527 - Standard pack.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 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 size of those in the remainder of the package. (3) “Well filled” means that the plums or prunes packed...

  12. 7 CFR 51.1527 - Standard pack.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 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 size of those in the remainder of the package. (3) “Well filled” means that the plums or prunes packed...

  13. 7 CFR 51.3055 - Standard pack.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ..., CERTIFICATION, AND STANDARDS) United States Standards for Florida Avocados Standard Pack § 51.3055 Standard pack. (a) The avocados shall be packed in accordance with good commercial practice and the pack shall be at... of the weight of the largest fruit in the container. Size of the avocados may be specified by...

  14. 7 CFR 51.1217 - Standard pack.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ..., CERTIFICATION, AND STANDARDS) United States Standards for Grades of Peaches Standard Pack § 51.1217 Standard pack. (a) Each package shall be packed so that the peaches in the shown face shall be reasonably representative in size, color and quality of the contents of the package. (b) Peaches packed in U.S. Standard...

  15. 7 CFR 51.1217 - Standard pack.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... Standards for Grades of Peaches Standard Pack § 51.1217 Standard pack. (a) Each package shall be packed so that the peaches in the shown face shall be reasonably representative in size, color and quality of the contents of the package. (b) Peaches packed in U.S. Standard bushel baskets, or half-bushel baskets, shall...

  16. 7 CFR 51.1217 - Standard pack.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... Standards for Grades of Peaches Standard Pack § 51.1217 Standard pack. (a) Each package shall be packed so that the peaches in the shown face shall be reasonably representative in size, color and quality of the contents of the package. (b) Peaches packed in U.S. Standard bushel baskets, or half-bushel baskets, shall...

  17. 7 CFR 51.1217 - Standard pack.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ..., CERTIFICATION, AND STANDARDS) United States Standards for Grades of Peaches Standard Pack § 51.1217 Standard pack. (a) Each package shall be packed so that the peaches in the shown face shall be reasonably representative in size, color and quality of the contents of the package. (b) Peaches packed in U.S. Standard...

  18. 7 CFR 51.1311 - Packing.

    Code of Federal Regulations, 2010 CFR

    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...

  19. 7 CFR 51.1270 - Packing.

    Code of Federal Regulations, 2010 CFR

    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...

  20. 7 CFR 51.310 - Packing requirements.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... (INSPECTION, CERTIFICATION, AND STANDARDS) United States Standards for Grades of Apples Packing Requirements § 51.310 Packing requirements. (a) Apples tray packed or cell packed in cartons shall be arranged.... 3 2 “Fairly tight” means that apples are of the proper size for molds or cell compartments in which...

  1. 7 CFR 51.310 - Packing requirements.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... (INSPECTION, CERTIFICATION, AND STANDARDS) United States Standards for Grades of Apples Packing Requirements § 51.310 Packing requirements. (a) Apples tray packed or cell packed in cartons shall be arranged.... 3 2 “Fairly tight” means that apples are of the proper size for molds or cell compartments in which...

  2. Bernal's road to random packing and the structure of liquids

    NASA Astrophysics Data System (ADS)

    Finney, John L.

    2013-11-01

    Until the 1960s, liquids were generally regarded as either dense gases or disordered solids, and theoretical attempts at understanding their structures and properties were largely based on those concepts. Bernal, himself a crystallographer, was unhappy with either approach, preferring to regard simple liquids as 'homogeneous, coherent and essentially irregular assemblages of molecules containing no crystalline regions'. He set about realizing this conceptual model through a detailed examination of the structures and properties of random packings of spheres. In order to test the relevance of the model to real liquids, ways had to be found to realize and characterize random packings. This was at a time when computing was slow and in its infancy, so he and his collaborators set about building models in the laboratory, and examining aspects of their structures in order to characterize them in ways which would enable comparison with the properties of real liquids. Some of the imaginative - often time consuming and frustrating - routes followed are described, as well the comparisons made with the properties of simple liquids. With the increase of the power of computers in the 1960s, computational approaches became increasingly exploited in random packing studies. This enabled the use of packing concepts, and the tools developed to characterize them, in understanding systems as diverse as metallic glasses, crystal-liquid interfaces, protein structures, enzyme-substrate interactions and the distribution of galaxies, as well as their exploitation in, for example, oil extraction, understanding chromatographic separation columns, and packed beds in industrial processes.

  3. Dielectrophoretic assembly of dimpled colloids into open packing structures.

    PubMed

    Jia, Zhuoqiang; Sacanna, Stefano; Lee, Stephanie S

    2017-08-30

    Reversible solid-state phase transitions between open- and close-packed structures in two-dimensional colloidal crystals comprising 1.8 μm dimpled spherical colloids were observed using negative dielectrophoresis. These asymmetrically-shaped colloids adopted lattices with cmm plane group symmetry and a packing fraction, ϕ, of 0.68 at low electric field strengths. At high electric field strengths, the close-packed p6m symmetry was observed, with ϕ = 0.90. The transition between open and close-packed structures was found to be reversible, depending on the applied electric field strength and frequency. Finite Fourier transform analysis and COMSOL simulations revealed the existence of repulsive interactions between colloids perpendicular to the electric field lines due to a concentration of the electric field at the edges of the dimpled regions of the colloids. The repulsive interactions resulted in a stretching of the hexagonal lattice perpendicular to the electric field lines, the magnitude of which depended on the electric field strength. By screening the colloids from the electric field in local potential wells, the entropically favored close-packed hexagonal lattice with ϕ = 0.91 was recovered.

  4. Molecular packing in bone collagen fibrils prior to mineralization

    NASA Astrophysics Data System (ADS)

    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.

  5. An observation of nanotwin lamellae in Cd 0.6Mn 0.4Te crystal by atomic force microscopy

    NASA Astrophysics Data System (ADS)

    George, M. A.; Azoulay, M.; Collins, W. E.; Burger, A.; Silberman, E.

    1993-05-01

    Atomic force microscopy (AFM) is used to examine the structure of freshly cleaved Cd 0.6Mn 0.4Te surfaces. The present report complements previous results obtained with X-ray diffraction and optical microscopy which showed the existence of microtwins. The AFM analysis was performed under ambient conditions and yielded nanometer scale resolution images of single twin lamellae that ranged between 20 and 100 nm in width. This is a first observation using AFM of such a substructure, which we interpret as evidence for the presence of nonotwins.

  6. Development of a Specialized Pack for Shipping Water Specimens in Glass Bottles.

    DTIC Science & Technology

    1982-08-01

    AD-R120 514 DEVELOPMENT OF A SPECIALIZED PACK FOR SHIPPING WATER ji’j SPECIMENS IN GLASS BOTTLES (U) AIR FORCE PACKAGING EVALUATION AGENCY WRIGHT...787-4519 immi Commercial (513) 257-4234 DIVIUCINT (W A SPICIALIZED PACK FOR SHIPING MATh SPECIMUS IN GLASS BOTTLS • S I) Air Force Packaging...breakage, during shipment, of glass bottles filled with water specimens. A prototype of the specialized container, employing the proposed Poly-Foam

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

    PubMed

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

    NASA Astrophysics Data System (ADS)

    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.

  9. Valve packings conquer fugitive emissions

    SciTech Connect

    1995-11-01

    In the early 1990s, when the US Environmental Protection Agency (EPA; Washington, D.C.) declared its intent to regulate fugitive emissions from valve-stem leakage, much of the chemical process industries (CPI) responded with fear and uncertainty. The biggest fear was that valve packing would not meet the required limits on leak rates and that expensive bellows seals may be required on many applications. The uncertainly was about how much it would cost. Today, for the most part, these concerns have been mitigated. It is estimated that about 80--90% of valves satisfy the emission requirements. The rest need some improvement in their packing systems to meet the regulations. Generally, these valves can be brought within compliance if the packing designers follow a few basic principles: Employ less-pliable outer rings and more-pliable inner rings; and don`t use excessive packing. While interest in valve packing remains high, mechanical seals continue to become more user-friendly. Many of those covered below are designed to run dry, and some can even tolerate high shaft-wobble without damage. Also look for improved flange gaskets and a host of seals to protect bearings. Twenty-one summaries are presented on new products and services.

  10. Packing loops into annular cavities

    NASA Astrophysics Data System (ADS)

    Sobral, T. A.; Gomes, M. A. F.

    2017-02-01

    The continuous packing of a flexible rod in two-dimensional cavities yields a countable set of interacting domains that resembles nonequilibrium cellular systems and belongs to a new class of lightweight material. However, the link between the length of the rod and the number of domains requires investigation, especially in the case of non-simply connected cavities, where the number of avoided regions emulates an effective topological temperature. In the present article we report the results of an experiment of injection of a single flexible rod into annular cavities in order to find the total length needed to insert a given number of loops (domains of one vertex). Using an exponential model to describe the experimental data we quite minutely analyze the initial conditions, the intermediary behavior, and the tight packing limit. This method allows the observation of a new fluctuation phenomenon associated with instabilities in the dynamic evolution of the packing process. Furthermore, the fractal dimension of the global pattern enters the discussion under a novel point of view. A comparison with the classical problems of the random close packing of disks and jammed disk packings is made.

  11. Determining the sputter yields of molybdenum in low-index crystal planes via electron backscattered diffraction, focused ion beam and atomic force microscope

    SciTech Connect

    Huang, H.S.; Chiu, C.H.; Hong, I.T.; Tung, H.C.; Chien, F.S.-S.

    2013-09-15

    Previous literature has used several monocrystalline sputtering targets with various crystalline planes, respectively, to investigate the variations of the sputter yield of materials in different crystalline orientations. This study presents a method to measure the sputtered yields of Mo for the three low-index planes (100), (110), and (111), through using an easily made polycrystalline target. The procedure was firstly to use electron backscattered diffraction to identify the grain positions of the three crystalline planes, and then use a focused ion beam to perform the micro-milling of each identified grain, and finally the sputter yields were calculated from the removed volumes, which were measured by atomic force microscope. Experimental results showed that the sputter yield of the primary orientations for Mo varied as Y{sub (110)} > Y{sub (100)} > Y{sub (111)}, coincidental with the ranking of their planar atomic packing densities. The concept of transparency of ion in the crystalline substance was applied to elucidate these results. In addition, the result of (110) orientation exhibiting higher sputter yield is helpful for us to develop a Mo target with a higher deposition rate for use in industry. By changing the deformation process from straight rolling to cross rolling, the (110) texture intensity of the Mo target was significantly improved, and thus enhanced the deposition rate. - Highlights: • We used EBSD, FIB and AFM to measure the sputter yields of Mo in low-index planes. • The sputter yield of the primary orientations for Mo varied as Y{sub (110)} > Y{sub (100)} > Y{sub (111)}. • The transparency of ion was used to elucidate the differences in the sputter yield. • We improved the sputter rate of polycrystalline Mo target by adjusting its texture.

  12. Close packing effects on clean and dirty snow albedo and associated climatic implications

    NASA Astrophysics Data System (ADS)

    He, Cenlin; Takano, Yoshi; Liou, Kuo-Nan

    2017-04-01

    Previous modeling of snow albedo, a key climate feedback parameter, follows the independent scattering approximation (ISA) such that snow grains are considered as a number of separate units with distances longer than wavelengths. Here we develop a new snow albedo model for widely observed close-packed snow grains internally mixed with black carbon (BC) and demonstrate that albedo simulations match closer to observations. Close packing results in a stronger light absorption for clean and BC-contaminated snow. Compared with ISA, close packing reduces pure snow albedos by up to 0.05, whereas it enhances BC-induced snow albedo reduction and associated surface radiative forcing by up to 15% (20%) for fresh (old) snow, with larger enhancements for stronger structure packing. Finally, our results suggest that BC-snow albedo forcing and snow albedo feedback (climate sensitivity) are underestimated in previous modeling studies, making snow close packing consideration a necessity in climate modeling and analysis.

  13. Preliminary investigation of labyrinth packing pressure drops at onset of swirl-induced rotor instability

    NASA Technical Reports Server (NTRS)

    Miller, E. H.; Vohr, J. H.

    1984-01-01

    Backward and forward subsynchronous instability was observed in a flexible model test rotor under the influence of swirl flow in a straight-through labyrinth packing. The packing pressure drop at the onset of instability was then measured for a range of operating speeds, clearances and inlet swirl conditions. The trend in these measurements for forward swirl and forward instability is generally consistent with the short packing rotor force formulations of Benchert and Wachter. Diverging clearances were also destabilizing and had a forward orbit with forward swirl and a backward orbit with reverse swirl. A larger, stiff rotor model system is now being assembled which will permit testing steam turbine-type straight-through and hi-lo labyrinth packings. With calibrated and adjustable bearings in this new apparatus, direct measure of the net destabilizing force generated by the packings can be made.

  14. Pack structure and genetic relatedness among wolf packs in a naturally-regulated population

    USGS Publications Warehouse

    Meier, Thomas J.; Burch, John W.; Mech, L. David; Adams, Layne G.; Carbyn, Ludwig N.; Fritts, Steven H.; Seip, Dale R.

    1995-01-01

    Observations of wolf pack dynamics over a six-year period in Denali National Park and Preserve, Alaska, found high rates of intraspecific strife, wolf pack dissolution and new pack formation, and the acceptance of new wolves into established packs. These observations corroborate genetic studies that found more genetic links between packs, and more genetic diversity within packs, than would be expected if most packs were composed of an unrelated breeding pair and their offspring. Longevity of packs, stability of pack territories, and the incidence of inbreeding all appear to be less than previously suggested, even in the absence of significant human disturbance. The formation of new packs by two or more local dispersers, the acceptance of unrelated wolves into existing packs, and the presence of multiple breeding females within packs would tend to blur genetic distinctions between the packs in a population.

  15. Computational crystallization

    PubMed Central

    Altan, Irem; Charbonneau, Patrick; Snell, Edward H.

    2016-01-01

    Crystallization is a key step in macromolecular structure determination by crystallography. While a robust theoretical treatment of the process is available, due to the complexity of the system, the experimental process is still largely one of trial and error. In this article, efforts in the field are discussed together with a theoretical underpinning using a solubility phase diagram. Prior knowledge has been used to develop tools that computationally predict the crystallization outcome and define mutational approaches that enhance the likelihood of crystallization. For the most part these tools are based on binary outcomes (crystal or no crystal), and the full information contained in an assembly of crystallization screening experiments is lost. The potential of this additional information is illustrated by examples where new biological knowledge can be obtained and where a target can be sub-categorized to predict which class of reagents provides the crystallization driving force. Computational analysis of crystallization requires complete and correctly formatted data. While massive crystallization screening efforts are under way, the data available from many of these studies are sparse. The potential for this data and the steps needed to realize this potential are discussed. PMID:26792536

  16. Computational crystallization.

    PubMed

    Altan, Irem; Charbonneau, Patrick; Snell, Edward H

    2016-07-15

    Crystallization is a key step in macromolecular structure determination by crystallography. While a robust theoretical treatment of the process is available, due to the complexity of the system, the experimental process is still largely one of trial and error. In this article, efforts in the field are discussed together with a theoretical underpinning using a solubility phase diagram. Prior knowledge has been used to develop tools that computationally predict the crystallization outcome and define mutational approaches that enhance the likelihood of crystallization. For the most part these tools are based on binary outcomes (crystal or no crystal), and the full information contained in an assembly of crystallization screening experiments is lost. The potential of this additional information is illustrated by examples where new biological knowledge can be obtained and where a target can be sub-categorized to predict which class of reagents provides the crystallization driving force. Computational analysis of crystallization requires complete and correctly formatted data. While massive crystallization screening efforts are under way, the data available from many of these studies are sparse. The potential for this data and the steps needed to realize this potential are discussed.

  17. Sleeping distance in wild wolf packs

    USGS Publications Warehouse

    Knick, S.T.; Mech, L.D.

    1980-01-01

    Sleeping distances were observed among members of 13 wild wolf (Canis lupus) packs and 11 pairs in northeastern Minnesota to determine if the distances correlated with pack size and composition. The study utilized aerial radio-tracking and observation during winter. Pack size and number of adults per pack were inversely related to pack average sleeping distance and variability. No correlation between sleeping distance and microclimate was observed. Possible relationships between social bonding and our results are discussed.

  18. DEM simulation of dendritic grain random packing: application to metal alloy solidification

    NASA Astrophysics Data System (ADS)

    Olmedilla, Antonio; Založnik, Miha; Combeau, Hervé

    2017-06-01

    The random packing of equiaxed dendritic grains in metal-alloy solidification is numerically simulated and validated via an experimental model. This phenomenon is characterized by a driving force which is induced by the solid-liquid density difference. Thereby, the solid dendritic grains, nucleated in the melt, sediment and pack with a relatively low inertia-to-dissipation ratio, which is the so-called Stokes number. The characteristics of the particle packed porous structure such as solid packing fraction affect the final solidified product. A multi-sphere clumping Discrete Element Method (DEM) approach is employed to predict the solid packing fraction as function of the grain geometry under the solidification conditions. Five different monodisperse noncohesive frictionless particle collections are numerically packed by means of a vertical acceleration: a) three dendritic morphologies; b) spheres and c) one ellipsoidal geometry. In order to validate our numerical results with solidification conditions, the sedimentation and packing of two monodisperse collections (spherical and dendritic) is experimentally carried out in a viscous quiescent medium. The hydrodynamic similarity is respected between the actual phenomenon and the experimental model, that is a low Stokes number, o(10-3). In this way, the experimental average solid packing fraction is employed to validate the numerical model. Eventually, the average packing fraction is found to highly depend on the equiaxed dendritic grain sphericity, with looser packings for lower sphericity.

  19. The interplay between hydrogen bonding and π-π stacking interactions in the crystal packing of N1-thyminyl derivatives, and implications for the photo-chemical [2π + 2π]-cycloaddition of thyminyl compounds.

    PubMed

    Johnston, Priscilla; Izgorodina, Ekaterina I; Saito, Kei

    2012-12-01

    The solid-state photo-chemical dimerisation of thyminyl derivatives occurs when two thyminyl units are aligned in such a way that the olefinic moieties are separated by a distance of less than 4.2 Å. When irradiated with >270 nm UV, the thyminyl olefinic groups undergo [2π + 2π]-cycloaddition to form a dimeric cyclobutane derivative. However, the design and execution of [2π + 2π]-cycloaddition reactions can be challenging due to the requirement to produce molecular crystals with the necessary olefinic alignment. In this investigation, the crystallographic and solid-state photo-chemical reactions of six N1-thyminyl derivatives are studied. Only one derivative, thyminyl propanamide (), was found to undergo [2π + 2π]-cycloaddition in the crystalline state. As such, quantum chemical methods were employed to study the photo-chemical transition states of the derivatives, as well as the strengths of typical intermolecular interactions that were observed in their crystal structures (such as π-π stacking between the thyminyl rings, Watson and Crick style hydrogen bonding and hydrogen bonding between functional groups of N1 substituents). These results were used to rationalise the solid-state photo-reactivity of more complex bis-thyminyl monomers.

  20. MP:PD--a data base of internal packing densities, internal packing defects and internal waters of helical membrane proteins.

    PubMed

    Rose, Alexander; Theune, Dominic; Goede, Andrean; Hildebrand, Peter W

    2014-01-01

    The membrane protein packing database (MP:PD) (http://proteinformatics.charite.de/mppd) is a database of helical membrane proteins featuring internal atomic packing densities, cavities and waters. Membrane proteins are not tightly packed but contain a considerable number of internal cavities that differ in volume, polarity and solvent accessibility as well as in their filling with internal water. Internal cavities are supposed to be regions of high physical compressibility. By serving as mobile hydrogen bonding donors or acceptors, internal waters likely facilitate transition between different functional states. Despite these distinct functional roles, internal cavities of helical membrane proteins are not well characterized, mainly because most internal waters are not resolved by crystal structure analysis. Here we combined various computational biophysical techniques to characterize internal cavities, reassign positions of internal waters and calculate internal packing densities of all available helical membrane protein structures and stored them in MP:PD. The database can be searched using keywords and entries can be downloaded. Each entry can be visualized in Provi, a Jmol-based protein viewer that provides an integrated display of low energy waters alongside membrane planes, internal packing density, hydrophobic cavities and hydrogen bonds.

  1. Determining the Molecular Growth Mechanisms of Tetragonal Lysozyme Crystals

    NASA Technical Reports Server (NTRS)

    Li, Huayu; Nadarajah, Arunan; Konnert, John H.; Pusey, Marc L.

    1998-01-01

    Studies of the growth of tetragonal lysozyme crystals employing atomic force microscopy (AFM) have shown the advantages of this technique in investigating the growth mechanisms of protein crystals [1]. The resolution of these studies was in the micron range, which revealed surface features such as the occurrence of dislocations and 2D nucleation islands, similar to those found in inorganic systems. They clearly showed that the crystals grew by these surface growth mechanisms. However, the studies also revealed some surprising features, such as bimolecular growth step heights and pronounced growth anisotropies on the (110) face, which could not be explained. In previous studies we employed Periodic Bond Chain (PBC) theory to tetragonal lysozyme crystal growth and found that the crystals were constructed by strongly bonded molecular chains forming helices about the 43 axes [2,3]. The helices were connected to each other with weaker bonds. The growth process was shown to proceed by the formation of these 43 helices, resulting in bimolecular growth steps on the (110) face. It was also shown to explain many other observations on tetragonal lysozyme crystal growth. Although PBC analysis is not a new technique [4], it has not been widely used as the mechanisms predicted from it could not be experimentally verified. In this study the growth process of these crystals was investigated, particularly for the (110) face, employing some newly developed high resolution AFM techniques. These techniques allowed individual lysozyme molecules on the crystal faces to be resolved and predictions from PBC analyses to be tested. The analyses had shown that of the two possible packing arrangements on (110) faces, only one would actually occur. Employing the first of the newly developed techniques, these faces were scanned by high resolution AFM. The resulting images were then compared with the theoretically constructed images for the two possible packing arrangements on the (110) face

  2. Photovoltaic dryer with dual packed beds for drying medical herb

    SciTech Connect

    Abdel-Rehim, Z.S.; Fahmy, F.H.

    1998-03-01

    This work presents design and optimization of a cylindrical photovoltaic dryer with dual packed beds thermal energy storage for drying medical herb. The dryer is provided with electrical heater where the electrical energy is generated by using photovoltaic system. The electrical heater is designed and sized to realize continuous drying (day and night) to minimize the drying time. Two packed beds are used to fix the drying temperature in dryer during day and night. The main packed bed thermal energy storage is charged during the sunlight hours directly, to realize continued drying after sunset. An efficient PV dryer is devised to work under forced air created by air blower and heated by the electrical coils.

  3. Use of the Primitive Unit Cell in Understanding Subtle Features of the Cubic Closest-Packed Structure

    ERIC Educational Resources Information Center

    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…

  4. Use of the Primitive Unit Cell in Understanding Subtle Features of the Cubic Closest-Packed Structure

    ERIC Educational Resources Information Center

    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. Protein Crystallization

    NASA Technical Reports Server (NTRS)

    Chernov, Alexander A.

    2005-01-01

    Nucleation, growth and perfection of protein crystals will be overviewed along with crystal mechanical properties. The knowledge is based on experiments using optical and force crystals behave similar to inorganic crystals, though with a difference in orders of magnitude in growing parameters. For example, the low incorporation rate of large biomolecules requires up to 100 times larger supersaturation to grow protein, rather than inorganic crystals. Nucleation is often poorly reproducible, partly because of turbulence accompanying the mixing of precipitant with protein solution. Light scattering reveals fluctuations of molecular cluster size, its growth, surface energies and increased clustering as protein ages. Growth most often occurs layer-by-layer resulting in faceted crystals. New molecular layer on crystal face is terminated by a step where molecular incorporation occurs. Quantitative data on the incorporation rate will be discussed. Rounded crystals with molecularly disordered interfaces will be explained. Defects in crystals compromise the x-ray diffraction resolution crucially needed to find the 3D atomic structure of biomolecules. The defects are immobile so that birth defects stay forever. All lattice defects known for inorganics are revealed in protein crystals. Contribution of molecular conformations to lattice disorder is important, but not studied. This contribution may be enhanced by stress field from other defects. Homologous impurities (e.g., dimers, acetylated molecules) are trapped more willingly by a growing crystal than foreign protein impurities. The trapped impurities induce internal stress eliminated in crystals exceeding a critical size (part of mni for ferritin, lysozyme). Lesser impurities are trapped from stagnant, as compared to the flowing, solution. Freezing may induce much more defects unless quickly amorphysizing intracrystalline water.

  6. Cylinder valve packing nut studies

    SciTech Connect

    Blue, S.C.

    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.

  7. Structural characterization of submerged granular packings

    NASA Astrophysics Data System (ADS)

    Jakšić, Z. M.; Šćepanović, J. R.; Lončarević, I.; Budinski-Petković, Lj.; Vrhovac, S. B.; Belić, A.

    2014-12-01

    We consider the impact of the effective gravitational acceleration on microstructural properties of granular packings through experimental studies of spherical granular materials saturated within fluids of varying density. We characterize the local organization of spheres in terms of contact connectivity, distribution of the Delaunay free volumes, and the shape factor (parameter of nonsphericity) of the Voronoï polygons. The shape factor gives a clear physical picture of the competition between less and more ordered domains of particles in experimentally obtained packings. As the effective gravity increases, the probability distribution of the shape factor becomes narrower and more localized around the lowest values of the shape factor corresponding to regular hexagon. It is found that curves of the pore distributions are asymmetric with a long tail on the right-hand side, which progressively reduces while the effective gravity gets stronger for lower densities of interstitial fluid. We show that the distribution of local areas (Voronoï cells) broadens with decreasing value of the effective gravity due to the formation of lose structures such as large pores and chainlike structures (arches or bridges). Our results should be particularly helpful in testing the newly developed simulation techniques involving liquid-related forces associated with immersed granular particles.

  8. Structural characterization of submerged granular packings.

    PubMed

    Jakšić, Z M; Šćepanović, J R; Lončarević, I; Budinski-Petković, Lj; Vrhovac, S B; Belić, A

    2014-12-01

    We consider the impact of the effective gravitational acceleration on microstructural properties of granular packings through experimental studies of spherical granular materials saturated within fluids of varying density. We characterize the local organization of spheres in terms of contact connectivity, distribution of the Delaunay free volumes, and the shape factor (parameter of nonsphericity) of the Voronoï polygons. The shape factor gives a clear physical picture of the competition between less and more ordered domains of particles in experimentally obtained packings. As the effective gravity increases, the probability distribution of the shape factor becomes narrower and more localized around the lowest values of the shape factor corresponding to regular hexagon. It is found that curves of the pore distributions are asymmetric with a long tail on the right-hand side, which progressively reduces while the effective gravity gets stronger for lower densities of interstitial fluid. We show that the distribution of local areas (Voronoï cells) broadens with decreasing value of the effective gravity due to the formation of lose structures such as large pores and chainlike structures (arches or bridges). Our results should be particularly helpful in testing the newly developed simulation techniques involving liquid-related forces associated with immersed granular particles.

  9. 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

    NASA Astrophysics Data System (ADS)

    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.

  10. Fracture behavior of lithium single crystal in the framework of (semi-)empirical force field derived from first-principles

    NASA Astrophysics Data System (ADS)

    Groh, Sébastien; Alam, Masud

    2015-06-01

    An approach to derive, from first-principles data, accurate and reliable potentials in the modified embedded-atom method in view of modeling the mechanical behavior of metals is presented in this work and applied to the optimization of a potential representative of lithium (Li). Although the theoretical background of the modified embedded-atom method was considered in this work, the proposed method is general and it can be applied to any other functional form. The main feature of the method is to introduce several path transformations in the material database that are critical for plastic and failure behavior. As part of the potential validation, path transformations different from the ones used for the parameterization procedure are considered. Applied in the case of Li, the material database was enriched with the generalized stacking fault energy curve along the  <1 1 1>  -direction on the {1 1 0}-plane, and with the traction-separation behavior of a {1 0 0}-surface. The path transformations used to enrich the material database were initially derived from first-principles calculations. For validation, the generalized stacking fault energy curves along the  <1 1 1>  -direction on the {1 1 2}- and {1 2 3}-planes were considered for plasticity, while traction-separation behavior of {1 1 0} and {1 1 1}-planes were considered for failure behavior. As part of the validation procedure, the predictions made in the MEAM framework were validated by first-principles data. The final potential accurately reproduced basic equilibrium properties, elastic constants, surface energies in agreement with first-principles predictions, and transition energy between different crystal structures. Furthermore, generalized stacking fault energy curves along the  <1 1 1>  -direction on the {1 1 0}, {1 1 2}, and {1 2 3}-planes, and tensile cohesive stress, characteristic length of fracture, and work of separation of a

  11. Studies of Particle Packings in Mixtures of Pharmaceutical Excipients

    NASA Astrophysics Data System (ADS)

    Bentham, Craig; Dutt, Meenakshi; Hancock, Bruno; Elliott, James

    2005-03-01

    Pharmaceutical powder blends used to generate tablets are complex multicomponent mixtures of the drug powder and excipients which facilitate the delivery of the required drug. The individual constituents of these blends can be noncohesive and cohesive powders. We study the geometric and mechanical characteristics of idealized mixtures of excipient particle packings, for a small but representative number of dry noncohesive particles, generated via gravitational compaction followed by uniaxial compaction. We discuss particle packings in 2- and 3- component mixtures of microcrystalline cellulose (MCC) & lactose and MCC, starch & lactose, respectively. We have computed the evolution of the force and stress distributions in monodisperse and polydisperse mixtures comprised of equal parts of each excipient; comparisons are made with results for particles packings of pure blends of MCC and lactose. We also compute the stress-strain relations for these mixtures. In order to obtain insight into details of the particle packings, we calculate the coordination number, packing fraction, radial distribution functions and contact angle distributions for the various mixtures. The numerical experiments have been performed on spheroidal idealizations of the excipient grains using Discrete Element Method simulations (Dutt et al., 2004 to be published).

  12. Adsorption behavior of acetone solvent at the HMX crystal faces: A molecular dynamics study.

    PubMed

    Liu, Yingzhe; Yu, Tao; Lai, Weipeng; Ma, Yiding; Kang, Ying; Ge, Zhongxue

    2017-03-10

    Molecular dynamics simulations have been performed to understand the adsorption behavior of acetone (AC) solvent at the three surfaces of 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctan (HMX) crystal, i.e. (011), (110), and (020) faces. The simulation results show that the structural features and electrostatic potentials of crystal faces are determined by the HMX molecular packing, inducing distinct mass density distribution, dipole orientation, and diffusion of solvent molecules in the interfacial regions. The solvent adsorption is mainly governed by the van der Waals forces, and the crystal-solvent interaction energies among three systems are ranked as (020)≈(110)>(011). The adsorption sites for solvent incorporation at the crystal surface were found and visualized with the aid of occupancy analysis. A uniform arrangement of adsorption sites is observed at the rough (020) surface as a result of ordered adsorption motif.

  13. Magnetosomes and magnetite crystals produced by magnetotactic bacteria as resolved by atomic force microscopy and transmission electron microscopy.

    PubMed

    Oestreicher, Zachery; Valverde-Tercedor, Carmen; Chen, Lijun; Jimenez-Lopez, Concepcion; Bazylinski, Dennis A; Casillas-Ituarte, Nadia N; Lower, Steven K; Lower, Brian H

    2012-12-01

    Atomic force microscopy (AFM) was used in concert with transmission electron microscopy (TEM) to image magnetotactic bacteria (Magnetospirillum gryphiswaldense MSR-1 and Magnetospirillum magneticum AMB-1), magnetosomes, and purified Mms6 proteins. Mms6 is a protein that is associated with magnetosomes in M. magneticum AMB-1 and is believed to control the synthesis of magnetite (Fe(3)O(4)) within the magnetosome. We demonstrated how AFM can be used to capture high-resolution images of live bacteria and achieved nanometer resolution when imaging Mms6 protein molecules on magnetite. We used AFM to acquire simultaneous topography and amplitude images of cells that were combined to provide a three-dimensional reconstructed image of M. gryphiswaldense MSR-1. TEM was used in combination with AFM to image M. gryphiswaldense MSR-1 and magnetite-containing magnetosomes that were isolated from the bacteria. AFM provided information, such as size, location and morphology, which was complementary to the TEM images. Copyright © 2012 Elsevier Ltd. All rights reserved.

  14. Ionic Strength, Surface Charge, and Packing Density Effects on the Properties of Peptide Self-Assembled Monolayers.

    PubMed

    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

  15. Atomic force microscopy study of tooth surfaces.

    PubMed

    Farina, M; Schemmel, A; Weissmüller, G; Cruz, R; Kachar, B; Bisch, P M

    1999-03-01

    Atomic force microscopy (AFM) was used to study tooth surfaces in order to compare the pattern of particle distribution in the outermost layer of the tooth surfaces. Human teeth and teeth from a rodent (Golden hamster), from a fish (piranha), and from a grazing mollusk (chiton) with distinct feeding habits were analyzed in terms of particle arrangement, packing, and size distribution. Scanning electron microscopy and transmission electron microscopy were used for comparison. It was found that AFM gives high-contrast, high-resolution images and is an important tool as a source of complementary and/or new structural information. All teeth were cleaned and some were etched with acidic solutions before analysis. It was observed that human enamel (permanent teeth) presents particles tightly packed in the outer surface, whereas enamel from the hamster (continuously growing teeth) shows particles of less dense packing. The piranha teeth have a thin cuticle covering the long apatite crystals of the underlying enameloid. This cuticle has a rough surface of particles that have a globular appearance after the brief acidic treatment. The similar appearance of the in vivo naturally etched tooth surface suggests that the pattern of globule distribution may be due to the presence of an organic material. Elemental analysis of this cuticle indicated that calcium, phosphorus, and iron are the main components of the structure while electron microdiffraction of pulverized cuticle particles showed a pattern consistent with hydroxyapatite. The chiton mineralized tooth cusp had a smooth surface in an unabraded region and a very rough structure with the magnetite crystals (already known to make part of the structure) protruding from the surface. It was concluded that the structures analyzed are optimized for efficiency in feeding mechanism and life span of the teeth.

  16. Inverse statistical mechanics, lattice packings, and glasses

    NASA Astrophysics Data System (ADS)

    Marcotte, Etienne

    Computer simulation methods enable the investigation of systems and properties that are intractable by purely analytical or experimental approaches. Each chapter of this dissertation contains an application of simulation methods to solve complex physical problems consisting of interacting many-particle or many-spin systems. The problems studied in this dissertation can be divided up into the following two broad categories: inverse and forward problems. The inverse problems considered are those in which we construct an interaction potential such that the corresponding ground state is a targeted configuration. In Chapters 2 and 3, we devise convex pair-potential functions that result in low-coordinated ground states. Chapter 2 describes targeted ground states that are the square and honeycomb crystals, while in Chapter 3 the targeted ground state is the diamond crystal. Chapter 4 applies similar techniques to explicitly enumerate all unique ground states up to a given system size, for spin configurations that interact according to generalized isotropic Ising potentials with finite range. We also consider forward statistical-mechanical problems. In Chapter 5, we adapt a linear programming algorithm to find the densest lattice packings across Euclidean space dimensions. In Chapter 6, we demonstrate that for two different glass models a signature of the glass transition is apparent well before the transition temperature is reached. In both models, this signature appears as nonequilibrium length scales that grow upon supercooling.

  17. Crystal structure of bis­(fluoro­sulfato-κO)xenon(II), Xe(SO3F)2

    PubMed Central

    Malischewski, Moritz; Seppelt, Konrad

    2015-01-01

    Thermally unstable Xe(SO3F)2 has been prepared by the reaction of XeF2 with HSO3F. Single crystals were obtained from HSO3F by slow cooling in a sealed tube. The mol­ecular structure is characterized by the Xe atom covalently bonded to two O atoms of two fluoro­sulfate tetra­hedra in an almost linear fashion [O—Xe—O = 179.13 (4)°]. The crystal packing is strongly influenced by inter­molecular van der Waals forces. PMID:26029391

  18. Microfabricated packed gas chromatographic column

    DOEpatents

    Kottenstette, Richard; Matzke, Carolyn M.; Frye-Mason, Gregory C.

    2003-12-16

    A new class of miniaturized gas chromatographic columns has been invented. These chromatographic columns are formed using conventional micromachining techniques, and allow packed columns having lengths on the order of a meter to be fabricated with a footprint on the order of a square centimeter.

  19. Ecology and Energy Action Pack.

    ERIC Educational Resources Information Center

    McDonald's Corp., Oak Brook, IL.

    One of five McDonald's Action Packs, these elementary school-level instructional materials are for use as an introduction to existing units of study, supplements to a textbook, or a source of special projects for environmental education. Contents include these six units: Make Your Own Ecology Mini-spinner, Let's Look at a Food Chain, Drip the…

  20. Ecology and Energy Action Pack.

    ERIC Educational Resources Information Center

    McDonald's Corp., Oak Brook, IL.

    One of five McDonald's Action Packs, these elementary school-level instructional materials are for use as an introduction to existing units of study, supplements to a textbook, or a source of special projects for environmental education. Contents include these six units: Make Your Own Ecology Mini-spinner, Let's Look at a Food Chain, Drip the…

  1. Pack cementation coatings for alloys

    SciTech Connect

    He, Yi-Rong; Zheng, Minhui; Rapp, R.A.

    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.

  2. Wire and Packing Tape Sandwiches

    ERIC Educational Resources Information Center

    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.)

  3. Teflon-packed flexible joint

    NASA Technical Reports Server (NTRS)

    Belmont, G. E.

    1969-01-01

    Teflon-packed flexible joint separates the movement of the shaker from the liquid nitrogen hose during the ground testing of cryogenic zero-g equipment. The joint allows the hose to lie on the floor in a stationary position as the shaker moves back and forth, thus, the hose is not subject to violent motion.

  4. Wire and Packing Tape Sandwiches

    ERIC Educational Resources Information Center

    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. Transport and Morphology of Nanoparticle Aggregates in Packed Beds: Findings from LBM simulations

    NASA Astrophysics Data System (ADS)

    Pham, Ngoc; Papavassiliou, Dimitrios

    2016-11-01

    Aggregation of colloidal particles in porous media has attracted attention because of possible pore clogging and sedimentation, which reduces the particle breakthrough. In addition, in some systems, further attachment of colloidal particles on deposited aggregates is expected. In this study, the morphology of nanoparticle aggregates, propagating in beds packed with spheres under different electrolyte conditions, is numerically investigated. In our simulation, the nanoparticles are advanced by balancing forces such as drag, random force, buoyancy, gravitational force, electrostatic repulsion, and van der Waals attractive force. When the van der Waals forces take over, the aggregates are formed. The packed beds are made of spheres, either ideally packed or randomly packed in simulation boxes. Sequentially, the flow field of water inside the packed beds is generated, using the lattice Boltzmann method (LBM). In conjunction with that, a Lagrangian framework is applied to record the trajectories of the free nanoparticles and the aggregated nanoparticles. Within the scope of this study, we draw attention to the change of the morphology of the aggregates, reflected by their fractal dimension, under various electrolyte and packing conditions.

  6. Efficient algorithms for orthogonal packing problems

    NASA Astrophysics Data System (ADS)

    Chekanin, A. V.; Chekanin, V. A.

    2013-10-01

    The NP complete problem of the orthogonal packing of objects of arbitrary dimension is considered in the general form. A new model for representing objects in containers is proposed that ensures the fast design of an orthogonal packing. New heuristics for the placement of orthogonal packing are proposed. A single-pass heuristic algorithm and a multimethod genetic algorithm are developed that optimize an orthogonal packing solution by increasing the packing density. Numerical experiments for two- and three-dimensional orthogonal packing problems are performed.

  7. Packing hyperspheres in high-dimensional Euclidean spaces.

    PubMed

    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.

  8. Cationic metal complex, carbonatobis(1,10-phenanthroline)cobalt(III) as anion receptor: Synthesis, characterization, single crystal X-ray structure and packing analysis of [Co(phen) 2CO 3](3,5-dinitrobenzoate)·5H 2O

    NASA Astrophysics Data System (ADS)

    Sharma, Raj Pal; Singh, Ajnesh; Brandão, Paula; Felix, Vitor; Venugopalan, Paloth

    2009-03-01

    To explore the potential of [Co(phen) 2CO 3] + as anion receptor, red coloured single crystals of [Co(phen) 2CO 3](dnb)·5H 2O (dnb = 3,5-dinitrobenzoate) were obtained by recrystallizing the red microcrystalline product synthesised by the reaction of carbonatobis (1,10-phenanthroline)cobalt(III)chloride with sodium salt of 3,5-dinitrobenzoic acid in aqueous medium (1:1 molar ratio). The newly synthesized complex salt has been characterized by elemental analysis, spectroscopic studies (IR, UV/visible, 1H and 13C NMR), solubility and conductance measurements. The complex salt crystallizes in the triclinic crystal system with space group P1¯, having the cell dimensions a = 10.3140(8), b = 12.2885(11), c = 12.8747(13), α = 82.095(4), β = 85.617(4), γ = 79.221(4)°, V = 1585.6(2) Å 3, Z = 2. Single crystal X-ray structure determination revealed ionic structure consisting of cationic carbonatobis(1,10-phenanthroline)cobalt(III), dnb anion and five lattice water molecule. In the complex cation [Co(phen) 2CO 3] +, the cobalt(III) is bonded to four nitrogen atoms, originating from two phenanthroline ligands and two oxygen atoms from the bidentate carbonato group showing an octahedral geometry around cobalt(III) center. Supramolecular networks between ionic groups [ CHphen+⋯Xanion-] by second sphere coordination i.e. C sbnd H⋯O (benzoate), C sbnd H⋯O (nitro), C sbnd H⋯O (water) besides electrostatic forces of attraction alongwith π-π interactions stabilize the crystal lattice.

  9. Structures of cyano-biphenyl liquid crystals

    NASA Technical Reports Server (NTRS)

    Chu, Yuan-Chao; Tsang, Tung; Rahimzadeh, E.; Yin, L.

    1989-01-01

    The structures of p-alkyl- p'-cyano- bicyclohexanes, C(n)H(2n+1) (C6H10)(C6H10) CN (n-CCH), and p-alkyl- p'-cyano- biphenyls, C(n)H(2n+1) (C6H4)(C6H4) CN (n-CBP), were studied. It is convenient to use an x ray image intensification device to search for symmetric x ray diffraction patterns. Despite the similarities in molecular structures of these compounds, very different crystal structures were found. For the smectic phase of 2CCH, the structure is close to rhombohedral with threefold symmetry. In contrast, the structure is close to hexagonal close-packed with two molecules per unit cell for 4CCH. Since intermolecular forces may be quite weak for these liquid crystals systems, it appears that crystal structures change considerably when the alkyl chain length is slightly altered. Different structures were also found in the crystalline phase of n-CBP for n = 6 to 9. For n = 7 to 9, the structures are close to monclinic. The structures are reminiscent of the smectic-A liquid crystal structures with the linear molecules slightly tilted away from the c-axis. In contrast, the structure is quite different for n = 6 with the molecules nearly perpendicular to the c-axis.

  10. Measuring order in the isotropic packing of elastic rods

    NASA Astrophysics Data System (ADS)

    Bayart, E.; Deboeuf, S.; Corson, F.; Boudaoud, A.; Adda-Bedia, M.

    2011-08-01

    The packing of elastic bodies has emerged as a paradigm for the study of macroscopic disordered systems. However, progress is hampered by the lack of controlled experiments. Here we consider a model experiment for the isotropic two-dimensional confinement of a rod by a central force. We seek to measure how ordered is a folded configuration and we identify two key quantities. A geometrical characterization is given by the number of superposed layers in the configuration. Using temporal modulations of the confining force, we probe the mechanical properties of the configuration and we define and measure its effective susceptibility. These two quantities may be used to build a statistical framework for packed elastic systems.

  11. 7 CFR 984.15 - Pack.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... Orders; Fruits, Vegetables, Nuts), DEPARTMENT OF AGRICULTURE WALNUTS GROWN IN CALIFORNIA Order Regulating Handling Definitions § 984.15 Pack. Pack means to bleach, clean, grade, shell or otherwise prepare walnuts for market as inshell or shelled walnuts....

  12. 7 CFR 984.15 - Pack.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... Orders; Fruits, Vegetables, Nuts), DEPARTMENT OF AGRICULTURE WALNUTS GROWN IN CALIFORNIA Order Regulating Handling Definitions § 984.15 Pack. Pack means to bleach, clean, grade, shell or otherwise prepare walnuts for market as inshell or shelled walnuts....

  13. 7 CFR 984.15 - Pack.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... Orders; Fruits, Vegetables, Nuts), DEPARTMENT OF AGRICULTURE WALNUTS GROWN IN CALIFORNIA Order Regulating Handling Definitions § 984.15 Pack. Pack means to bleach, clean, grade, shell or otherwise prepare walnuts for market as inshell or shelled walnuts....

  14. 7 CFR 984.15 - Pack.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... ORDERS; FRUITS, VEGETABLES, NUTS), DEPARTMENT OF AGRICULTURE WALNUTS GROWN IN CALIFORNIA Order Regulating Handling Definitions § 984.15 Pack. Pack means to bleach, clean, grade, shell or otherwise prepare walnuts for market as inshell or shelled walnuts....

  15. 7 CFR 984.15 - Pack.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... ORDERS; FRUITS, VEGETABLES, NUTS), DEPARTMENT OF AGRICULTURE WALNUTS GROWN IN CALIFORNIA Order Regulating Handling Definitions § 984.15 Pack. Pack means to bleach, clean, grade, shell or otherwise prepare walnuts for market as inshell or shelled walnuts....

  16. An overview of gravel-packed completions

    SciTech Connect

    Heng, H.B.

    1987-05-01

    Sarawak Shell Bhd./Sabah Shell Petroleum Co. (SSB/SSPC) experience with gravel-packed completions covers some 12 years. During that period, some 290 gravel-packed zones have been completed, and about 400X10/sup 6/ bbl (64X10/sup 6/ m/sup 3/) of oil have been produced through gravel packs in 13 offshore fields. This paper presents an overview of the development of gravel-packing methods, with special reference to the new gravel-packing technique developed in early 1984 for the Bayan field gravel-packed completions. Productivity reduction resulting from gravel packing and the long-term performance of the packs are discussed briefly.

  17. Designing gravel pack for uranium ISL wells

    NASA Astrophysics Data System (ADS)

    Ber, A. A.; Minaev, K. M.; Ber, L. M.; Isaev, Ye D.; Ulyanova, O. S.

    2016-09-01

    The paper describes the improvement of gravel packing technique applied for the production wells. The authors have suggested new design of gravel pack for gravel packing of productive formations. The issue is currently topical because gravel packing at drillhole ISL is less time- and money-consuming. The subject of the research is gravel pack design and content. The purpose defined by the authors is to design the gravel pack and to suggest the composition of gravel cement agent. As a result of the research, the authors have described different designs of the gravel pack, its optimal shape, as well as a choice and justification of cement agents, a hold cover of the gravel pack, and suggested the methods of experimental research.

  18. Assembly of streptolysin O pores assessed by quartz crystal microbalance and atomic force microscopy provides evidence for the formation of anchored but incomplete oligomers.

    PubMed

    Stewart, Sarah E; D'Angelo, Michael E; Paintavigna, Stefania; Tabor, Rico F; Martin, Lisandra L; Bird, Phillip I

    2015-01-01

    Streptolysin O (SLO) is a bacterial pore forming protein that is part of the cholesterol dependent cytolysin (CDC) family. We have used quartz crystal microbalance with dissipation monitoring (QCM-D) to examine SLO membrane binding and pore formation. In this system, SLO binds tightly to cholesterol-containing membranes, and assembles into partial and complete pores confirmed by atomic force microscopy. SLO binds to the lipid bilayer at a single rate consistent with the Langmuir isotherm model of adsorption. Changes in dissipation illustrate that SLO alters the viscoelastic properties of the bilayer during pore formation, but there is no loss of material from the bilayer as reported for small membrane-penetrating peptides. SLO mutants were used to further dissect the assembly and insertion processes by QCM-D. This shows the signature of SLO in QCM-D changes when pore formation is inhibited, and that bound and inserted SLO forms can be distinguished. Furthermore a pre-pore locked SLO mutant binds reversibly to lipid, suggesting that the partially complete wtSLO forms observed by AFM are anchored to the membrane.

  19. Assessment of DNA binding to human Rad51 protein by using quartz crystal microbalance and atomic force microscopy: effects of ADP and BRC4-28 peptide inhibitor.

    PubMed

    Esnault, Charles; Renodon-Cornière, Axelle; Takahashi, Masayuki; Casse, Nathalie; Delorme, Nicolas; Louarn, Guy; Fleury, Fabrice; Pilard, Jean-François; Chénais, Benoît

    2014-12-01

    The interaction of human Rad51 protein (HsRad51) with single-stranded deoxyribonucleic acid (ssDNA) was investigated by using quartz crystal microbalance (QCM) monitoring and atomic force microscopy (AFM) visualization. Gold surfaces for QCM and AFM were modified by electrografting of the in situ generated aryldiazonium salt from the sulfanilic acid to obtain the organic layer Au-ArSO3 H. The Au-ArSO3 H layer was activated by using a solution of PCl5 in CH2 Cl2 to give a Au-ArSO2 Cl layer. The modified surface was then used to immobilize long ssDNA molecules. The results obtained showed that the presence of adenosine diphosphate promotes the protein autoassociation rather than nucleation around DNA. In addition, when the BRC4-28 peptide inhibitor was used, both QCM and AFM confirmed the inhibitory effect of BRC4-28 toward HsRad51 autoassociation. Altogether these results show the suitability of this modified surface to investigate the kinetics and structure of DNA-protein interactions and for the screening of inhibitors.

  20. Supramolecular Packing Controls H2 Photocatalysis in Chromophore Amphiphile Hydrogels

    PubMed Central

    2015-01-01

    Light harvesting supramolecular assemblies are potentially useful structures as components of solar-to-fuel conversion materials. The development of these functional constructs requires an understanding of optimal packing modes for chromophores. We investigated here assembly in water and the photocatalytic function of perylene monoimide chromophore amphiphiles with different alkyl linker lengths separating their hydrophobic core and the hydrophilic carboxylate headgroup. We found that these chromophore amphiphiles (CAs) self-assemble into charged nanostructures of increasing aspect ratio as the linker length is increased. The addition of salt to screen the charged nanostructures induced the formation of hydrogels and led to internal crystallization within some of the nanostructures. For linker lengths up to seven methylenes, the CAs were found to pack into 2D crystalline unit cells within ribbon-shaped nanostructures, whereas the nine methylene CAs assembled into long nanofibers without crystalline molecular packing. At the same time, the different molecular packing arrangements after charge screening led to different absorbance spectra, despite the identical electronic properties of all PMI amphiphiles. While the crystalline CAs formed electronically coupled H-aggregates, only CAs with intermediate linker lengths showed evidence of high intermolecular orbital overlap. Photocatalytic hydrogen production using a nickel-based catalyst was observed in all hydrogels, with the highest turnovers observed for CA gels having intermediate linker lengths. We conclude that the improved photocatalytic performance of the hydrogels formed by supramolecular assemblies of the intermediate linker CA molecules likely arises from improved exciton splitting efficiencies due to their higher orbital overlap. PMID:26593389

  1. Cell aggregation: Packing soft grains

    NASA Astrophysics Data System (ADS)

    Åström, J. A.; Karttunen, M.

    2006-06-01

    Cellular aggregates may be considered as collections of membrane enclosed units with a pressure difference between the internal and external liquid phases. Cells are kept together by membrane adhesion and/or confined space compression. Pattern formation and, in particular, intercellular spacing have important roles in controlling solvent diffusion within such aggregates. A physical approach is used to study generic aspects of cellular packings in a confined space. Average material properties are derived from the free energy. The appearance of penetrating intercellular void channels is found to be critically governed by the cell wall adhesion mechanisms during the formation of dense aggregates. A fully relaxed aggregate efficiently hinders solvent diffusion at high hydrostatic pressures, while a small fraction (˜0.1) of adhesion related packing frustration is sufficient for breaking such a blockage even at high a pressure.

  2. Packing nanomechanics of viral genomes

    NASA Astrophysics Data System (ADS)

    Iber, A. Å.; Dragar, M.; Parsegian, V. A.; Podgornik, R.

    2008-07-01

    We investigate the osmotic equilibrium between a bulk polyethylene glycol (PEG) solution and DNA tightly packed in a spherical capsid. We base our analysis on the equations of thermodynamic equilibrium in terms of osmotic pressure. The equality between external osmotic pressure of PEG and osmotic pressure of tightly packed DNA gives us the DNA encapsidation curves. In this way we directly connect the wealth of existing osmotic pressure data for DNA in the bulk with the DNA encapsidation curves within small viral capsids. Specific calculations are made for a monovalent salt, Na+ -DNA and a divalent salt, Mn2+ -DNA that have quite different DNA encapsidation behaviors. The main conclusion of our work is that bending energy of DNA is of minor importance regarding the encapsidated DNA length, but has a non-negligible influence on the density distribution of DNA within the capsid.

  3. Ammonium nitrate cold pack ingestion.

    PubMed

    Challoner, K R; McCarron, M M

    1988-01-01

    Disposable ammonium nitrate cold packs are widely used in emergency departments instead of ice bags. Five confused or suicidal patients who tore open a pack and ingested from 64 to 234 grams of ammonium nitrate in a single dose, and another patient who attempted to do so, are reported. It is known that chronic ingestion of 6 to 12 grams/day of ammonium nitrate may cause gastritis, acidosis, isosmotic diuresis, and nitrite toxicity manifesting as methemoglobinemia or vasodilatation. None of these patients developed severe toxicity, although three had symptoms of gastritis, three had slight methemoglobinemia, and two had mild hypotension. The product was removed from the stomach promptly in three of the five patients. None had pre-existing renal or intestinal dysfunction, which are known to enhance ammonium nitrate toxicity.

  4. 7 CFR 51.3055 - Standard pack.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... FRESH FRUITS, VEGETABLES AND OTHER PRODUCTS 1,2 (INSPECTION, CERTIFICATION, AND STANDARDS) United States Standards for Florida Avocados Standard Pack § 51.3055 Standard pack. (a) The avocados shall be packed in... smallest fruit in any container shall be not less than 75 percent of the weight of the largest fruit in the...

  5. 7 CFR 51.1527 - Standard pack.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ..., CERTIFICATION, AND STANDARDS) United States Standards for Grades of Fresh Plums and Prunes Standard Pack § 51... the approved and recognized methods. (2) The plums or prunes in the top layer of any package shall be...” means that the plums or prunes packed in loose or volume filled containers are packed within 1 inch of...

  6. 7 CFR 51.1527 - Standard pack.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ..., CERTIFICATION, AND STANDARDS) United States Standards for Grades of Fresh Plums and Prunes Standard Pack § 51... the approved and recognized methods. (2) The plums or prunes in the top layer of any package shall be...” means that the plums or prunes packed in loose or volume filled containers are packed within 1 inch of...

  7. Characteristics of fluidized-packed beds

    NASA Technical Reports Server (NTRS)

    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. Significance and technology of coal mine packing

    NASA Astrophysics Data System (ADS)

    Wang, Yunliang

    2017-08-01

    Packing is a kind of mining method which is used to fill the goaf with filling material to control the movement of overlying strata and reduce the deformation of the surface. This paper mainly discusses the significance of coal mine packing, and introduces the current method of filling and mining. Finally, the future of coal mine packing is forecasted.

  9. 7 CFR 906.10 - Pack.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... GRANDE VALLEY IN TEXAS Order Regulating Handling Definitions § 906.10 Pack. Pack means the specific grade... 7 Agriculture 8 2012-01-01 2012-01-01 false Pack. 906.10 Section 906.10 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Marketing Agreements and...

  10. 7 CFR 906.10 - Pack.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... GRANDE VALLEY IN TEXAS Order Regulating Handling Definitions § 906.10 Pack. Pack means the specific grade... 7 Agriculture 8 2011-01-01 2011-01-01 false Pack. 906.10 Section 906.10 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Marketing Agreements and...

  11. 7 CFR 906.10 - Pack.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... GRANDE VALLEY IN TEXAS Order Regulating Handling Definitions § 906.10 Pack. Pack means the specific grade... 7 Agriculture 8 2014-01-01 2014-01-01 false Pack. 906.10 Section 906.10 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (MARKETING AGREEMENTS AND...

  12. 7 CFR 966.11 - Pack.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... Orders; Fruits, Vegetables, Nuts), DEPARTMENT OF AGRICULTURE TOMATOES GROWN IN FLORIDA Order Regulating Handling Definitions § 966.11 Pack. Pack means any of the packs of tomatoes as defined and set forth in the United States Standards for Fresh Tomatoes issued by the United States Department of Agriculture (§§ 51...

  13. 7 CFR 966.11 - Pack.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... Orders; Fruits, Vegetables, Nuts), DEPARTMENT OF AGRICULTURE TOMATOES GROWN IN FLORIDA Order Regulating Handling Definitions § 966.11 Pack. Pack means any of the packs of tomatoes as defined and set forth in the United States Standards for Fresh Tomatoes issued by the United States Department of Agriculture (§§ 51...

  14. 7 CFR 966.11 - Pack.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... ORDERS; FRUITS, VEGETABLES, NUTS), DEPARTMENT OF AGRICULTURE TOMATOES GROWN IN FLORIDA Order Regulating Handling Definitions § 966.11 Pack. Pack means any of the packs of tomatoes as defined and set forth in the United States Standards for Fresh Tomatoes issued by the United States Department of Agriculture (§§ 51...

  15. 7 CFR 966.11 - Pack.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... Orders; Fruits, Vegetables, Nuts), DEPARTMENT OF AGRICULTURE TOMATOES GROWN IN FLORIDA Order Regulating Handling Definitions § 966.11 Pack. Pack means any of the packs of tomatoes as defined and set forth in the United States Standards for Fresh Tomatoes issued by the United States Department of Agriculture (§§ 51...

  16. 7 CFR 966.11 - Pack.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... ORDERS; FRUITS, VEGETABLES, NUTS), DEPARTMENT OF AGRICULTURE TOMATOES GROWN IN FLORIDA Order Regulating Handling Definitions § 966.11 Pack. Pack means any of the packs of tomatoes as defined and set forth in the United States Standards for Fresh Tomatoes issued by the United States Department of Agriculture (§§ 51...

  17. Diffusion in Jammed Particle Packs.

    PubMed

    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).

  18. Vibrational Collapse of Hexapod Packings

    NASA Astrophysics Data System (ADS)

    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.

  19. The role of filament-packing dynamics in powering amoeboid cell motility

    PubMed Central

    Miao, Long; Vanderlinde, Orion; Liu, Jun; Grant, Richard P.; Wouterse, Alan; Shimabukuro, Katsuya; Philipse, Albert; Stewart, Murray; Roberts, Thomas M.

    2008-01-01

    Although several models have been proposed to account for how cytoskeleton polymerization drives protrusion in cell motility, the precise mechanism remains controversial. Here, we show that, in addition to force exerted directly against the membrane by growing filaments, the way elongating filaments pack also contributes to protrusion by generating an expansion of the cytoskeleton gel. Tomography shows that filament packing in the major sperm protein (MSP) -based nematode sperm-motility machinery resembles that observed with rigid rods. Maximum rod-packing density decreases dramatically as the rods lengthen. Therefore, as filaments elongate, the cytoskeleton gel expands to accommodate their packing less densely. This volume expansion combines with polymerization to drive protrusion. Consistent with this hypothesis, an engineered MSP mutant that generates shorter filaments shows higher filament-packing density and slower movement. PMID:18385381

  20. The role of filament-packing dynamics in powering amoeboid cell motility.

    PubMed

    Miao, Long; Vanderlinde, Orion; Liu, Jun; Grant, Richard P; Wouterse, Alan; Shimabukuro, Katsuya; Philipse, Albert; Stewart, Murray; Roberts, Thomas M

    2008-04-08

    Although several models have been proposed to account for how cytoskeleton polymerization drives protrusion in cell motility, the precise mechanism remains controversial. Here, we show that, in addition to force exerted directly against the membrane by growing filaments, the way elongating filaments pack also contributes to protrusion by generating an expansion of the cytoskeleton gel. Tomography shows that filament packing in the major sperm protein (MSP) -based nematode sperm-motility machinery resembles that observed with rigid rods. Maximum rod-packing density decreases dramatically as the rods lengthen. Therefore, as filaments elongate, the cytoskeleton gel expands to accommodate their packing less densely. This volume expansion combines with polymerization to drive protrusion. Consistent with this hypothesis, an engineered MSP mutant that generates shorter filaments shows higher filament-packing density and slower movement.