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

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.

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 �

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

Insight into the defects of cage-type silica mesoporous crystals with Fd3m symmetry: TEM observations and a new proposal of "polyhedron packing" for the crystals.

PubMed

Han, Lu; Sakamoto, Yasuhiro; Che, Shunai; Terasaki, Osamu

2009-01-01

Silica mesoporous crystals were synthesized by using a gemini cationic surfactant (C(18-3-1)) as the directing agent, carboxyethylsilanetriol sodium salt as the co-structure directing agent (CSDA), and varying amounts of HCl. By using transmission electron microscopy (TEM) we observed 1) a structural change from the close-packed structures of spherical micelles--face-centered cubic (Fm3m) and hexagonal close-packed (P6(3)/mmc)--to Fd3m structures with an increase of HCl and 2) a few structural defects in the crystals with Fd3m symmetry. The structure of a crystal with Fd3m symmetry is described as one of the tetrahedrally close-packed (tcp) structures consisting of 5(12) and 5(12)6(4) polyhedra. The observed TEM images of the structural defects were explained well through use of simulated TEM images by introducing new 13-15 polyhedra comprising 5(12)6(2), 5(12)6(3), 4(1)5(10)6(2), 4(2)5(8)6(5), and 4(1)5(10)6(4), which have been observed in bubbles by Matzke. The mesostructural changes and defect formation are discussed in terms of the hardness of micelles composed of surfactant/CSDA/silica species that have formed through a change of the interaction between the surfactant and CSDA, which causes the micelles to change from a regime of close-packing to one of minimum-area packing.

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.

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 (k BT) 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

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kennedy, Robert D.; Halim, Merissa; Khan, Saeed I.

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 seriesmore » 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.« less

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.

Crystal Engineering; How molecules build solids

NASA Astrophysics Data System (ADS)

Williams, Jeffrey H.

2017-09-01

There are more than 20 million chemicals in the literature, with new materials being synthesized each week. Most of these molecules are stable, and the 3-dimensional arrangement of the atoms in the molecules, in the various solids may be determined by routine x-ray crystallography. When this is done, it is found that this vast range of molecules, with varying sizes and shapes can be accommodated by only a handful of solid structures. This limited number of architectures for the packing of molecules of all shapes and sizes, to maximize attractive intermolecular forces and minimizing repulsive intermolecular forces, allows us to develop simple models of what holds the molecules together in the solid. In this volume we look at the origin of the molecular architecture of crystals; a topic that is becoming increasingly important and is often termed, crystal engineering. Such studies are a means of predicting crystal structures, and of designing crystals with particular properties by manipulating the structure and interaction of large molecules. That is, creating new crystal architectures with desired physical characteristics in which the molecules pack together in particular architectures; a subject of particular interest to the pharmaceutical industry.

Molecular mechanism of melting of a helical polymer crystal: Role of conformational order, packing and mobility of polymers

NASA Astrophysics Data System (ADS)

Cheerla, Ramesh; Krishnan, Marimuthu

2018-03-01

The molecular mechanism of melting of a superheated helical polymer crystal has been investigated using isothermal-isobaric molecular dynamics simulation that allows anisotropic deformation of the crystal lattice. A detailed microscopic analysis of the onset and progression of melting and accompanying changes in the polymer conformational order, translational, and orientation order of the solid along the melting pathway is presented. Upon gradual heating from room temperature to beyond the melting point at ambient pressure, the crystal exhibits signatures of premelting well below the solid-to-liquid melting transition at the melting point. The melting transition is manifested by abrupt changes in the crystal volume, lattice energy, polymer conformation, and dynamical properties. In the premelting stage, the crystal lattice structure and backbone orientation of the polymer chains are retained but with the onset of weakening of long-range helical order and interchain packing of polymers perpendicular to the fibre axis of the crystal. The premelting also marks the onset of conformational defects and anisotropic solid-state diffusion of polymers along the fibre axis. The present study underscores the importance of the interplay between intermolecular packing, interactions, and conformational dynamics at the atomic level in determining the macroscopic melting behavior of polymer crystals.

Visualising crystal packing interactions in solid-state NMR: Concepts and applications

NASA Astrophysics Data System (ADS)

Zilka, Miri; Sturniolo, Simone; Brown, Steven P.; Yates, Jonathan R.

2017-10-01

In this article, we introduce and apply a methodology, based on density functional theory and the gauge-including projector augmented wave approach, to explore the effects of packing interactions on solid-state nuclear magnetic resonance (NMR) parameters. A visual map derived from a so-termed "magnetic shielding contribution field" can be made of the contributions to the magnetic shielding of a specific site—partitioning the chemical shift to specific interactions. The relation to the established approaches of examining the molecule to crystal change in the chemical shift and the nuclear independent chemical shift is established. The results are applied to a large sample of 71 molecular crystals and three further specific examples from supermolecular chemistry and pharmaceuticals. This approach extends the NMR crystallography toolkit and provides insight into the development of both cluster based approaches to the predictions of chemical shifts and for empirical predictions of chemical shifts in solids.

Crystal packing modifies ligand binding affinity: the case of aldose reductase.

PubMed

Cousido-Siah, Alexandra; Petrova, Tatiana; Hazemann, Isabelle; Mitschler, André; Ruiz, Francesc X; Howard, Eduardo; Ginell, Stephan; Atmanene, Cédric; Van Dorsselaer, Alain; Sanglier-Cianférani, Sarah; Joachimiak, Andrzej; Podjarny, Alberto

2012-11-01

The relationship between the structures of protein-ligand complexes existing in the crystal and in solution, essential in the case of fragment-based screening by X-ray crystallography (FBS-X), has been often an object of controversy. To address this question, simultaneous co-crystallization and soaking of two inhibitors with different ratios, Fidarestat (FID; K(d) = 6.5 nM) and IDD594 (594; K(d) = 61 nM), which bind to h-aldose reductase (AR), have been performed. The subatomic resolution of the crystal structures allows the differentiation of both inhibitors, even when the structures are almost superposed. We have determined the occupation ratio in solution by mass spectrometry (MS) Occ(FID)/Occ(594) = 2.7 and by X-ray crystallography Occ(FID)/Occ(594) = 0.6. The occupancies in the crystal and in solution differ 4.6 times, implying that ligand binding potency is influenced by crystal contacts. A structural analysis shows that the Loop A (residues 122-130), which is exposed to the solvent, is flexible in solution, and is involved in packing contacts within the crystal. Furthermore, inhibitor 594 contacts the base of Loop A, stabilizing it, while inhibitor FID does not. This is shown by the difference in B-factors of the Loop A between the AR-594 and AR-FID complexes. A stable loop diminishes the entropic energy barrier to binding, favoring 594 versus FID. Therefore, the effect of the crystal environment should be taken into consideration in the X-ray diffraction analysis of ligand binding to proteins. This conclusion highlights the need for additional methodologies in the case of FBS-X to validate this powerful screening technique, which is widely used. Copyright © 2012 Wiley Periodicals, Inc.

Protein crystals as scanned probes for recognition atomic force microscopy.

PubMed

Wickremasinghe, Nissanka S; Hafner, Jason H

2005-12-01

Lysozyme crystal growth has been localized at the tip of a conventional silicon nitride cantilever through seeded nucleation. After cross-linking with glutaraldehyde, lysozyme protein crystal tips image gold nanoparticles and grating standards with a resolution comparable to that of conventional tips. Force spectra between the lysozyme crystal tips and surfaces covered with antilysozyme reveal an adhesion force that drops significantly upon blocking with free lysozyme, thus confirming that lysozyme crystal tips can detect molecular recognition interactions.

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

The effect of ligand substituent on crystal packing: Structural and theoretical studies of two Ga(III) supramolecular compounds

NASA Astrophysics Data System (ADS)

Soleimannejad, Janet; Nazarnia, Esfandiar

2016-07-01

A new Ga(III) supramolecular compound (4,4‧-bipyH2)[Ga(hpydc)2]2·7H2O (2) (where H2hpydc = 4-hydroxy-pyridine-2,6-dicarboxylic acid and 4,4‧-bipy = 4,4‧-bipyridine) was synthesized using the proton transfer reaction. Compound 2 was structurally characterized using single crystal X-ray diffraction, and it was shown that its asymmetric unit consists of two independent anionic Ga(III) complexes, one fully protonated 4,4‧-bipyridine and seven uncoordinated water molecules. In order to understand the effect of pyridine OH substituent on supramolecular interactions and crystal packing, compound 2 was compared with (bipyH2)[Ga(pydc)2]·(H2pydc)·4H2O (1) (where H2pydc = pyridine-2,6-dicarboxylic acid), that does not have an OH group on the pyridine ligand. The Density Functional Theory (DFT) and Natural Bond Orbital (NBO) calculations and also Atoms in Molecules (AIM) analysis were used to analyze the non-covalent interactions in both complexes. The calculation of non-covalent interactions' energy provides a useful means to investigate their effects in the crystal packing.

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.

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.

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…

Shearing single crystal magnesium in the close-packed basal plane at different temperatures

NASA Astrophysics Data System (ADS)

Han, Ming; Li, Lili; Zhao, Guangming

2018-05-01

Shear behaviors of single crystal magnesium (Mg) in close-packed (0001) basal plane along the [ 1 bar 2 1 bar 0 ], [ 1 2 bar 10 ], [ 10 1 bar 0 ] and [ 1 bar 010 ] directions were studied using molecular dynamics simulations via EAM potential. The results show that both shear stress-strain curves along the four directions and the motion path of free atoms during shearing behave periodic characteristics. It reveals that the periodic shear displacement is inherently related to the crystallographic orientation in single crystal Mg. Moreover, different temperatures in a range from 10 to 750 K were considered, demonstrating that shear modulus decreases with increasing temperatures. The results agree well with the MTS model. It is manifested that the modulus is independent with the shear direction and the size of the atomic model. This work also demonstrates that the classical description of shear modulus is still effective at the nanoscale.

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.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

McMahon, Roisin M., E-mail: r.mcmahon1@uq.edu.au; Coinçon, Mathieu; Tay, Stephanie

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 discoverymore » 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.« less

Approaching an experimental electron density model of the biologically active trans -epoxysuccinyl amide group-Substituent effects vs. crystal packing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shi, Ming W.; Stewart, Scott G.; Sobolev, Alexandre N.

The trans-epoxysuccinyl amide group as a biologically active moiety in cysteine protease inhibitors such as loxistatin acid E64c has been used as a benchmark system for theoretical studies of environmental effects on the electron density of small active ingredients in relation to their biological activity. Here, the synthesis and the electronic properties of the smallest possible active site model compound are reported to close the gap between the unknown experimental electron density of trans-epoxysuccinyl amides and the well-known function of related drugs. Intramolecular substituent effects are separated from intermolecular crystal packing effects on the electron density, which allows us tomore » predict the conditions under which an experimental electron density investigation on trans-epoxysuccinyl amides will be possible. In this context, the special importance of the carboxylic acid function in the model compound for both crystal packing and biological activity is revealed through the novel tool of model energy analysis.« less

Variability of the contrail radiative forcing due to crystal shape

NASA Astrophysics Data System (ADS)

Markowicz, K. M.; Witek, M. L.

2011-12-01

The aim of this study is to examine the influence of particles' shape and particles' optical properties on the contrail radiative forcing. Contrail optical properties in the shortwave and longwave range are derived using a ray-tracing geometric method and the discrete dipole approximation method, respectively. Both methods present good correspondence of the single scattering albedo and the asymmetry parameter in a transition range (3-7μm). We compare optical properties defined following simple 10 crystals habits randomly oriented: hexagonal plates, hexagonal columns with different aspect ratio, and spherical. There are substantial differences in single scattering properties between ten crystal models investigated here (e.g. hexagonal columns and plates with different aspect ratios, spherical particles). The single scattering albedo and the asymmetry parameter both vary up to 0.1 between various crystal shapes. Radiative forcing calculations were performed using a model which includes an interface between the state-of-the-art radiative transfer model Fu-Liou and databases containing optical properties of the atmosphere and surface reflectance and emissivity. This interface allows to determine radiative fluxes in the atmosphere and to estimate the contrail radiative forcing for clear- and all-sky (including natural clouds) conditions for various crystal shapes. The Fu-Liou code is fast and therefore it is suitable for computing radiative forcing on a global scale. At the same time it has sufficiently good accuracy for such global applications. A noticeable weakness of the Fu-Liou code is that it does not take into account the 3D radiative effects, e.g. cloud shading and horizontal. Radiative transfer model calculations were performed at horizontal resolution of 5x5 degree and time resolution of 20 min during day and 3 h during night. In order to calculate a geographic distribution of the global and annual mean contrail radiative forcing, the contrail cover must be

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.

A method for fast safety screening of explosives in terms of crystal packing and molecular stability.

PubMed

Hu, Xiaohua; Chen, Nana; Li, Weichen

2016-07-01

Safety prediction is crucial to the molecular design or the material design of explosives, and the predictions based on any single factor alone will cause much inaccuracy, leading to a desire for a method on multi-bases. The presented proposes an improved method for fast screening explosive safety by combining a crystal packing factor and a molecular one, that is, steric hindrance against shear slide in crystal and molecular stability, denoted by intermolecular friction symbol (IFS) and bond dissociation energy (BDE) of trigger linkage respectively. Employing this BDE-IFS combined method, we understand the impact sensitivities of 24 existing explosives, and predict those of two energetic-energetic cocrystals of the observed CL-20/BTF and the supposed HMX/TATB. As a result, a better understanding is implemented by the combined method relative to molecular stability alone, verifying its improvement of more accurate predictions and the feasibility of IFS to graphically reflect molecular stacking in crystals. Also, this work verifies that the explosive safety is strongly related with its crystal stacking, which determines steric hindrance and influences shear slide.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cinacchi, Giorgio, E-mail: giorgio.cinacchi@uam.es; Torquato, Salvatore, E-mail: torquato@princeton.edu

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 themore » 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.« less

Self-assembly modes of glycyrrhetinic acid esters in view of the crystal packing of related triterpene molecules.

PubMed

Langer, Dominik; Wicher, Barbara; Szczołko, Wojciech; Gdaniec, Maria; Tykarska, Ewa

2016-08-01

The crystal structures of three ester derivatives of glycyrrhetinic acid (GE) are reported. X-ray crystallography revealed that despite differences in the size of the ester substituents (ethyl, isopropyl and 2-morpholinoethyl) the scheme of molecular self-assembly is similar in all three cases but differs significantly from that observed in other known GE esters. According to our analysis, the two basic patterns of self-assembly of GE esters observed in their unsolvated crystals correspond to two distinct orientations of the ester groups relative to the triterpene backbone. Moreover, comparison of the self-assembly modes of GE esters in their unsolvated forms with the supramolecular organization of GE and carbenoxolone in their solvated crystals revealed that ester substituents replace solvent molecules hydrogen bonded to the COOH group at the triterpene skeleton, resulting in similar packing arrangements of these compounds.

Synthesis and Crystal Structure of a Chalcone Derivative

NASA Astrophysics Data System (ADS)

Singh, Vikram D.; Salian, Vinutha V.; Narayana, B.; Sarojini, B. K.; Kamni; Anthal, Sumati; Kant, Rajni

2017-12-01

(2E)-3-(anthrance-9-yl)-1-(3,4-dichlorophenyl)prop-2-en-1-one [C23H14OCl2] is synthesized and its crystal structure is determined by single X-ray diffraction. There exist two molecules in the asymmetric unit. The dihedral angle between the benzene and anthracene moiety of the molecule A and B is 86.51(12)° and 76.42(13)°, respectively. No classical hydrogen bonds are observed and only van der Waals forces stabilize the crystal packing.

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…

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.

Random close packing in protein cores.

PubMed

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.

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.

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.

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.

Learning from oligosaccharide soaks of crystals of an AA13 lytic polysaccharide monooxygenase: crystal packing, ligand binding and active-site disorder.

PubMed

Frandsen, Kristian E H; Poulsen, Jens Christian Navarro; Tovborg, Morten; Johansen, Katja S; Lo Leggio, Leila

2017-01-01

Lytic polysaccharide monooxygenases (LPMOs) are a class of copper-dependent enzymes discovered within the last ten years. They oxidatively cleave polysaccharides (chitin, lignocellulose, hemicellulose and starch-derived), presumably making recalcitrant substrates accessible to glycoside hydrolases. Recently, the first crystal structure of an LPMO-substrate complex was reported, giving insights into the interaction of LPMOs with β-linked substrates (Frandsen et al., 2016). The LPMOs acting on α-linked glycosidic bonds (family AA13) display binding surfaces that are quite different from those of LPMOs that act on β-linked glycosidic bonds (families AA9-AA11), as revealed from the first determined structure (Lo Leggio et al., 2015), and thus presumably the AA13s interact with their substrate in a distinct fashion. Here, several new structures of the same AA13 enzyme, Aspergillus oryzae AA13, are presented. Crystals obtained in the presence of high zinc-ion concentrations were used, as they can be obtained more reproducibly than those used to refine the deposited copper-containing structure. One structure with an ordered zinc-bound active site was solved at 1.65 Å resolution, and three structures from crystals soaked with maltooligosaccharides in solutions devoid of zinc ions were solved at resolutions of up to 1.10 Å. Despite similar unit-cell parameters, small rearrangements in the crystal packing occur when the crystals are depleted of zinc ions, resulting in a more occluded substrate-binding surface. In two of the three structures maltooligosaccharide ligands are bound, but not at the active site. Two of the structures presented show a His-ligand conformation that is incompatible with metal-ion binding. In one of these structures this conformation is the principal one (80% occupancy), giving a rare atomic resolution view of a substantially misfolded enzyme that is presumably rendered inactive.

Crystal structures of 6-chloro­indan-1-one and 6-bromo­indan-1-one exhibit different inter­molecular packing inter­actions

PubMed Central

Caruso, Alessio; Blair, Benjamin; Tanski, Joseph M.

2016-01-01

The two title compounds are analogs of 1-indanone that are substituted at the 6-position with chlorine and bromine. Although very similar in mol­ecular structure, the crystal structures are not isomorphous and reveal that 6-chloro­indan-1-one, C9H7ClO (I), and 6-bromo­indan-1-one, C9H7BrO (II), exhibit unique inter­molecular packing motifs. The mol­ecules of the chloro analog (I) pack with a herringbone packing motif of C—H⋯O inter­actions, whereas the bromo derivative (II) packs with offset face-to-face π-stacking, C—H⋯O, C—H⋯Br and Br⋯O inter­actions. Compound (II) was refined as a two-component non-merohedral twin, BASF 0.0762 (5). PMID:27840702

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.

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.

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.

Dynamic Simulation of Random Packing of Polydispersive Fine Particles

NASA Astrophysics Data System (ADS)

Ferraz, Carlos Handrey Araujo; Marques, Samuel Apolinário

2018-02-01

In this paper, we perform molecular dynamic (MD) simulations to study the two-dimensional packing process of both monosized and random size particles with radii ranging from 1.0 to 7.0 μm. The initial positions as well as the radii of five thousand fine particles were defined inside a rectangular box by using a random number generator. Both the translational and rotational movements of each particle were considered in the simulations. In order to deal with interacting fine particles, we take into account both the contact forces and the long-range dispersive forces. We account for normal and static/sliding tangential friction forces between particles and between particle and wall by means of a linear model approach, while the long-range dispersive forces are computed by using a Lennard-Jones-like potential. The packing processes were studied assuming different long-range interaction strengths. We carry out statistical calculations of the different quantities studied such as packing density, mean coordination number, kinetic energy, and radial distribution function as the system evolves over time. We find that the long-range dispersive forces can strongly influence the packing process dynamics as they might form large particle clusters, depending on the intensity of the long-range interaction strength.

Magnetic assembly of nonmagnetic particles into photonic crystal structures.

PubMed

He, Le; Hu, Yongxing; Kim, Hyoki; Ge, Jianping; Kwon, Sunghoon; Yin, Yadong

2010-11-10

We report the rapid formation of photonic crystal structures by assembly of uniform nonmagnetic colloidal particles in ferrofluids using external magnetic fields. Magnetic manipulation of nonmagnetic particles with size down to a few hundred nanometers, suitable building blocks for producing photonic crystals with band gaps located in the visible regime, has been difficult due to their weak magnetic dipole moment. Increasing the dipole moment of magnetic holes has been limited by the instability of ferrofluids toward aggregation at high concentration or under strong magnetic field. By taking advantage of the superior stability of highly surface-charged magnetite nanocrystal-based ferrofluids, in this paper we have been able to successfully assemble 185 nm nonmagnetic polymer beads into photonic crystal structures, from 1D chains to 3D assemblies as determined by the interplay of magnetic dipole force and packing force. In a strong magnetic field with large field gradient, 3D photonic crystals with high reflectance (83%) in the visible range can be rapidly produced within several minutes, making this general strategy promising for fast creation of large-area photonic crystals using nonmagnetic particles as building blocks.

Direction-specific interaction forces underlying zinc oxide crystal growth by oriented attachment

DOE PAGES

Zhang, X.; Shen, Z.; Liu, J.; ...

2017-10-10

Here, crystallization by particle attachment is impacting our understanding of natural mineralization processes and holds promise for novel materials design. When particles assemble in crystallographic registry, expulsion of the intervening solvent and particle coalescence is enabled by near-perfect co-alignment via interparticle forces that remain poorly quantified. Here we report measurement and simulation of these nanoscale aligning forces for the ZnO(0001)-ZnO(000¯1) system in aqueous solution. Dynamic force spectroscopy using nanoengineered single crystal probes reveals an attractive force with 60o rotational periodicity. Calculated distance and orientation-dependent potentials of mean force show several attractive free energy wells distinguished by numbers of intervening watermore » layers, which reach a minimum when aligned. The calculated activation energy to separate the attractively bound solvated interfaces perfectly reproduces the measured 60o periodicity, revealing the key role of intervening water structuring as a basis to generate the interparticle torque that completes alignment and enables coalescence.« less

Direction-specific interaction forces underlying zinc oxide crystal growth by oriented attachment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, X.; Shen, Z.; Liu, J.

Here, crystallization by particle attachment is impacting our understanding of natural mineralization processes and holds promise for novel materials design. When particles assemble in crystallographic registry, expulsion of the intervening solvent and particle coalescence is enabled by near-perfect co-alignment via interparticle forces that remain poorly quantified. Here we report measurement and simulation of these nanoscale aligning forces for the ZnO(0001)-ZnO(000¯1) system in aqueous solution. Dynamic force spectroscopy using nanoengineered single crystal probes reveals an attractive force with 60o rotational periodicity. Calculated distance and orientation-dependent potentials of mean force show several attractive free energy wells distinguished by numbers of intervening watermore » layers, which reach a minimum when aligned. The calculated activation energy to separate the attractively bound solvated interfaces perfectly reproduces the measured 60o periodicity, revealing the key role of intervening water structuring as a basis to generate the interparticle torque that completes alignment and enables coalescence.« less

Fabrication of oriented crystals as force measurement tips via focused ion beam and microlithography methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Zhigang; Chun, Jaehun; Chatterjee, Sayandev

Detailed knowledge of the forces between nanocrystals is very crucial for understanding many generic (e.g., random aggregation/assembly and rheology) and specific (e.g., oriented attachment) phenomena at macroscopic length scales, especially considering the additional complexities involved in nanocrystals such as crystal orientation and corresponding orientation-dependent physicochemical properties. Because there are a limited number of methods to directly measure the forces, little is known about the forces that drive the various emergent phenomena. Here we report on two methods of preparing crystals as force measurement tips used in an atomic force microscope (AFM): the focused ion beam method and microlithography method. Themore » desired crystals are fabricated using these two methods and are fixed to the AFM probe using platinum deposition, ultraviolet epoxy, or resin, which allows for the orientation-dependent force measurements. These two methods can be used to attach virtually any solid particles (from the size of a few hundreds of nanometers to millimeters). We demonstrate the force measurements between aqueous media under different conditions such as pH.« less

Particle packing from an earth science viewpoint

NASA Astrophysics Data System (ADS)

Rogers, C. D. F.; Dijkstra, T. A.; Smalley, I. J.

1994-04-01

Particle packings are relevant to many aspects of the Earth sciences, and there is a long history of the study of packings from an Earth science viewpoint. Packings have also been studied in connection with other subjects and disciplines. Allen (1982) produced a major review which provides a solid base for Earth science related studies. This review complements Allen's work and in particular focuses on advances in the study of random packings over the last ten years. Transitions from packing to packing may be as important as the packings themselves, and possibly easier to model. This paper places emphasis on certain neglected works, in particular Morrow and Graves (1969) and the packing transition envelope, Kahn (1956) and the measurement of packing parameters, Griffiths (1962) on packings in one-dimension, and Getis and Boots (1978) on packings in two dimensions. Certain packing problems are relevant to current areas of study including structure collapse in loess (hydroconsolidation), flowslides in very sensitive soils, wind erosion, jewel quality in opals and the structure and functions of sand dunes. The region where interparticle forces become active (particles < 200 μm) is considered and the implications for packing are examined.

Investigation of Artificial Forced Cooling in the Bridgman Crystal Growth of Cadmium Zinc Telluride

NASA Astrophysics Data System (ADS)

Liu, Juncheng; Li, Jiao; Zhang, Guodong; Li, Changxing; Lennon, Craig; Sivananthan, Siva

2007-08-01

The effects of artificial forced cooling on the solid liquid interface and on solute segregation were investigated by modeling the vertical Bridgman method for the single-crystal growth of CdZnTe, taking into consideration effects such as increasing the axial outward heat flux from the crucible bottom, the radial outward heat flux from the crucible wall, and the carbon film thickness on the crucible inner wall. Axial artificially forced cooling noticeably increases convection and the temperature gradient in the melt next to the solid liquid interface, and substantially reduces interface concavity at the initial solidification stage. Interface concavity increases a little when the solidification proceeds further, however. Axial artificially forced cooling reduces radial solute segregation of the initial segment of the grown crystal and slightly increases the solute iso-concentration segment. Radial artificially forced cooling enhances melt convection substantially, affects solid liquid interface concavity only slightly, and hardly affects solute segregation in the grown crystal. Doubling the carbon film thickness weakens convection of the melt in front of the interface, substantially increases interface concavity, and hardly affects solute segregation in the grown crystal.

Communication: From close-packed to topologically close-packed: Formation of Laves phases in moderately polydisperse hard-sphere mixtures

NASA Astrophysics Data System (ADS)

Lindquist, Beth A.; Jadrich, Ryan B.; Truskett, Thomas M.

2018-05-01

Particle size polydispersity can help to inhibit crystallization of the hard-sphere fluid into close-packed structures at high packing fractions and thus is often employed to create model glass-forming systems. Nonetheless, it is known that hard-sphere mixtures with modest polydispersity still have ordered ground states. Here, we demonstrate by computer simulation that hard-sphere mixtures with increased polydispersity fractionate on the basis of particle size and a bimodal subpopulation favors the formation of topologically close-packed C14 and C15 Laves phases in coexistence with a disordered phase. The generality of this result is supported by simulations of hard-sphere mixtures with particle-size distributions of four different forms.

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.

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.

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

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

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.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Land, T.A.; De Yoreo, J.J.; Malkin, A.J.

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 determinemore » 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.« less

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.

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.

Crystallization of micrometer-sized particles with molecular contours.

PubMed

Song, Pengcheng; Olmsted, Brian K; Chaikin, Paul; Ward, Michael D

2013-11-12

The crystallization of micrometer-sized particles with shapes mimicking those of tetrabenzoheptacene (TBH) and 1,2:5,6-dibenzanthracene (DBT), both flat polyacenes, in an electric field results in the formation of ordered 2D packings that mimic the plane group symmetries in their respective molecular crystal equivalents. Whereas the particles packed in low-density disordered arrangements under a gravitational gradient, dielectrophoresis (under an ac electric field) produced ordered high-density packings with readily identifiable plane group symmetry. The ordered colloidal assemblies were stable for hours, with the packing density decreasing slowly but with recognizable symmetry for up to 12 h for the TBH-shaped particles and up to 4 h for the DBT-shaped particles. This unexpected stability is attributed to jamming behavior associated with interlocking of the dogbone-shaped (TBH) and Z-block (DBT) particles, contrasting with the more rapid reduction of packing density and loss of hexagonal symmetry for disk-shaped particles upon removal of the electric field. The TBH-shaped and DBT-shaped particles assemble into the p2 plane group, which corresponds to the densest particle packing among the possible close-packed plane groups for these particle symmetries. The p2 symmetry observed for the TBH-shaped and DBT-shaped colloid crystal emulates the p2 symmetry of the (010) layers in their respective molecular crystals, which crystallize in monoclinic lattices. Notably, DBT-shaped particles also form ordered domains with pgg symmetry, replicating the plane group symmetry of the (100) layer in the orthorhombic polymorph of DBT. These observations illustrate that the 2D ordering of colloid particles can mimic the packing of molecules with similar shapes, demonstrating that packing can transcend length scales from the molecular to the colloidal.

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, CO 2 sequestration inmore » 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.« less

Quantitative single molecule measurements on the interaction forces of poly(L-glutamic acid) with calcite crystals.

PubMed

Sonnenberg, Lars; Luo, Yufei; Schlaad, Helmut; Seitz, Markus; Cölfen, Helmut; Gaub, Hermann E

2007-12-12

The interaction between poly(L-glutamic acid) (PLE) and calcite crystals was studied with AFM-based single molecule force spectroscopy. Block copolymers of poly(ethylene oxide) (PEO) and PLE were synthesized and covalently attached to the tip of an AFM cantilever. In desorption measurements the molecules were allowed to adsorb on the calcite crystal faces and afterward successively desorbed. The corresponding desorption forces were detected with high precision, showing for example a force transition between the two blocks. Because of its importance in the crystallization process in biominerals, the PLE-calcite interaction was investigated as a function of the pH as well as the calcium concentration of the aqueous solution. The sensitivity of the technique was underlined by resolving different interaction forces for calcite (104) and calcite (100).

SdsA polymorph isolation and improvement of their crystal quality using nonconventional crystallization techniques

DOE Office of Scientific and Technical Information (OSTI.GOV)

De la Mora, Eugenio; Flores-Hernández, Edith; Jakoncic, Jean

SdsA, a sodium dodecyl sulfate hydrolase, from Pseudomonas aeruginosa was crystallized in three different crystal polymorphs and their three-dimensional structure was determined. The different polymorphs present different crystal packing habits. One of the polymorphs suggests the existence of a tetramer, an oligomeric state not observed previously, while the crystal packing of the remaining two polymorphs obstructs the active site entrance but stabilizes flexible regions of the protein. Nonconventional crystallization methods that minimize convection, such as counterdiffusion in polyvinyl alcohol gel coupled with the influence of a 500 MHz (10.2 T) magnetic field, were necessary to isolate the poorest diffracting polymorphmore » and increase its internal order to determine its structure by X-ray diffraction. In conclusion, the results obtained show the effectiveness of nonconventional crystallographic methods to isolate different crystal polymorphs.« less

Force production in the rugby union scrum.

PubMed

Quarrie, K L; Wilson, B D

2000-04-01

In this study, we examined the relationship between anthropometric, strength and power characteristics of rugby forwards, their body position when scrummaging, and their ability to apply force when scrummaging. Force applied to an instrumented scrum machine was measured for 56 players, both individually and as scrum packs. Measurements of body position for individuals were made by digitizing videotape records of the trials. Forty players subsequently had their anthropometry assessed and completed several strength and power tests. Body mass, each component of somatotype, maximal anaerobic power developed on a cycle ergometer, and isokinetic knee extension strength correlated significantly with individual scrummaging force. A regression model (P < 0.001) including body mass, mesomorphy, maximal anaerobic power and hip angle while in the scrummaging position accounted for 45% of the variance in individual scrummaging force. The packs that produced the largest scrummaging forces were, in general, characterized by a greater pack force to sum of individual force ratio than the packs producing lower forces. Our results emphasize the need for a scrum pack to develop technique and coordination as a unit to maximize scrummaging force.

Order - disorder transitions in granular sphere packings

NASA Astrophysics Data System (ADS)

Panaitescu, Andreea M.

Granular materials are ubiquitous in many industrial and natural processes, yet their complex behaviors characterized by unusual static and dynamic properties are still poorly understood. In this dissertation we investigate both the geometrical structure and the dynamical properties (the response to shear deformations, disorder-order transition and crystallization) of packings of mono-sized spheres as a function of the packing volume fraction. Different average packing fractions were obtained by submitting a dense granular material to periodic shear deformations and by epitaxy. Using advanced imaging techniques including the refractive index matched imaging (RIM) and X-ray computed tomography (CT) enables us to determine the three dimensional particles position inside the packing. From positions we obtain the Voronoi tessellation corresponding to the particles in the bulk and calculate the radial distribution and the bond-order metric. These two parameters are widely used to quantify the structure of the spherical particle systems. A granular packing undergoing periodic shear deformations is observed to slowly evolve towards crystallization and the packing fraction is correspondingly observed to increase smoothly from loose packing fraction, 0.59, well above the random close packing fraction, 0.637. Tracking the particles over several shear cycles allows us to obtain the probability distributions of particle displacements and the mean-square displacements and to compute the components of the diffusion tensor. We find that in a shear flow, the initial self-diffusion of the particles is anisotropic with diffusion greater in the flow direction compared with the velocity gradient direction which in turn is greater than in the vorticity direction. We further find that the granular matter under cyclic shear shows reversible as well as irreversible or plastic response for small enough strain amplitude. The appearance and the propagation of the crystalline order were

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 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

Structural, crystal structure, Hirshfeld surface analysis and physicochemical studies of a new chlorocadmate template by 1-(2-hydroxyethyl)piperazine

NASA Astrophysics Data System (ADS)

Soudani, S.; Jeanneau, E.; Jelsch, C.; Lefebvre, F.; Ben Nasr, C.

2016-11-01

The synthesis, crystal structure and spectroscopic characterization of a new chlorocadmate template by the 1-(2-hydroxyethyl)piperazine ligand are reported. In the atomic arrangement, the CdCl5O entities are deployed in corrugated rows along the a-axis at y = 1/4 and y = 3/4 to form layers parallel to the (a,b) plane. In these crystals, piperazinediium cations are in a chair conformation and are inserted between these layers through Nsbnd H⋯Cl, Csbnd H⋯Cl, Osbnd H⋯Cl and Nsbnd H⋯O hydrogen bonds to form infinite three-dimensional network. Investigation of intermolecular interactions and crystal packing via Hirshfeld surface analysis reveals that H⋯Cl and Csbnd H⋯Hsbnd C intermolecular interactions are the most abundant contacts of the organic cation in the crystal packing. The crystal contacts enrichments reveals that, the Cd++ … Cl- salt bridges, the Cd⋯O complexation and Osbnd H⋯Cl- and Nsbnd H⋯Cl-strong H-bonds are the driving forces in the packing formation. The presence of twelve independent chloride anions and four organic cation in the asymmetric unit allowed comparing their contact propensities. The 13C and 15N CP-MAS NMR spectra are in agreement with the X-ray structure. Additional characterization of this compound has also been performed by IR spectroscopy.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chuvildeev, V.N., E-mail: chuvildeev@gmail.com; Semenycheva, A.V., E-mail: avsemenycheva@gmail.com

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.

Simulations of wave propagation and disorder in 3D non-close-packed colloidal photonic crystals with low refractive index contrast.

PubMed

Glushko, O; Meisels, R; Kuchar, F

2010-03-29

The plane-wave expansion method (PWEM), the multiple-scattering method (MSM) and the 3D finite-difference time-domain method (FDTD) are applied for simulations of propagation of electromagnetic waves through 3D colloidal photonic crystals. The system investigated is not a "usual" artificial opal with close-packed fcc lattice but a dilute bcc structure which occurs due to long-range repulsive interaction between electrically charged colloidal particles during the growth process. The basic optical properties of non-close-packed colloidal PhCs are explored by examining the band structure and reflection spectra for a bcc lattice of silica spheres in an aqueous medium. Finite size effects and correspondence between the Bragg model, band structure and reflection spectra are discussed. The effects of size, positional and missing-spheres disorder are investigated. In addition, by analyzing the results of experimental work we show that the fabricated structures have reduced plane-to-plane distance probably due to the effect of gravity during growth.

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

2018-01-01

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.

Characterization of the crystal structure, kinematics, stresses and rotations in angular granular quartz during compaction

DOE PAGES

Hurley, Ryan C.; Herbold, Eric B.; Pagan, Darren C.

2018-06-28

Three-dimensional X-ray diffraction (3DXRD), a method for quantifying the position, orientation and elastic strain of large ensembles of single crystals, has recently emerged as an important tool for studying the mechanical response of granular materials during compaction. Applications have demonstrated the utility of 3DXRD and X-ray computed tomography (XRCT) for assessing strains, particle stresses and orientations, inter-particle contacts and forces, particle fracture mechanics, and porosity evolution in situ . Although past studies employing 3DXRD and XRCT have elucidated the mechanics of spherical particle packings and angular particle packings with a small number of particles, there has been limited effort tomore » date in studying angular particle packings with a large number of particles and in comparing the mechanics of these packings with those composed of a large number of spherical particles. Therefore, the focus of the present paper is on the mechanics of several hundred angular particles during compaction using in situ 3DXRD to study the crystal structure, kinematics, stresses and rotations of angular quartz grains. Comparisons are also made between the compaction response of angular grains and that of spherical grains, and stress-induced twinning within individual grains is discussed.« less

Characterization of the crystal structure, kinematics, stresses and rotations in angular granular quartz during compaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hurley, Ryan C.; Herbold, Eric B.; Pagan, Darren C.

Three-dimensional X-ray diffraction (3DXRD), a method for quantifying the position, orientation and elastic strain of large ensembles of single crystals, has recently emerged as an important tool for studying the mechanical response of granular materials during compaction. Applications have demonstrated the utility of 3DXRD and X-ray computed tomography (XRCT) for assessing strains, particle stresses and orientations, inter-particle contacts and forces, particle fracture mechanics, and porosity evolution in situ . Although past studies employing 3DXRD and XRCT have elucidated the mechanics of spherical particle packings and angular particle packings with a small number of particles, there has been limited effort tomore » date in studying angular particle packings with a large number of particles and in comparing the mechanics of these packings with those composed of a large number of spherical particles. Therefore, the focus of the present paper is on the mechanics of several hundred angular particles during compaction using in situ 3DXRD to study the crystal structure, kinematics, stresses and rotations of angular quartz grains. Comparisons are also made between the compaction response of angular grains and that of spherical grains, and stress-induced twinning within individual grains is discussed.« less

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 T substrate = 0.78T g to 1.02T g, where T g (=330 K) is the glass transition temperature. The films were characterized using X-ray scattering techniques. For T substrate near and below T g, glasses with layered smectic-like structures can be prepared and the layer spacing can be tuned by 16% through the choice of T substrate. Remarkably, glasses prepared with T substrate values above T g exhibit levels of structural organization much higher than that of a thermally annealedmore » 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.« less

Lateral shearing optical gradient force in coupled nanobeam photonic crystal cavities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Du, Han; Zhang, Xingwang; Chau, Fook Siong

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 futuremore » nanooptoelectromechanical systems.« less

Range of motion exercise of temporo-mandibular joint with hot pack increases occlusal force in patients with Duchenne muscular dystrophy.

PubMed

Nozaki, S; Kawai, M; Shimoyama, R; Futamura, N; Matsumura, T; Adachi, K; Kikuchi, Y

2010-12-01

The purpose of this study is to evaluate whether the range of motion exercise of the temporo-mandibular joint (jaw ROM exercise) with a hot pack and massage of the masseter muscle improve biting disorder in Duchenne muscular dystrophy (DMD). The subjects were 18 DMD patients (21.3+/- 4.1 years old). The jaw ROM exercise consisted of therapist-assisted training (2 times a week) and self-training (before each meal every day). The therapist-assisted training consisted of the application of a hot pack on the cheek of the masseter muscle region (15 minutes), the massage of the masseter (10 minutes), and jaw ROM exercise (5 minutes). The self-training involved jaw ROM exercise by opening the mouth to the maximum degree, ten times. These trainings continued for six months. Outcomes were evaluated by measuring the greatest occlusal force and the distance at the maximum degree of mouth opening between an incisor of the top and that of the bottom. Six months later, the greatest occlusal force had increased significantly compared with that at the start of jaw ROM exercise (intermediate values: from 73.8N to 97.3N) (p = 0.005) as determined by the Friedman test and Scheffi's nonparametric test. The patients' satisfaction with meals increased. However, the maximum degree of mouth opening did not change after six months of jaw ROM exercise. Jaw ROM exercise in DMD is effective for increasing the greatest occlusal force.

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)

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.).

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.

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.

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

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

PubMed

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

2016-06-01

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 ( a w ) > 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.

Packing of muscles in the rabbit shank influences three-dimensional architecture of M. soleus.

PubMed

Wick, Carolin; Böl, Markus; Müller, Florian; Blickhan, Reinhard; Siebert, Tobias

2018-07-01

Isolated and packed muscles (e.g. in the calf) exhibit different three-dimensional muscle shapes. In packed muscles, cross-sections are more angular compared to the more elliptical ones in isolated muscles. As far as we know, it has not been examined yet, whether the shape of the muscle in its packed condition influences its internal arrangement of muscle fascicles and accordingly the contraction behavior in comparison to the isolated condition. To evaluate the impact of muscle packing, we examined the three-dimensional muscle architecture of isolated and packed rabbit M. soleus for different ankle angles (65°, 75°, 85°, 90°, and 95°) using manual digitization (MicroScribe ® MLX). In general, significantly increased values of pennation angle and fascicle curvature were found in packed compared to isolated M. soleus (except for fascicle curvature at 90° ankle angle). On average, fascicle length of isolated muscles exceeded fascicle lengths of packed muscles by 2.6%. Reduction of pennation angle in the packed condition had only marginal influence on force generation (about 1% of maximum isometric force) in longitudinal direction (along the line of action) although an increase of transversal force component (perpendicular to the line of action) of about 26% is expected. Results of this study provide initial evidence that muscle packing limits maximum muscle performance observed in isolated M. soleus. Besides an enhanced understanding of the impact of muscle packing on architectural parameters, the outcomes of this study are essential for realistic three-dimensional muscle modeling and model validation. Copyright © 2018 Elsevier Ltd. All rights reserved.

Stress Transmission in Granular Packings: Localization and Cooperative Response

NASA Astrophysics Data System (ADS)

Ramola, Kabir

We develop a framework for stress transmission in two dimensional granular media that respects vector force balance at the microscopic level. For a packing of grains interacting via pairwise contact forces, we introduce local gauge degrees of freedom that determine the response of the system to external perturbations. This allows us to construct unique force-balanced solutions that determine the change in contact forces as a response to external stress. By mapping this response to diffusion in the underlying contact network, we show that this naturally leads to spatial localization of forces. We present numerical evidence for stress localization using exact diagonalization studies of network Laplacians associated with soft disk packings. We use this formalism to characterize the deviation from elastic behaviour as the amount of disorder in the underlying network is varied. We discuss generalizations to systems with large friction between grains and other networks that display topological disorder. This work has been supported by NSF-DMR 1409093 and the W. M. Keck Foundation.

Quasi-Dual-Packed-Kerneled Au49 (2,4-DMBT)27 Nanoclusters and the Influence of Kernel Packing on the Electrochemical Gap.

PubMed

Liao, Lingwen; Zhuang, Shengli; Wang, Pu; Xu, Yanan; Yan, Nan; Dong, Hongwei; Wang, Chengming; Zhao, Yan; Xia, Nan; Li, Jin; Deng, Haiteng; Pei, Yong; Tian, Shi-Kai; Wu, Zhikun

2017-10-02

Although face-centered cubic (fcc), body-centered cubic (bcc), hexagonal close-packed (hcp), and other structured gold nanoclusters have been reported, it was unclear whether gold nanoclusters with mix-packed (fcc and non-fcc) kernels exist, and the correlation between kernel packing and the properties of gold nanoclusters is unknown. A Au 49 (2,4-DMBT) 27 nanocluster with a shell electron count of 22 has now been been synthesized and structurally resolved by single-crystal X-ray crystallography, which revealed that Au 49 (2,4-DMBT) 27 contains a unique Au 34 kernel consisting of one quasi-fcc-structured Au 21 and one non-fcc-structured Au 13 unit (where 2,4-DMBTH=2,4-dimethylbenzenethiol). Further experiments revealed that the kernel packing greatly influences the electrochemical gap (EG) and the fcc structure has a larger EG than the investigated non-fcc structure. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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. © 2014 Wiley Periodicals, Inc.

A Constant-Force Resistive Exercise Unit

NASA Technical Reports Server (NTRS)

Colosky, Paul; Ruttley, Tara

2010-01-01

A constant-force resistive exercise unit (CFREU) has been invented for use in both normal gravitational and microgravitational environments. In comparison with a typical conventional exercise machine, this CFREU weighs less and is less bulky: Whereas weight plates and associated bulky supporting structures are used to generate resistive forces in typical conventional exercise machines, they are not used in this CFREU. Instead, resistive forces are generated in this CFREU by relatively compact, lightweight mechanisms based on constant-torque springs wound on drums. Each such mechanism is contained in a module, denoted a resistive pack, that includes a shaft for making a torque connection to a cable drum. During a stroke of resistive exercise, the cable is withdrawn from the cable drum against the torque exerted by the resistance pack. The CFREU includes a housing, within which can be mounted one or more resistive pack(s). The CFREU also includes mechanisms for engaging any combination of (1) one or more resistive pack(s) and (2) one or more spring(s) within each resistive pack to obtain a desired level of resistance.

Pore configuration landscape of granular crystallization.

PubMed

Saadatfar, M; Takeuchi, H; Robins, V; Francois, N; Hiraoka, Y

2017-05-12

Uncovering grain-scale mechanisms that underlie the disorder-order transition in assemblies of dissipative, athermal particles is a fundamental problem with technological relevance. To date, the study of granular crystallization has mainly focussed on the symmetry of crystalline patterns while their emergence and growth from irregular clusters of grains remains largely unexplored. Here crystallization of three-dimensional packings of frictional spheres is studied at the grain-scale using X-ray tomography and persistent homology. The latter produces a map of the topological configurations of grains within static partially crystallized packings. Using numerical simulations, we show that similar maps are measured dynamically during the melting of a perfect crystal. This map encodes new information on the formation process of tetrahedral and octahedral pores, the building blocks of perfect crystals. Four key formation mechanisms of these pores reproduce the main changes of the map during crystallization and provide continuous deformation pathways representative of the crystallization dynamics.

Pore configuration landscape of granular crystallization

PubMed Central

Saadatfar, M.; Takeuchi, H.; Robins, V.; Francois, N.; Hiraoka, Y.

2017-01-01

Uncovering grain-scale mechanisms that underlie the disorder–order transition in assemblies of dissipative, athermal particles is a fundamental problem with technological relevance. To date, the study of granular crystallization has mainly focussed on the symmetry of crystalline patterns while their emergence and growth from irregular clusters of grains remains largely unexplored. Here crystallization of three-dimensional packings of frictional spheres is studied at the grain-scale using X-ray tomography and persistent homology. The latter produces a map of the topological configurations of grains within static partially crystallized packings. Using numerical simulations, we show that similar maps are measured dynamically during the melting of a perfect crystal. This map encodes new information on the formation process of tetrahedral and octahedral pores, the building blocks of perfect crystals. Four key formation mechanisms of these pores reproduce the main changes of the map during crystallization and provide continuous deformation pathways representative of the crystallization dynamics. PMID:28497794

Pore configuration landscape of granular crystallization

NASA Astrophysics Data System (ADS)

Saadatfar, M.; Takeuchi, H.; Robins, V.; Francois, N.; Hiraoka, Y.

2017-05-01

Uncovering grain-scale mechanisms that underlie the disorder-order transition in assemblies of dissipative, athermal particles is a fundamental problem with technological relevance. To date, the study of granular crystallization has mainly focussed on the symmetry of crystalline patterns while their emergence and growth from irregular clusters of grains remains largely unexplored. Here crystallization of three-dimensional packings of frictional spheres is studied at the grain-scale using X-ray tomography and persistent homology. The latter produces a map of the topological configurations of grains within static partially crystallized packings. Using numerical simulations, we show that similar maps are measured dynamically during the melting of a perfect crystal. This map encodes new information on the formation process of tetrahedral and octahedral pores, the building blocks of perfect crystals. Four key formation mechanisms of these pores reproduce the main changes of the map during crystallization and provide continuous deformation pathways representative of the crystallization dynamics.

Crystallization of dienelactone hydrolase in two space groups: structural changes caused by crystal packing

PubMed Central

Porter, Joanne L.; Carr, Paul D.; Collyer, Charles A.; Ollis, David L.

2014-01-01

Dienelactone hydrolase (DLH) is a monomeric protein with a simple α/β-hydrolase fold structure. It readily crystallizes in space group P212121 from either a phosphate or ammonium sulfate precipitation buffer. Here, the structure of DLH at 1.85 Å resolution crystallized in space group C2 with two molecules in the asymmetric unit is reported. When crystallized in space group P212121 DLH has either phosphates or sulfates bound to the protein in crucial locations, one of which is located in the active site, preventing substrate/inhibitor binding. Another is located on the surface of the enzyme coordinated by side chains from two different molecules. Crystallization in space group C2 from a sodium citrate buffer results in new crystallographic protein–protein interfaces. The protein backbone is highly similar, but new crystal contacts cause changes in side-chain orientations and in loop positioning. In regions not involved in crystal contacts, there is little change in backbone or side-chain configuration. The flexibility of surface loops and the adaptability of side chains are important factors enabling DLH to adapt and form different crystal lattices. PMID:25005082

Exploring the folding pattern of a polymer chain in a single crystal by combining single-molecule force spectroscopy and steered molecular dynamics simulations.

PubMed

Song, Yu; Feng, Wei; Liu, Kai; Yang, Peng; Zhang, Wenke; Zhang, Xi

2013-03-26

Understanding the folding pattern of a single polymer chain within its single crystal will shed light on the mechanism of crystallization. Here, we use the combined techniques of atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) and steered molecular dynamics (SMD) simulations to study the folding pattern of a polyethylene oxide (PEO) chain in its single crystal. Our results show that the folding pattern of a PEO chain in the crystal formed in dilute solution follows the adjacent re-entry folding model. While in the crystal obtained from the melt, the nonadjacent folding with large and irregular loops contributes to big force fluctuations in the force-extension curves. The method established here can offer a novel strategy to directly unravel the chain-folding pattern of polymer single crystals at single-molecule level.

Icosahedral and decagonal quasicrystals of intermetallic compounds are multiple twins of cubic or orthorhombic crystals composed of very large atomic complexes with icosahedral point-group symmetry in cubic close packing or body-centered packing: Structure of decagonal Al6Pd

PubMed Central

Pauling, Linus

1989-01-01

A doubly icosahedral complex involves roughly spherical clusters of atoms with icosahedral point-group symmetry, which are themselves, in parallel orientation, icosahedrally packed. These complexes may form cubic crystallites; three structures of this sort have been identified. Analysis of electron diffraction photographs of the decagonal quasicrystal Al6Pd has led to its description as involving pentagonal twinning of an orthorhombic crystal with a = 51.6 Å, b = 37.6 Å, and c = 33.24 Å, with about 4202 atoms in the unit, comprising two 1980-atom doubly icosahedral complexes, each involving icosahedral packing of 45 44-atom icosahedral complexes (at 0 0 0 and 1/2 1/2 1/2) and 242 interstitial atoms. The complexes and clusters are oriented with one of their fivefold axes in the c-axis direction. Images PMID:16594092

Icosahedral and decagonal quasicrystals of intermetallic compounds are multiple twins of cubic or orthorhombic crystals composed of very large atomic complexes with icosahedral point-group symmetry in cubic close packing or body-centered packing: Structure of decagonal Al(6)Pd.

PubMed

Pauling, L

1989-12-01

A doubly icosahedral complex involves roughly spherical clusters of atoms with icosahedral point-group symmetry, which are themselves, in parallel orientation, icosahedrally packed. These complexes may form cubic crystallites; three structures of this sort have been identified. Analysis of electron diffraction photographs of the decagonal quasicrystal Al(6)Pd has led to its description as involving pentagonal twinning of an orthorhombic crystal with a = 51.6 A, b = 37.6 A, and c = 33.24 A, with about 4202 atoms in the unit, comprising two 1980-atom doubly icosahedral complexes, each involving icosahedral packing of 45 44-atom icosahedral complexes (at 0 0 0 and 1/2 1/2 1/2) and 242 interstitial atoms. The complexes and clusters are oriented with one of their fivefold axes in the c-axis direction.

Manipulating Light and Matter with Photonic Structures: Numerical Investigations on Photonic Crystals and Optical Forces

NASA Astrophysics Data System (ADS)

Zhang, Peng

The highly developed nano-fabrication techniques allow light to be modulated with photonic structures in a more intensive way. These photonic structures involve photonic crystals, metals supporting surface plasmon polaritons, metamaterials, etc. In this thesis work, three different ways for light manipulation are numerically investigated. First, the light propagation is modulated using a photonic crystal with Dirac cones. It is demonstrated that the zero-index behavior of this photonic crystal which happens for normal incident waves, is lost at oblique incidence. A new method combining complex-k band calculations and absorbing boundary conditions for Bloch modes is developed to analyze the Bloch mode interaction in details. Second, the mechanic states of graphene are modulated through the optical gradient force. This force is induced by the coupled surface plasmons on the double graphene sheets and is greatly enhanced in comparison to the regular waveguides. By applying different strengths of forces in accordance to the input power, the mechanic state transition is made possible, accompanied by an abrupt change in the transmission and reflection spectra. Third, the helicity/chirality of light is studied to modulate the lateral force on a small particle. A left-hand material slab which supports coherent TE ad TM plasmons simultaneously is introduced. By mixing the TE and TM surface plasmons with different relative phases, the lateral force on a chiral particle can be changed, which will be beneficial for chiral particle sorting.

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).

Cooperative Effects in Closely Packed Quantum Emitters with Collective Dephasing

NASA Astrophysics Data System (ADS)

Prasanna Venkatesh, B.; Juan, M. L.; Romero-Isart, O.

2018-01-01

In a closely packed ensemble of quantum emitters, cooperative effects are typically suppressed due to the dephasing induced by the dipole-dipole interactions. Here, we show that by adding sufficiently strong collective dephasing, cooperative effects can be restored. Specifically, we show that the dipole force on a closely packed ensemble of strongly driven two-level quantum emitters, which collectively dephase, is enhanced in comparison to the dipole force on an independent noninteracting ensemble. Our results are relevant to solid-state systems with embedded quantum emitters such as color centers in diamond and superconducting qubits in microwave cavities and waveguides.

Close packing effects on clean and dirty snow albedo and associated climatic implications

NASA Astrophysics Data System (ADS)

He, C.; Liou, K. N.; Takano, Y.

2017-12-01

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.

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.

Molecular packing in virus crystals: geometry, chemistry, and biology.

PubMed

Natarajan, P; Johnson, J E

1998-01-01

An automated procedure was developed to determine the geometrical and chemical interactions of crystalline virus particles using the crystal parameters, particle position, orientation, and atomic coordinates for an icosahedral asymmetric unit. Two applications of the program are reported: (1) An analysis of a novel pseudo-rhombohedral (R32) symmetry present in the monoclinic crystal lattices of both Nodamura Virus (NOV) and Coxsackie virus B3 (CVB3). The study shows that in both cases the interactions between particles is substantially increased by minor deviations from exact R32 symmetry and that only particles with the proper ratio of dimensions along twofold and fivefold symmetry axes (such as southern bean mosaic virus) can achieve comparable buried surface area in the true R32 space group. (2) An attempt was made to correlate biological function with remarkably conserved interparticle contact regions found in different crystal forms of three members of the nodavirus family, NOV, Flock House Virus (FHV), and Black Beetle Virus (BBV). Mutational evidence implicates the quasi-threefold region on the viral surface in receptor binding in nodaviruses and this region is dominant in particle contacts in all three virus crystals. Examination of particle contacts in numerous crystal structures of viruses in the picornavirus super-family showed that portions of the capsid surface known to interact with a receptor or serve as an epitope for monoclonal antibodies frequently stabilize crystal contacts.

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.

USDC based rapid penetrator of packed soil

NASA Technical Reports Server (NTRS)

Bao, Xiaoqi; Bar-Cohen, Yoseph; Chang, Zensheu; Sherrit, Stewart; Badescu, Mircea

2006-01-01

Environment protection requires more testing and analysis tools. To detect buried chemical containers or other objects embedded in soil and avoid possible damages of them, a penetrator of packed soil operated using low pushing force was developed. The design was based on a novel driving mechanism of the ultrasonic/sonic driller/corer (USDC) device developed in the NDEAA lab at JPL [Bar-Cohen et al 2001, Bao et al 2003]. In the penetrator, a small free-flying mass is energized by a piezoelectric transducer and impacts a rod probe on its shoulder at frequencies of hundreds times per second. The impacts help the probe to penetrate the packed soil rapidly. A great reduction of the needed pushing force for penetration was achieved. The details of the design of the prototype penetrator and the results of performance tests are presented.

Traceable atomic force microscopy of high-quality solvent-free crystals of [6,6]-phenyl-C61-butyric acid methyl ester

NASA Astrophysics Data System (ADS)

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

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.

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

Langevin dynamics simulations of genome packing in bacteriophage.

PubMed

Forrey, Christopher; Muthukumar, M

2006-07-01

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.

Biogenic twinned crystals exhibiting unique morphological symmetry

NASA Astrophysics Data System (ADS)

Hirsch, Anna; Gur, Dvir; Palmer, Ben; Addadi, Lia; Leiserowitz, Leslie; Kronik, Leeor

Guanine crystals are widely used in nature as components of multilayer reflectors. Organisms control the size, morphology, and arrangement of these crystals, to obtain a variety of optical ''devices''. The reflection systems found in the lens of the scallop eye and in the copepod cuticle are unique in that the multilayered reflectors are tiled together to form a contiguous packed array. In the former, square crystals are tiled to form a reflecting mirror. In the latter, hexagonal crystals are closely packed to produce brilliant colors. Based on electron diffraction, morphology considerations, and density functional theory, these crystals were shown to possess similar monoclinic crystal symmetry, which we have previously identified as different from that of synthetic anhydrous guanine. However, the crystals are different in that multiple twinning about the {012} and the {011} crystallographic planes results in square and hexagonal morphology, respectively. This is a unique example where controlled twinning is used as a strategy to form a morphology with higher symmetry than that of the underlying crystal, allowing for tilling that facilitates optical functionality.

Fluorescence Approaches to Growing Macromolecule Crystals

NASA Technical Reports Server (NTRS)

Pusey, Marc; Forsythe, Elizabeth; Achari, Aniruddha

2006-01-01

Trace fluorescent labeling, typically < 1%, can be a powerful aid in macromolecule crystallization. Precipitation concentrates a solute, and crystals are the most densely packed solid form. The more densely packed the fluorescing material, the more brightly the emission from it, and thus fluorescence intensity of a solid phase is a good indication of whether one has crystals or not. The more brightly fluorescing crystalline phase is easily distinguishable, even when embedded in an amorphous precipitate. This approach conveys several distinct advantages: one can see what the protein is doing in response to the imposed conditions, and distinguishing between amorphous and microcrystalline precipitated phases are considerably simpler. The higher fluorescence intensity of the crystalline phase led us to test if we could derive crystallization conditions from screen outcomes which had no obvious crystalline material, but simply "bright spots" in the precipitated phase. Preliminary results show that the presence of these bright spots, not observable under white light, is indeed a good indicator of potential crystallization conditions.

Mechanochemical Synthesis of Carbon Nanothread Single Crystals.

PubMed

Li, Xiang; Baldini, Maria; Wang, Tao; Chen, Bo; Xu, En-Shi; Vermilyea, Brian; Crespi, Vincent H; Hoffmann, Roald; Molaison, Jamie J; Tulk, Christopher A; Guthrie, Malcolm; Sinogeikin, Stanislav; Badding, John V

2017-11-15

Synthesis of well-ordered reduced dimensional carbon solids with extended bonding remains a challenge. For example, few single-crystal organic monomers react under topochemical control to produce single-crystal extended solids. We report a mechanochemical synthesis in which slow compression at room temperature under uniaxial stress can convert polycrystalline or single-crystal benzene monomer into single-crystalline packings of carbon nanothreads, a one-dimensional sp 3 carbon nanomaterial. The long-range order over hundreds of microns of these crystals allows them to readily exfoliate into fibers. The mechanochemical reaction produces macroscopic single crystals despite large dimensional changes caused by the formation of multiple strong, covalent C-C bonds to each monomer and a lack of reactant single-crystal order. Therefore, it appears not to follow a topochemical pathway, but rather one guided by uniaxial stress, to which the nanothreads consistently align. Slow-compression room-temperature synthesis may allow diverse molecular monomers to form single-crystalline packings of polymers, threads, and higher dimensional carbon networks.

DHS Internship Summary-Crystal Assembly at Different Length Scales

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mishchenko, L

2009-08-06

Table 1. 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.« less

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.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Agarkar, Vinod B.; Kimani, Serah W.; Cowan, Donald A.

2006-12-01

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

Surface force and vibrational spectroscopic analyses of interfacial water molecules in the vicinity of methoxy-tri(ethylene glycol)-terminated monolayers: mechanisms underlying the effect of lateral packing density on bioinertness.

PubMed

Sekine, Taito; Asatyas, Syifa; Sato, Chikako; Morita, Shigeaki; Tanaka, Masaru; Hayashi, Tomohiro

Unequivocal dependence of bioinertness of self-assembled monolayers of methoxy-tri(ethylene glycol)-terminated alkanethiol (EG3-OMe SAMs) on their packing density has been a mystery for more than two decades. We tackled this long-standing question by performing surface force and surface-enhanced infrared absorption (SEIRA) spectroscopic measurements. Our surface force measurements revealed a physical barrier of interfacial water in the vicinity of the Au-supported EG3-OMe SAM (low packing density), whereas the Ag-supported one (high packing density) did not possess such interfacial water. In addition, the results of SEIRA measurements clearly exhibited that hydrogen bonding states of the interfacial water differ depending on the substrates. We also characterized the bioinertness of these SAMs by protein adsorption tests and adhesion assays of platelet and human umbilical vein endothelial cells. The hydrogen bonding states of the interfacial water and water-induced interaction clearly correlated with the bioinertness of the SAMs, suggesting that the interfacial water plays an important role determining the interaction of the SAMs with biomolecules and cells.

Can Csbnd H⋯Fsbnd C hydrogen bonds alter crystal packing features in the presence of Nsbnd H⋯Odbnd C hydrogen bond?

NASA Astrophysics Data System (ADS)

Yadav, Hare Ram; Choudhury, Angshuman Roy

2017-12-01

Intermolecular interactions involving organic fluorine have been the contemporary field of research in the area of organic solid state chemistry. While a group of researchers had refuted the importance of "organic fluorine" in guiding crystal structures, others have provided evidences for in favor of fluorine mediated interactions in the solid state. Many systematic studies have indicated that the "organic fluorine" is capable of offering weak hydrogen bonds through various supramolecular synthons, mostly in the absence of other stronger hydrogen bonds. Analysis of fluorine mediated interaction in the presence of strong hydrogen bonds has not been highlighted in detail. Hence a thorough structural investigation is needed to understand the role of "organic fluorine" in crystal engineering of small organic fluorinated molecules having the possibility of strong hydrogen bond formation in the solution and in the solid state. To fulfil this aim, we have synthesized a series of fluorinated amides using 3-methoxyphenylacetic acid and fluorinated anilines and studied their structural properties through single crystal and powder X-ray diffraction methods. Our results indicated that the "organic fluorine" plays a significant role in altering the packing characteristics of the molecule in building specific crystal lattices even in the presence of strong hydrogen bond.

Surface force analysis of glycine adsorption on different crystal surfaces of titanium dioxide (TiO2).

PubMed

Ganbaatar, Narangerel; Imai, Kanae; Yano, Taka-Aki; Hara, Masahiko

2017-01-01

Surface force analysis with atomic force microscope (AFM) in which a single amino acid residue was mounted on the tip apex of AFM probe was carried out for the first time at the molecular level on titanium dioxide (TiO 2 ) as a representative mineral surface for prebiotic chemical evolution reactions. The force analyses on surfaces with three different crystal orientations revealed that the TiO 2 (110) surface has unique characteristics for adsorbing glycine molecules showing different features compared to those on TiO 2 (001) and (100). To examine this difference, we investigated thermal desorption spectroscopy (TDS) and the interaction between the PEG cross-linker and the three TiO 2 surfaces. Our data suggest that the different single crystal surfaces would provide different chemical evolution field for amino acid molecules.

Epitaxial growth of ordered and disordered granular sphere packings

NASA Astrophysics Data System (ADS)

Panaitescu, Andreea; Kudrolli, Arshad

2014-09-01

We demonstrate that epitaxy can be used to obtain a wide range of ordered to disordered granular packings by simply changing the deposition flux. We show that a defect-free face-centered-cubic (fcc) monocrystal can be obtained by depositing athermal granular spheres randomly into a container with a templated surface in a gravitational field without direct manipulation. This packing corresponds to the maximum sphere packing fraction and is obtained when the substrate is templated corresponding to the (100) plane of a fcc crystal and the container side is an integer multiple of the sphere diameter. We find that the maximum sphere packing is obtained when the deposited grains come to rest, one at a time, without damaging the substrate. A transition to a disordered packing is observed when the flux is increased. Using micro x-ray computed tomography, we find that defects nucleate at the boundaries of the container in which the packing is grown as grains cooperatively come to rest above their local potential minimum. This leads to a transition from ordered to disordered loose packings that grow in the form of an inverted cone, with the apex located at the defect nucleation site. We capture the observed decrease in order using a minimal model in which a defect leads to growth of further defects in the neighboring sites in the layer above with a probability that increases with the deposition flux.

Epitaxial growth of ordered and disordered granular sphere packings.

PubMed

Panaitescu, Andreea; Kudrolli, Arshad

2014-09-01

We demonstrate that epitaxy can be used to obtain a wide range of ordered to disordered granular packings by simply changing the deposition flux. We show that a defect-free face-centered-cubic (fcc) monocrystal can be obtained by depositing athermal granular spheres randomly into a container with a templated surface in a gravitational field without direct manipulation. This packing corresponds to the maximum sphere packing fraction and is obtained when the substrate is templated corresponding to the (100) plane of a fcc crystal and the container side is an integer multiple of the sphere diameter. We find that the maximum sphere packing is obtained when the deposited grains come to rest, one at a time, without damaging the substrate. A transition to a disordered packing is observed when the flux is increased. Using micro x-ray computed tomography, we find that defects nucleate at the boundaries of the container in which the packing is grown as grains cooperatively come to rest above their local potential minimum. This leads to a transition from ordered to disordered loose packings that grow in the form of an inverted cone, with the apex located at the defect nucleation site. We capture the observed decrease in order using a minimal model in which a defect leads to growth of further defects in the neighboring sites in the layer above with a probability that increases with the deposition flux.

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.

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 [Br 2 C 6 H 2 (OC n H 2n + 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.

The Use of Atomic-Force Microscopy for Studying the Crystallization Process of Amorphous Alloys

NASA Astrophysics Data System (ADS)

Elmanov, G. N.; Ivanitskaya, E. A.; Dzhumaev, P. S.; Skrytniy, V. I.

The crystallization process of amorphous alloys is accompanied by the volume changes as a result of structural phase transitions. This leads to changes in the surface topography, which was studied by atomic force microscopy (AFM). The changes of the surface topography, structure and phase composition during multistage crystallization process of the metallic glasses with composition Ni71,5Cr6,8Fe2,7B11,9Si7,1 and Ni63,4Cr7,4Fe4,3Mn0,8B15,6Si8,5 (AWS BNi2) has been investigated. The obtained results on changing of the surface topography in crystallization process are in good agreement with the data of X-ray diffraction analysis (XRD). The nature of redistribution of some alloy components in the crystallization process has been suggested.

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

2017-06-01

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. Copyright © 2017 Elsevier Inc. All rights reserved.

The influence of crystal habit on the prediction of dry powder inhalation formulation performance using the cohesive-adhesive force balance approach.

PubMed

Hooton, Jennifer C; Jones, Matthew D; Harris, Haggis; Shur, Jagdeep; Price, Robert

2008-09-01

The aim of this investigation was to study the influence of crystalline habit of active pharmaceutical ingredients on the cohesive-adhesive force balance within model dry powder inhaler (DPI) formulations and the corresponding affect on DPI formulation performance. The cohesive-adhesive balance (CAB) approach to colloid probe atomic force microscopy (AFM) was employed to determine the cohesive and adhesive interactions of micronized budesonide particles against the {102} and {002} faces of budesonide single crystals and crystalline substrates of different sugars (cyclodextrin, lactose, trehalose, raffinose, and xylitol), respectively. These data were used to measure the relative level of cohesion and adhesion via CAB and the possible influence on in vitro performance of a carrier-based DPI formulation. Varying the crystal habit of the drug had a significant effect on the cohesive measurement of micronized budesonide probes, with the cohesive values on the {102} faces being approximately twice that on the {002} crystal faces. However, although different CAB values were measured with the sugars with respect to the crystal faces chosen for the cohesive-based measurement, the overall influence on the rank order of the CAB values was not directly influenced. For these data sets, the CAB gradient indicated that a decrease in the dominance of the adhesive forces led to a concomitant increase in fine particle delivery, reaching a plateau as the cohesive forces became dominant. The study suggested that crystal habit of the primary drug crystals influences the cohesive interactions and the resulting force balance measurements of colloid probe CAB analysis.

vGNM: a better model for understanding the dynamics of proteins in crystals.

PubMed

Song, Guang; Jernigan, Robert L

2007-06-08

The dynamics of proteins are important for understanding their functions. In recent years, the simple coarse-grained Gaussian Network Model (GNM) has been fairly successful in interpreting crystallographic B-factors. However, the model clearly ignores the contribution of the rigid body motions and the effect of crystal packing. The model cannot explain the fact that the same protein may have significantly different B-factors under different crystal packing conditions. In this work, we propose a new GNM, called vGNM, which takes into account both the contribution of the rigid body motions and the effect of crystal packing, by allowing the amplitude of the internal modes to be variables. It hypothesizes that the effect of crystal packing should cause some modes to be amplified and others to become less important. In doing so, vGNM is able to resolve the apparent discrepancy in experimental B-factors among structures of the same protein but with different crystal packing conditions, which GNM cannot explain. With a small number of parameters, vGNM is able to reproduce experimental B-factors for a large set of proteins with significantly better correlations (having a mean value of 0.81 as compared to 0.59 by GNM). The results of applying vGNM also show that the rigid body motions account for nearly 60% of the total fluctuations, in good agreement with previous findings.

Tribochemical wear of single crystal aluminum in NaCl solution studied by atomic force microscopy

NASA Astrophysics Data System (ADS)

Cai, M.; Langford, S. C.; Dickinson, J. T.

2011-09-01

We report a systematic study of chemically enhanced wear of single crystal aluminum surfaces in aqueous solutions using an environmentally equipped atomic force microscope (AFM). The experiments were conducted by using a standard Si3N4 AFM tip to apply a localized force on a polished, single crystal aluminum (110) surface. Most measurements were performed in 0.5 M NaCl solution. We show the effect of applied force, number of scans, chemical solution, and temperature on the chemical-mechanical wear of aluminum on the nanometer scale. Aggressive chemical environments significantly enhance the wear of aluminum relative to scanning in dry air. Quantitative measurements show that the wear volume increases in proportion to the square root of force and the number of scans (or time). Arrhenius plots of wear volume versus temperature are consistent with an activation energy of 31 kJ/mol for scanning in 0.5 M NaCl. The wear of the AFM tip and the aluminum substrate is explained in terms of the synergistic surface chemical reactions and mechanical action of the tip. We compare these results to previous studies of AFM wear of silicate glass.

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…

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lazzerini, Giovanni Mattia; Yacoot, Andrew; Paternò, Giuseppe Maria

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 surfacemore » 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.« less

Crystal structure of simple metals at high pressures

NASA Astrophysics Data System (ADS)

Degtyareva, Olga

2010-09-01

The effects of pressure on the crystal structure of simple (or sp-) elements are analysed in terms of changes in coordination number, packing density, and interatomic distances, and general rules are established. In the polyvalent elements from groups 14-17, the covalently bonded structures tend to transform to metallic phases with a gradual increase in coordination number and packing density, a behaviour normally expected under pressure. Group 1 and 2 metallic elements, however, show a reverse trend towards structures with low packing density due to intricate changes in their electronic structure. Complex crystal structures such as host-guest and incommensurately modulated structures found in these elements are given special attention in this review in an attempt to determine their role in the observed phase-transition sequences.

The crystal chemistry of inorganic metal borohydrides and their relation to metal oxides.

PubMed

Černý, Radovan; Schouwink, Pascal

2015-12-01

The crystal structures of inorganic homoleptic metal borohydrides are analysed with respect to their structural prototypes found amongst metal oxides in the inorganic databases such as Pearson's Crystal Data [Villars & Cenzual (2015). Pearson's Crystal Data. Crystal Structure Database for Inorganic Compounds, Release 2014/2015, ASM International, Materials Park, Ohio, USA]. The coordination polyhedra around the cations and the borohydride anion are determined, and constitute the basis of the structural systematics underlying metal borohydride chemistry in various frameworks and variants of ionic packing, including complex anions and the packing of neutral molecules in the crystal. Underlying nets are determined by topology analysis using the program TOPOS [Blatov (2006). IUCr CompComm. Newsl. 7, 4-38]. It is found that the Pauling rules for ionic crystals apply to all non-molecular borohydride crystal structures, and that the latter can often be derived by simple deformation of the close-packed anionic lattices c.c.p. and h.c.p., by partially removing anions and filling tetrahedral or octahedral sites. The deviation from an ideal close packing is facilitated in metal borohydrides with respect to the oxide due to geometrical and electronic considerations of the BH4(-) anion (tetrahedral shape, polarizability). This review on crystal chemistry of borohydrides and their similarity to oxides is a contribution which should serve materials engineers as a roadmap to design new materials, synthetic chemists in their search for promising compounds to be prepared, and materials scientists in understanding the properties of novel materials.

On Retaining the Seat Pack After Ejection when Landing in Trees

DTIC Science & Technology

2010-11-01

défense Canada – CARO; Novembre 2010. Introduction : la formation actuelle des membres de la force aérienne prévoit que les membres d’équipage qui...pack status on tree landing injuries ...................................................... 13 3.3.1 Causal relationships between seat pack status and...tree landing injuries....... 13 3.3.2 Significance of tree landing injury severity distributions ............................. 14 3.4 Discussion

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 water

Crystallization, structure and dynamics of the proton-translocating P-type ATPase.

PubMed

Scarborough, G A

2000-01-01

Large single three-dimensional crystals of the dodecylmaltoside complex of the Neurospora crassa plasma membrane H(+)-ATPase (H(+) P-ATPase) can be grown in polyethylene-glycol-containing solutions optimized for moderate supersaturation of both the protein surfaces and detergent micellar region. Large two-dimensional H(+) P-ATPase crystals also grow on the surface of such mixtures and on carbon films located at such surfaces. Electron crystallographic analysis of the two-dimensional crystals grown on carbon films has recently elucidated the structure of the H(+) P-ATPase at a resolution of 0.8 nm in the membrane plane. The two-dimensional crystals comprise two offset layers of ring-shaped ATPase hexamers with their exocytoplasmic surfaces face to face. Side-to-side interactions between the cytoplasmic regions of the hexamers in each layer can be seen, and an interaction between identical exocytoplasmic loops in opposing hexamer layers holds the two layers together. Detergent rings around the membrane-embedded region of the hexamers are clearly visible, and detergent-detergent interactions between the rings are also apparent. The crystal packing forces thus comprise both protein-protein and detergent-detergent interactions, supporting the validity of the original crystallization strategy. Ten transmembrane helices in each ATPase monomer are well-defined in the structure map. They are all relatively straight, closely packed, moderately tilted at various angles with respect to a plane normal to the membrane surface and average approximately 3.5 nm in length. The transmembrane helix region is connected in at least three places to the larger cytoplasmic region, which comprises several discrete domains separated by relatively wide, deep clefts. Previous work has shown that the H(+) P-ATPase undergoes substantial conformational changes during its catalytic cycle that are not changes in secondary structure. Importantly, the results of hydrogen/deuterium exchange

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.

Standard atomic volumes in double-stranded DNA and packing in protein–DNA interfaces

PubMed Central

Nadassy, Katalin; Tomás-Oliveira, Isabel; Alberts, Ian; Janin, Joël; Wodak, Shoshana J.

2001-01-01

Standard volumes for atoms in double-stranded B-DNA are derived using high resolution crystal structures from the Nucleic Acid Database (NDB) and compared with corresponding values derived from crystal structures of small organic compounds in the Cambridge Structural Database (CSD). Two different methods are used to compute these volumes: the classical Voronoi method, which does not depend on the size of atoms, and the related Radical Planes method which does. Results show that atomic groups buried in the interior of double-stranded DNA are, on average, more tightly packed than in related small molecules in the CSD. The packing efficiency of DNA atoms at the interfaces of 25 high resolution protein–DNA complexes is determined by computing the ratios between the volumes of interfacial DNA atoms and the corresponding standard volumes. These ratios are found to be close to unity, indicating that the DNA atoms at protein–DNA interfaces are as closely packed as in crystals of B-DNA. Analogous volume ratios, computed for buried protein atoms, are also near unity, confirming our earlier conclusions that the packing efficiency of these atoms is similar to that in the protein interior. In addition, we examine the number, volume and solvent occupation of cavities located at the protein–DNA interfaces and compared them with those in the protein interior. Cavities are found to be ubiquitous in the interfaces as well as inside the protein moieties. The frequency of solvent occupation of cavities is however higher in the interfaces, indicating that those are more hydrated than protein interiors. Lastly, we compare our results with those obtained using two different measures of shape complementarity of the analysed interfaces, and find that the correlation between our volume ratios and these measures, as well as between the measures themselves, is weak. Our results indicate that a tightly packed environment made up of DNA, protein and solvent atoms plays a significant role

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.

Second harmonic generation efficiency affected by radiation force of a high-energy laser beam through stress within a mounted potassium dihydrogen phosphate crystal

NASA Astrophysics Data System (ADS)

Su, Ruifeng; Zhu, Mingzhi; Huang, Zhan; Wang, Baoxu; Wu, Wenkai

2018-01-01

Influence of radiation force of a high-energy laser beam on the second harmonic generation (SHG) efficiency through stress within a mounted potassium dihydrogen phosphate (KDP) crystal is studied, as well as an active method of improving the SHG efficiency by controlling the stress is proposed. At first, the model for studying the influence of the radiation force on the SHG efficiency is established, where the radiation force is theoretically analyzed, the stress caused by the radiation force is theoretically analyzed and numerically calculated using the finite-element method, and the influence of the stress on the SHG efficiency is theoretically analyzed. Then, a method of improving the SHG efficiency by controlling the stress through adjusting the structural parameters of the mounting set of the KDP crystal is examined. It demonstrates that the radiation force causes stress within the KDP crystal and further militates against the SHG efficiency; however, the SHG efficiency could be improved by controlling the stress through adjusting the structural parameters of the mounting set of the KDP crystal.

Conformational flexibility and packing plausibility of repaglinide polymorphs

NASA Astrophysics Data System (ADS)

Rani, Dimpy; Goyal, Parnika; Chadha, Renu

2018-04-01

The present manuscript highlights the structural insight into the repaglinide polymorphs. The experimental screening for the possible crystal forms were carried out using various solvents, which generated three forms. The crystal structure of Form II and III was determined using PXRD pattern whereas structural analysis of Form I has already been reported. Form I, II and II was found to exist in P212121, PNA21 and P21/c space groups respectively. Conformational analysis was performed to account the conformational flexibility of RPG. The obtained conformers were further utilized to obtain the information about the crystal packing pattern of RPG polymorphs by polymorph prediction module. The lattice energy landscape, depicting the relationship between lattice energy and density of the polymorphs has been obtained for various possible polymorphs. The experimentally isolated polymorphs were successfully fitted into lattice energy landscape.

On crystal versus fiber formation in dipeptide hydrogelator systems.

PubMed

Houton, Kelly A; Morris, Kyle L; Chen, Lin; Schmidtmann, Marc; Jones, James T A; Serpell, Louise C; Lloyd, Gareth O; Adams, Dave J

2012-06-26

Naphthalene dipeptides have been shown to be useful low-molecular-weight gelators. Here we have used a library to explore the relationship between the dipeptide sequence and the hydrogelation efficiency. A number of the naphthalene dipeptides are crystallizable from water, enabling us to investigate the comparison between the gel/fiber phase and the crystal phase. We succeeded in crystallizing one example directly from the gel phase. Using X-ray crystallography, molecular modeling, and X-ray fiber diffraction, we show that the molecular packing of this crystal structure differs from the structure of the gel/fiber phase. Although the crystal structures may provide important insights into stabilizing interactions, our analysis indicates a rearrangement of structural packing within the fibers. These observations are consistent with the fibrillar interactions and interatomic separations promoting 1D assembly whereas in the crystals the peptides are aligned along multiple axes, allowing 3D growth. This observation has an impact on the use of crystal structures to determine supramolecular synthons for gelators.

Crystal structure of simple metals at high pressures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Degtyareva, Olga

2010-10-22

The effects of pressure on the crystal structure of simple (or sp-) elements are analysed in terms of changes in coordination number, packing density, and interatomic distances, and general rules are established. In the polyvalent elements from groups 14-17, the covalently bonded structures tend to transform to metallic phases with a gradual increase in coordination number and packing density, a behaviour normally expected under pressure. Group 1 and 2 metallic elements, however, show a reverse trend towards structures with low packing density due to intricate changes in their electronic structure. Complex crystal structures such as host-guest and incommensurately modulated structuresmore » found in these elements are given special attention in this review in an attempt to determine their role in the observed phase-transition sequences.« less

Protein crystal growth

NASA Technical Reports Server (NTRS)

2001-01-01

Atomic force microscopy uses laser technology to reveal a defect, a double-screw dislocation, on the surface of this crystal of canavalin, a major source of dietary protein for humans and domestic animals. When a crystal grows, attachment kinetics and transport kinetics are competing for control of the molecules. As a molecule gets close to the crystal surface, it has to attach properly for the crystal to be usable. NASA has funded investigators to look at those attachment kinetics from a theoretical standpoint and an experimental standpoint. Dr. Alex McPherson of the University of California, Irvine, is one of those investigators. He uses X-ray diffraction and atomic force microscopy in his laboratory to answer some of the many questions about how protein crystals grow. Atomic force microscopy provides a means of looking at how individual molecules are added to the surface of growing protein crystals. This helps McPherson understand the kinetics of protein crystal growth. McPherson asks, How fast do crystals grow? What are the forces involved? Investigators funded by NASA have clearly shown that such factors as the level of supersaturation and the rate of growth all affect the habit [characteristic arrangement of facets] of the crystal and the defects that occur in the crystal.

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.

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.

Relating protein conformational changes to packing efficiency and disorder

PubMed Central

Bhardwaj, Nitin; Gerstein, Mark

2009-01-01

Changes in protein conformation play key roles in facilitating various biochemical processes, ranging from signaling and phosphorylation to transport and catalysis. While various factors that drive these motions such as environmental changes and binding of small molecules are well understood, specific causative effects on the structural features of the protein due to these conformational changes have not been studied on a large scale. Here, we study protein conformational changes in relation to two key structural metrics: packing efficiency and disorder. Packing has been shown to be crucial for protein stability and function by many protein design and engineering studies. We study changes in packing efficiency during conformational changes, thus extending the analysis from a static context to a dynamic perspective and report some interesting observations. First, we study various proteins that adopt alternate conformations and find that tendencies to show motion and change in packing efficiency are correlated: residues that change their packing efficiency show larger motions. Second, our results suggest that residues that show higher changes in packing during motion are located on the changing interfaces which are formed during these conformational changes. These changing interfaces are slightly different from shear or static interfaces that have been analyzed in previous studies. Third, analysis of packing efficiency changes in the context of secondary structure shows that, as expected, residues buried in helices show the least change in packing efficiency, whereas those embedded in bends are most likely to change packing. Finally, by relating protein disorder to motions, we show that marginally disordered residues which are ordered enough to be crystallized but have sequence patterns indicative of disorder show higher dislocation and a higher change in packing than ordered ones and are located mostly on the changing interfaces. Overall, our results demonstrate

Effect of Chain Conformation on the Single-Molecule Melting Force in Polymer Single Crystals: Steered Molecular Dynamics Simulations Study.

PubMed

Feng, Wei; Wang, Zhigang; Zhang, Wenke

2017-02-28

Understanding the relationship between polymer chain conformation as well as the chain composition within the single crystal and the mechanical properties of the corresponding single polymer chain will facilitate the rational design of high performance polymer materials. Here three model systems of polymer single crystals, namely poly(ethylene oxide) (PEO), polyethylene (PE), and nylon-66 (PA66) have been chosen to study the effects of chain conformation, helical (PEO) versus planar zigzag conformation (PE, PA66), and chain composition (PE versus PA66) on the mechanical properties of a single polymer chain. To do that, steered molecular dynamics simulations were performed on those polymer single crystals by pulling individual polymer chains out of the crystals. Our results show that the patterns of force-extension curve as well as the chain moving mode are closely related to the conformation of the polymer chain in the single crystal. In addition, hydrogen bonds can enhance greatly the force required to stretch the polymer chain out of the single crystal. The dynamic breaking and reformation of multivalent hydrogen bonds have been observed for the first time in PA66 at the single molecule level.

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).

Marginal stability in jammed packings: Quasicontacts and weak contacts

NASA Astrophysics Data System (ADS)

Kallus, Yoav; Torquato, Salvatore

2014-08-01

Maximally random jammed (MRJ) sphere packing is a prototypical example of a system naturally poised at the margin between underconstraint and overconstraint. This marginal stability has traditionally been understood in terms of isostaticity, the equality of the number of mechanical contacts and the number of degrees of freedom. Quasicontacts, pairs of spheres on the verge of coming in contact, are irrelevant for static stability, but they come into play when considering dynamic stability, as does the distribution of contact forces. We show that the effects of marginal dynamic stability, as manifested in the distributions of quasicontacts and weak contacts, are consequential and nontrivial. We study these ideas first in the context of MRJ packing of d-dimensional spheres, where we show that the abundance of quasicontacts grows at a faster rate than that of contacts. We reexamine a calculation of Jin et al. [Phys. Rev. E 82, 051126 (2010), 10.1103/PhysRevE.82.051126], where quasicontacts were originally neglected, and we explore the effect of their inclusion in the calculation. This analysis yields an estimate of the asymptotic behavior of the packing density in high dimensions. We argue that this estimate should be reinterpreted as a lower bound. The latter part of the paper is devoted to Bravais lattice packings that possess the minimum number of contacts to maintain mechanical stability. We show that quasicontacts play an even more important role in these packings. We also show that jammed lattices are a useful setting for studying the Edwards ensemble, which weights each mechanically stable configuration equally and does not account for dynamics. This ansatz fails to predict the power-law distribution of near-zero contact forces, P(f )˜fθ.

Packing Regularities in Biological Structures Relate to Their Dynamics

PubMed Central

Jernigan, Robert L.; Kloczkowski, Andrzej

2007-01-01

The high packing density inside proteins leads to certain geometric regularities and also is one of the most important contributors to the high extent of cooperativity manifested by proteins in their cohesive domain motions. The orientations between neighboring non-bonded residues in proteins substantially follow the similar geometric regularities, regardless of whether the residues are on the surface or buried - a direct result of hydrophobicity forces. These orientations are relatively fixed and correspond closely to small deformations from those of the face-centered cubic lattice, which is the way in which identical spheres pack at the highest density. Packing density also is related to the extent of conservation of residues, and we show this relationship for residue packing densities by averaging over a large sample or residue packings. There are three regimes: 1) over a broad range of packing densities the relationship between sequence entropy and inverse packing density is nearly linear, 2) over a limited range of low packing densities the sequence entropy is nearly constant, and 3) at extremely low packing densities the sequence entropy is highly variable. These packing results provide important justification for the simple elastic network models that have been shown for a large number of proteins to represent protein dynamics so successfully, even when the models are extremely coarse-grained. Elastic network models for polymeric chains are simple and could be combined with these protein elastic networks to represent partially denatured parts of proteins. Finally, we show results of applications of the elastic network model to study the functional motions of the ribosome, based on its known structure. These results indicate expected correlations among its components for the step-wise processing steps in protein synthesis, and suggest ways to use these elastic network models to develop more detailed mechanisms - an important possibility, since most

Young adult smokers' perceptions of plain packs, numbered packs and pack inserts in Turkey: a focus group study.

PubMed

Mucan, Burcu; Moodie, Crawford

2017-11-09

The Turkish Government's 'National Tobacco Control Program 2015-2018' included plans to introduce plain packaging and also a ban on brand names on cigarette packs, allowing only assigned numbers on packs. We explored perceptions of these proposed measures, and also pack inserts with cessation messages, another novel way of using the packaging to communicate with consumers. Eight focus groups were conducted with 47 young adult smokers in Manisa and Kutahya (Turkey) in December 2016. Participants were shown three straight-edged plain cigarette packs, as required in Australia, and then three bevelled-edged plain packs, as permitted in the UK. They were then shown plain packs with numbers rather than brand names, and finally three pack inserts with messages encouraging quitting or offering tips on how to do so. Participants were asked about their perceptions of each. Plain packs were considered unappealing and off-putting, although the bevelled-edged packs were viewed more favourably than the straight-edged packs. Numbered packs were thought by some to diminish the appeal created by the brand name and potentially decrease interest among never smokers and newer smokers. Pack inserts were thought to have less of an impact than the on-pack warnings, but could potentially help discourage initiation and encourage cessation. That bevelled-edged plain packs were perceived more positively than straight-edged plain packs is relevant to countries planning to introduce plain packaging. The study provides a first insight into smokers' perceptions of a ban on brand names, which was perceived to reduce appeal among young people. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Atomistic polarizable force field for molecular dynamics simulations of azide anion containing ionic liquids and crystals.

NASA Astrophysics Data System (ADS)

Starovoytov, Oleg; Hooper, Justin; Borodin, Oleg; Smith, Grant

2010-03-01

Atomistic polarizable force field has been developed for a number of azide anion containing ionic liquids and crystals. Hybrid Molecular Dynamics/Monte Carlo (MD/MC) simulations were performed on methylguanazinium azide and 1-(2-butynyl)-3-methyl-imidazolium azide crystals, while 1-butyl-2,3-dimethylimidazolium azide and 1-amino-3-methyl-1,2,3-triazolium azide ionic liquids were investigated using MD simulations. Crystal cell parameters and crystal structures of 1-(2-butynyl)-3-methyl-imidazolium azide were found in good agreement with X-ray experimental data. Density and ion transport of 1-butyl-2,3-dimethylimidazolium azide predicted from MD simulations were in good agreement with experiments. Details of the ionic liquid structure and relaxation mechanism will be discussed.

Ellipsoids beat Spheres: Experiments with Candies, Colloids and Crystals

NASA Astrophysics Data System (ADS)

Chaikin, Paul

2006-04-01

How many gumballs fit in the glass sphere of a gumball machine? Scientists have been puzzling over problems like this since the Ancient Greeks. Yet it was only recently proven that the standard way of stacking oranges at a grocery store--with one orange on top of each set of three below--is the densist packing for spheres, with a packing fraction φ˜ 0.74. Random (amorphous) packings of spheres have a lower density, with φ ˜0.64. The density of crystalline and random packings of atoms is intimately related to the melting transition in matter. We have studied the crystal-liquid transition in spherical colloidal systems on earth and in microgravity. The simplest objects to study after spheres are squashed spheres -- ellipsoids. Surprisingly we find that ellipsoids can randomly pack more densely than spheres, up to φ˜0.68 - 0.71 for a shape close to that of M&M's^ Candies, and even approach φ˜0.75 for general ellipsoids. The higher density relates directly to the higher number of neighbors needed to prevent the more asymetric ellipsoid from rotating. We have also found the ellipsoids can be packed in a crystalline array to a density, φ˜.7707 which exceeds the highest previous packing. Our findings provide insights into granular materials, rigidity, crystals and glasses, and they may lead to higher quality ceramic materials.

Effect of the Crystal Environment on Side-Chain Conformational Dynamics in Cyanovirin-N Investigated through Crystal and Solution Molecular Dynamics Simulations

PubMed Central

Ahlstrom, Logan S.; Vorontsov, Ivan I.; Shi, Jun; Miyashita, Osamu

2017-01-01

Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure. This agreement is most striking for crystal-contacting residues during crystal simulation. Given the high level of correspondence between our simulations and the X-ray data, we compare side-chain ensembles in solution and crystal simulations. We observe large decreases in conformational entropy in the crystal for several long, polar and contacting residues on the protein surface. Such cases agree well with the average loss in conformational entropy per residue upon protein folding and are accompanied by a change in side-chain conformation. This finding supports the application of surface engineering to facilitate crystallization. Our simulation-based approach demonstrated here with Cyanovirin-N establishes a framework for quantitatively comparing side-chain ensembles in solution and in the crystal across a larger set of proteins to elucidate the effect of the crystal environment on protein conformations. PMID:28107510

Effect of the Crystal Environment on Side-Chain Conformational Dynamics in Cyanovirin-N Investigated through Crystal and Solution Molecular Dynamics Simulations.

PubMed

Ahlstrom, Logan S; Vorontsov, Ivan I; Shi, Jun; Miyashita, Osamu

2017-01-01

Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure. This agreement is most striking for crystal-contacting residues during crystal simulation. Given the high level of correspondence between our simulations and the X-ray data, we compare side-chain ensembles in solution and crystal simulations. We observe large decreases in conformational entropy in the crystal for several long, polar and contacting residues on the protein surface. Such cases agree well with the average loss in conformational entropy per residue upon protein folding and are accompanied by a change in side-chain conformation. This finding supports the application of surface engineering to facilitate crystallization. Our simulation-based approach demonstrated here with Cyanovirin-N establishes a framework for quantitatively comparing side-chain ensembles in solution and in the crystal across a larger set of proteins to elucidate the effect of the crystal environment on protein conformations.

Photovoltaic dryer with dual packed beds for drying medical herb

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 devisedmore » to work under forced air created by air blower and heated by the electrical coils.« less

Synthesis, electronic structure, molecular packing/morphology evolution, and carrier mobilities of pure oligo-/poly(alkylthiophenes).

PubMed

Zhang, Lei; Colella, Nicholas S; Liu, Feng; Trahan, Stephan; Baral, Jayanta K; Winter, H Henning; Mannsfeld, Stefan C B; Briseno, Alejandro L

2013-01-16

Monodispersed conjugated oligothiophenes are receiving attention in fundamental and applied science due to their interesting optical, optoelectronic, and charge transport properties. These "low molecular weight" polymers serve as model structures for the corresponding polymer analogues, which are inherently polydispersed. Here we report the synthesis, electronic structure, molecular packing/morphology, and charge transport properties of monodispersed oligothiophenes with up to six didodecylquaterthiophene (DDQT) building block repeat units (i.e., 24 thiophene units). At the point where the effective conjugation length is reached, the electronic structure showed convergence behavior to the corresponding polymer, poly(3,3"-didodecyl-quaterthiophene) (PQT-12). X-ray crystal structure analysis of the dimer (DDQT-2) showed that terminal thiophenes exhibit syn-conformations, similar to the terminal syn-conformations observed in the trimer (DDQT-3). The dimer also exhibits a rare bending of the terminal alkyl side chains in order to prevent steric hindrance with neighboring hydrogens attached to core thiophenes. Grazing incidence X-ray scattering measurements revealed a morphology evolution from small molecule-like packing to polymer-like packing in thin films, with a morphology transition occurring near the effective conjugation length. Charge transport measurements showed a mobility increase with decreasing chain length. We correlated the molecular packing and morphology to charge transport and determined that carrier mobilities are most sensitive to crystallinity and crystal grain misorientation. This indicates that molecular weight is not a decisive factor for improved carrier mobility in the low molecular weight region, but rather the degree in crystallinity and in-plane crystal orientation. These results represent a fundamental advancement in understanding the relationship between conjugation length and carrier mobilities in oligothiophene semiconductors.

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.

Hydrodynamics of Packed Bed Reactor in Low Gravity

NASA Technical Reports Server (NTRS)

Motil, Brian J.; Nahra, Henry K.; Balakotaiah, Vemuri

2005-01-01

Packed bed reactors are well known for their vast and diverse applications in the chemical industry; from gas absorption, to stripping, to catalytic conversion. Use of this type of reactor in terrestrial applications has been rather extensive because of its simplicity and relative ease of operation. Developing similar reactors for use in microgravity is critical to many space-based advanced life support systems. However, the hydrodynamics of two-phase flow packed bed reactors in this new environment and the effects of one physiochemical process on another has not been adequately assessed. Surface tension or capillary forces play a much greater role which results in a shifting in flow regime transitions and pressure drop. Results from low gravity experiments related to flow regimes and two-phase pressure drop models are presented in this paper along with a description of plans for a flight experiment on the International Space Station (ISS). Understanding the packed bed hydrodynamics and its effects on mass transfer processes in microgravity is crucial for the design of packed bed chemical or biological reactors to be used for water reclamation and other life support processes involving water purification.

Viral capsomere structure, surface processes and growth kinetics in the crystallization of macromolecular crystals visualized by in situ atomic force microscopy

NASA Astrophysics Data System (ADS)

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

2001-11-01

In situ atomic force microscopy (AFM) was used to investigate surface evolution during the growth of single crystals of turnip yellow mosaic virus (TYMV), cucumber mosaic virus (CMV) and glucose isomerase. Growth of these crystals proceeded by two-dimensional (2D) nucleation. For glucose isomerase, from supersaturation dependencies of tangential step rates and critical step length, the kinetic coefficients of the steps and the surface free energy of the step edge were calculated for different crystallographic directions. The molecular structure of the step edges, the adsorption of individual virus particles and their aggregates, and the initial stages of formation of 2D nuclei on the surfaces of TYMV and CMV crystals were recorded. The surfaces of individual TYMV virions within crystals were visualized, and hexameric and pentameric capsomers of the T=3 capsids were clearly resolved. This, so far as we are aware, is the first direct visualization of the capsomere structure of a virus by AFM. In the course of recording the in situ development of the TYMV crystals, a profound restructuring of the surface arrangement was observed. This transformation was highly cooperative in nature, but the transitions were unambiguous and readily explicable in terms of an organized loss of classes of virus particles from specific lattice positions.

A unified picture of the crystal structures of metals

NASA Astrophysics Data System (ADS)

Söderlind, Per; Eriksson, Olle; Johansson, Börje; Wills, J. M.; Boring, A. M.

1995-04-01

THE crystal structures of the light actinides have intrigued physicists and chemists for several decades1. Simple metals and transition metals have close-packed, high-symmetry structures, such as body-centred cubic, face-centred cubic and hexagonal close packing. In contrast, the structures of the light actinides are very loosely packed and of low symmetry-tetragonal, orthorhombic and monoclinic. To understand these differences, we have performed total-energy calculations, as a function of volume, for both high-and low-symmetry structures of a simple metal (aluminium), a non-magnetic transition metal (niobium), a ferromagnetic transition metal (iron) and a light actinide (uranium). We find that the crystal structure of all of these metals is determined by the balance between electrostatic (Madelung) interactions, which favour high symmetry, and a Peierls distortion of the crystal lattice, which favours low symmetry. We show that simple metals and transition metals can adopt low-symmetry structures on expansion of the lattice; and we predict that, conversely, the light actinides will undergo transitions to structures of higher symmetry on compression.

A multistep single-crystal-to-single-crystal bromodiacetylene dimerization

NASA Astrophysics Data System (ADS)

Hoheisel, Tobias N.; Schrettl, Stephen; Marty, Roman; Todorova, Tanya K.; Corminboeuf, Clémence; Sienkiewicz, Andrzej; Scopelliti, Rosario; Schweizer, W. Bernd; Frauenrath, Holger

2013-04-01

Packing constraints and precise placement of functional groups are the reason that organic molecules in the crystalline state often display unusual physical or chemical properties not observed in solution. Here we report a single-crystal-to-single-crystal dimerization of a bromodiacetylene that involves unusually large atom displacements as well as the cleavage and formation of several bonds. Density functional theory computations support a mechanism in which the dimerization is initiated by a [2 + 1] photocycloaddition favoured by the nature of carbon-carbon short contacts in the crystal structure. The reaction proceeded up to the theoretical degree of conversion without loss of crystallinity, and it was also performed on a preparative scale with good yield. Moreover, it represents the first synthetic pathway to (E)-1,2-dibromo-1,2-diethynylethenes, which could serve as synthetic intermediates for the preparation of molecular carbon scaffolds. Our findings both extend the scope of single-crystal-to-single-crystal reactions and highlight their potential as a synthetic tool for complex transformations.

Mechanisms for pressure-induced crystal-crystal transition, amorphization, and devitrification of SnI4.

PubMed

Liu, H; Tse, J S; Hu, M Y; Bi, W; Zhao, J; Alp, E E; Pasternak, M; Taylor, R D; Lashley, J C

2015-10-28

The pressure-induced amorphization and subsequent recrystallization of SnI4 have been investigated using first principles molecular dynamics calculations together with high-pressure (119)Sn nuclear resonant inelastic x-ray scattering measurements. Above ∼8 GPa, we observe a transformation from an ambient crystalline phase to an intermediate crystal structure and a subsequent recrystallization into a cubic phase at ∼64 GPa. The crystalline-to-amorphous transition was identified on the basis of elastic compatibility criteria. The measured tin vibrational density of states shows large amplitude librations of SnI4 under ambient conditions. Although high pressure structures of SnI4 were thought to be determined by random packing of equal-sized spheres, we detected electron charge transfer in each phase. This charge transfer results in a crystal structure packing determined by larger than expected iodine atoms.

Spherical shock-wave propagation in three-dimensional granular packings.

PubMed

Xue, Kun; Bai, Chun-Hua

2011-02-01

We investigate numerically the spherical shock-wave propagation in an open dense granular packing perturbed by the sudden expansion of a spherical intruder in the interior of the pack, focusing on the correlation between geometrical fabrics and propagating properties. The measurements of the temporal and spatial variations in a variety of propagating properties define a consistent serrated wave substructure with characteristic length on the orders of particle diameters. Further inspection of particle packing reveals a well-defined particle layering that persists several particle diameters away from the intruder, although its dominant effects are only within one to two diameters. This interface-induced layering not only exactly coincides with the serrated wave profile, but also highlights the competition between two energy transmission mechanisms involving distinct transport speeds. The alternating dominances between these two mechanisms contribute to the nonlinear wave propagation on the particle scale. Moreover, the proliferation of intricate three-dimensional contact force networks suggests the anisotropic stress transmission, which is found to also arise from the localized packing structure in the vicinity of the intruder.

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

Crystal packing analysis of 1-(3,4-dimethoxyphenyl)-3-(4-bromophenyl)prop-2-en-1-one exhibiting a putative halogen bond Csbnd Br⋯O

NASA Astrophysics Data System (ADS)

Madan Kumar, Shankar; Fares Hezam, Al-Ostoot; Manjunath, B. C.; Shamprasad, Varija Raghu; Eissa Mohammed, Yasser Hussein; Mahesh, N.; Zabiulla; Shaukath, A. K.; Lokanath, N. K.; Byrappa, K.

2018-03-01

The title compound, 1-(3,4-dimethoxyphenyl)-3-(4-bromophenyl) prop-2-en-1-one (1DBr) was synthesized and characterized based on spectroscopic analysis (MS, FT-IR, Elemental analysis, UV-visible, 1H NMR and 13C NMR) and finally the three-dimensional structure is confirmed using single crystal X-ray diffraction studies. The molecule is almost planar and the C--H⋯O intramolecular hydrogen bond closes the ring S(5). In the crystal structure, the molecules are connected through intermolecular hydrogen bond C--H⋯O (R22(14) ring motif) and intermolecular interactions (C--H⋯π and C--O⋯π). Hirshfeld surfaces computational method was employed to quantify the inter-contacts (2D Fingerprint plots) and calculate enrichment ratio (E). The highest value of E is calculated for the contact Br⋯O (1.65) followed by C⋯C (1.02) and have high propensity for forming contacts in the crystal. This provides the basis for the existence of putative halogen bond of the type C-Br⋯O. In addition, the Energy-framework analysis was used to analyze and visualize the 3D-topology of the crystal packing. The dispersion energy framework is dominated over the electrostatic energy-frameworks. The thermogravimetric analysis (TGA) provided the thermal degradation of the 1DBr to be from 230 to 320 °C.

Determination of structure and properties of molecular crystals from first principles.

PubMed

Szalewicz, Krzysztof

2014-11-18

CONSPECTUS: Until recently, it had been impossible to predict structures of molecular crystals just from the knowledge of the chemical formula for the constituent molecule(s). A solution of this problem has been achieved using intermolecular force fields computed from first principles. These fields were developed by calculating interaction energies of molecular dimers and trimers using an ab initio method called symmetry-adapted perturbation theory (SAPT) based on density-functional theory (DFT) description of monomers [SAPT(DFT)]. For clusters containing up to a dozen or so atoms, interaction energies computed using SAPT(DFT) are comparable in accuracy to the results of the best wave function-based methods, whereas the former approach can be applied to systems an order of magnitude larger than the latter. In fact, for monomers with a couple dozen atoms, SAPT(DFT) is about equally time-consuming as the supermolecular DFT approach. To develop a force field, SAPT(DFT) calculations are performed for a large number of dimer and possibly also trimer configurations (grid points in intermolecular coordinates), and the interaction energies are then fitted by analytic functions. The resulting force fields can be used to determine crystal structures and properties by applying them in molecular packing, lattice energy minimization, and molecular dynamics calculations. In this way, some of the first successful determinations of crystal structures were achieved from first principles, with crystal densities and lattice parameters agreeing with experimental values to within about 1%. Crystal properties obtained using similar procedures but empirical force fields fitted to crystal data have typical errors of several percent due to low sensitivity of empirical fits to interactions beyond those of the nearest neighbors. The first-principles approach has additional advantages over the empirical approach for notional crystals and cocrystals since empirical force fields can only be

Plastic deformation of tubular crystals by dislocation glide.

PubMed

Beller, Daniel A; Nelson, David R

2016-09-01

Tubular crystals, two-dimensional lattices wrapped into cylindrical topologies, arise in many contexts, including botany and biofilaments, and in physical systems such as carbon nanotubes. The geometrical principles of botanical phyllotaxis, describing the spiral packings on cylinders commonly found in nature, have found application in all these systems. Several recent studies have examined defects in tubular crystals associated with crystalline packings that must accommodate a fixed tube radius. Here we study the mechanics of tubular crystals with variable tube radius, with dislocations interposed between regions of different phyllotactic packings. Unbinding and separation of dislocation pairs with equal and opposite Burgers vectors allow the growth of one phyllotactic domain at the expense of another. In particular, glide separation of dislocations offers a low-energy mode for plastic deformations of solid tubes in response to external stresses, reconfiguring the lattice step by step. Through theory and simulation, we examine how the tube's radius and helicity affects, and is in turn altered by, the mechanics of dislocation glide. We also discuss how a sufficiently strong bending rigidity can alter or arrest the deformations of tubes with small radii.

Plastic deformation of tubular crystals by dislocation glide

NASA Astrophysics Data System (ADS)

Beller, Daniel A.; Nelson, David R.

2016-09-01

Tubular crystals, two-dimensional lattices wrapped into cylindrical topologies, arise in many contexts, including botany and biofilaments, and in physical systems such as carbon nanotubes. The geometrical principles of botanical phyllotaxis, describing the spiral packings on cylinders commonly found in nature, have found application in all these systems. Several recent studies have examined defects in tubular crystals associated with crystalline packings that must accommodate a fixed tube radius. Here we study the mechanics of tubular crystals with variable tube radius, with dislocations interposed between regions of different phyllotactic packings. Unbinding and separation of dislocation pairs with equal and opposite Burgers vectors allow the growth of one phyllotactic domain at the expense of another. In particular, glide separation of dislocations offers a low-energy mode for plastic deformations of solid tubes in response to external stresses, reconfiguring the lattice step by step. Through theory and simulation, we examine how the tube's radius and helicity affects, and is in turn altered by, the mechanics of dislocation glide. We also discuss how a sufficiently strong bending rigidity can alter or arrest the deformations of tubes with small radii.

Supersonic N-Crowdions in a Two-Dimensional Morse Crystal

NASA Astrophysics Data System (ADS)

Dmitriev, S. V.; Korznikova, E. A.; Chetverikov, A. P.

2018-03-01

An interstitial atom placed in a close-packed atomic row of a crystal is called crowdion. Such defects are highly mobile; they can move along the row, transferring mass and energy. We generalize the concept of a classical supersonic crowdion to an N-crowdion in which not one but N atoms move simultaneously with a high velocity. Using molecular dynamics simulations for a close-packed two-dimensional Morse crystal, we show that N-crowdions transfer mass much more efficiently, because they are capable of covering large distances while having a lower total energy than that of a classical 1-crowdion.

Conversion of NO with a catalytic packed-bed dielectric barrier discharge reactor

NASA Astrophysics Data System (ADS)

Xu, CAO; Weixuan, ZHAO; Renxi, ZHANG; Huiqi, HOU; Shanping, CHEN; Ruina, ZHANG

2017-11-01

This paper discusses the conversion of nitric oxide (NO) with a low-temperature plasma induced by a catalytic packed-bed dielectric barrier discharge (DBD) reactor. Alumina oxide (Al2O3), glass (SiO2) and zirconium oxide (ZrO2), three different spherical packed materials of the same size, were each present in the DBD reactor. The NO conversion under varying input voltage and specific energy density, and the effects of catalysts (titanium dioxide (TiO2) and manganese oxide (MnO x ) coated on Al2O3) on NO conversion were investigated. The experimental results showed that NO conversion was greatly enhanced in the presence of packed materials in the reactor, and the catalytic packed bed of MnO x /Al2O3 showed better performance than that of TiO2/Al2O3. The surface and crystal structures of the materials and catalysts were characterized through scanning electron microscopy analysis. The final products were clearly observed by a Fourier transform infrared spectrometer and provided a better understanding of NO conversion.

3D investigation on polystyrene colloidal crystals by floatage self-assembly with mixed solvent via synchrotron radiation x-ray phase-contrast computed tomography

NASA Astrophysics Data System (ADS)

Fu, Yanan; Xie, Honglan; Deng, Biao; Du, Guohao; Xiao, Tiqiao

2017-06-01

The floatage self-assembly method was introduced with mixed solvent as the medium of polystyrene sphere suspension to fabricate the colloidal crystal. The three dimensional (3D) void system of the colloidal crystal was noninvasively characterized by synchrotron radiation phase-contrast computed tomography, and the quantitative image analysis was implemented aiming to the polystyrene sphere colloidal crystal. Comparing with gravity sedimentation method, the three samples fabricated from floatage self-assembly with mixed solvents have the lowest porosity, and when ethylene glycol and water were mixed with ratio of 1:1, the lowest porosity of 27.49% could be achieved, that has been very close to the minimum porosity of ordered 3D monodisperse sphere array (26%). In single slices, the porosities and fractal dimension for the voids were calculated. The results showed that two factors would significantly influence the porosity of the whole colloidal crystal: the first deposited sphere layer's orderliness and the sedimentation speed of the spheres. The floatage self-assembly could induce a stable close-packing process, resulted from the powerful nucleation force-lateral capillary force coupled with the mixed solvent to regulate the floating upward speed for purpose of matching the assembly rate.

Dynamic Properties of DNA-Programmable Nanoparticle Crystallization.

PubMed

Yu, Qiuyan; Zhang, Xuena; Hu, Yi; Zhang, Zhihao; Wang, Rong

2016-08-23

The dynamics of DNA hybridization is very important in DNA-programmable nanoparticle crystallization. Here, coarse-grained molecular dynamics is utilized to explore the structural and dynamic properties of DNA hybridizations for a self-complementary DNA-directed nanoparticle self-assembly system. The hexagonal close-packed (HCP) and close-packed face-centered cubic (FCC) ordered structures are identified for the systems of different grafted DNA chains per nanoparticle, which are in good agreement with the experimental results. Most importantly, the dynamic crystallization processes of DNA hybridizations are elucidated by virtue of the mean square displacement, the percentage of hybridizations, and the lifetime of DNA bonds. The lifetime can be modeled by the DNA dehybridization, which has an exponential form. The lifetime of DNA bonds closely depends on the temperature. A suitable temperature for the DNA-nanoparticle crystallization is obtained in the work. Moreover, a too large volume fraction hinders the self-assembly process due to steric effects. This work provides some essential information for future design of nanomaterials.

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.

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

NASA Technical Reports Server (NTRS)

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

2002-01-01

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

Organic semiconductor crystals.

PubMed

Wang, Chengliang; Dong, Huanli; Jiang, Lang; Hu, Wenping

2018-01-22

Organic semiconductors have attracted a lot of attention since the discovery of highly doped conductive polymers, due to the potential application in field-effect transistors (OFETs), light-emitting diodes (OLEDs) and photovoltaic cells (OPVs). Single crystals of organic semiconductors are particularly intriguing because they are free of grain boundaries and have long-range periodic order as well as minimal traps and defects. Hence, organic semiconductor crystals provide a powerful tool for revealing the intrinsic properties, examining the structure-property relationships, demonstrating the important factors for high performance devices and uncovering fundamental physics in organic semiconductors. This review provides a comprehensive overview of the molecular packing, morphology and charge transport features of organic semiconductor crystals, the control of crystallization for achieving high quality crystals and the device physics in the three main applications. We hope that this comprehensive summary can give a clear picture of the state-of-art status and guide future work in this area.

Controlling Chirality of Entropic Crystals.

PubMed

Damasceno, Pablo F; Karas, Andrew S; Schultz, Benjamin A; Engel, Michael; Glotzer, Sharon C

2015-10-09

Colloidal crystal structures with complexity and diversity rivaling atomic and molecular crystals have been predicted and obtained for hard particles by entropy maximization. However, thus far homochiral colloidal crystals, which are candidates for photonic metamaterials, are absent. Using Monte Carlo simulations we show that chiral polyhedra exhibiting weak directional entropic forces self-assemble either an achiral crystal or a chiral crystal with limited control over the crystal handedness. Building blocks with stronger faceting exhibit higher selectivity and assemble a chiral crystal with handedness uniquely determined by the particle chirality. Tuning the strength of directional entropic forces by means of particle rounding or the use of depletants allows for reconfiguration between achiral and homochiral crystals. We rationalize our findings by quantifying the chirality strength of each particle, both from particle geometry and potential of mean force and torque diagrams.

Controlling Chirality of Entropic Crystals

NASA Astrophysics Data System (ADS)

Damasceno, Pablo F.; Karas, Andrew S.; Schultz, Benjamin A.; Engel, Michael; Glotzer, Sharon C.

2015-10-01

Colloidal crystal structures with complexity and diversity rivaling atomic and molecular crystals have been predicted and obtained for hard particles by entropy maximization. However, thus far homochiral colloidal crystals, which are candidates for photonic metamaterials, are absent. Using Monte Carlo simulations we show that chiral polyhedra exhibiting weak directional entropic forces self-assemble either an achiral crystal or a chiral crystal with limited control over the crystal handedness. Building blocks with stronger faceting exhibit higher selectivity and assemble a chiral crystal with handedness uniquely determined by the particle chirality. Tuning the strength of directional entropic forces by means of particle rounding or the use of depletants allows for reconfiguration between achiral and homochiral crystals. We rationalize our findings by quantifying the chirality strength of each particle, both from particle geometry and potential of mean force and torque diagrams.

DNA Brick Crystals with Prescribed Depth

PubMed Central

Ke, Yonggang; Ong, Luvena L.; Sun, Wei; Song, Jie; Dong, Mingdong; Shih, William M.; Yin, Peng

2014-01-01

We describe a general framework for constructing two-dimensional crystals with prescribed depth and sophisticated three-dimensional features. These crystals may serve as scaffolds for the precise spatial arrangements of functional materials for diverse applications. The crystals are self-assembled from single-stranded DNA components called DNA bricks. We demonstrate the experimental construction of DNA brick crystals that can grow to micron-size in the lateral dimensions with precisely controlled depth up to 80 nanometers. They can be designed to display user-specified sophisticated three-dimensional nanoscale features, such as continuous or discontinuous cavities and channels, and to pack DNA helices at parallel and perpendicular angles relative to the plane of the crystals. PMID:25343605

Mechanisms for pressure-induced crystal-crystal transition, amorphization, and devitrification of SnI{sub 4}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, H.; Tse, J. S., E-mail: john.tse@usask.ca; Hu, M. Y.

2015-10-28

The pressure-induced amorphization and subsequent recrystallization of SnI{sub 4} have been investigated using first principles molecular dynamics calculations together with high-pressure {sup 119}Sn nuclear resonant inelastic x-ray scattering measurements. Above ∼8 GPa, we observe a transformation from an ambient crystalline phase to an intermediate crystal structure and a subsequent recrystallization into a cubic phase at ∼64 GPa. The crystalline-to-amorphous transition was identified on the basis of elastic compatibility criteria. The measured tin vibrational density of states shows large amplitude librations of SnI{sub 4} under ambient conditions. Although high pressure structures of SnI{sub 4} were thought to be determined by randommore » packing of equal-sized spheres, we detected electron charge transfer in each phase. This charge transfer results in a crystal structure packing determined by larger than expected iodine atoms.« less

Centrifugal sedimentation for selectively packing channels with silica microbeads in three-dimensional micro/nanofluidic devices.

PubMed

Gong, Maojun; Bohn, Paul W; Sweedler, Jonathan V

2009-03-01

Incorporation of nanofluidic elements into microfluidic channels is one approach for adding filtration and partition functionality to planar microfluidic devices, as well as providing enhanced biomolecular separations. Here we introduce a strategy to pack microfluidic channels with silica nanoparticles and microbeads, thereby indirectly producing functional nanostructures; the method allows selected channels to be packed, here demonstrated so that a separation channel is packed while keeping an injection channel unpacked. A nanocapillary array membrane is integrated between two patterned microfluidic channels that cross each other in vertically separated layers. The membrane serves both as a frit for bead packing and as a fluid communication conduit between microfluidic channels. Centrifugal force-assisted sedimentation is then used to selectively pack the microfluidic channels using an aqueous silica bead suspension loaded into the appropriate inlet reservoirs. This packing approach may be used to simultaneously pack multiple channels with silica microbeads having different sizes and surface properties. The chip design and packing method introduced here are suitable for packing silica particles in sizes ranging from nanometers to micrometers and allow rapid (approximately 10 min) packing with high quality. The liquid/analyte transport characteristics of these packed micro/nanofluidic devices have potential utility in a wide range of applications, including electroosmotic pumping, liquid chromatographic separations, and electrochromatography.

Control of piezoelectricity in amino acids by supramolecular packing

NASA Astrophysics Data System (ADS)

Guerin, Sarah; Stapleton, Aimee; Chovan, Drahomir; Mouras, Rabah; Gleeson, Matthew; McKeown, Cian; Noor, Mohamed Radzi; Silien, Christophe; Rhen, Fernando M. F.; Kholkin, Andrei L.; Liu, Ning; Soulimane, Tewfik; Tofail, Syed A. M.; Thompson, Damien

2018-02-01

Piezoelectricity, the linear relationship between stress and induced electrical charge, has attracted recent interest due to its manifestation in biological molecules such as synthetic polypeptides or amino acid crystals, including gamma (γ) glycine. It has also been demonstrated in bone, collagen, elastin and the synthetic bone mineral hydroxyapatite. Piezoelectric coefficients exhibited by these biological materials are generally low, typically in the range of 0.1-10 pm V-1, limiting technological applications. Guided by quantum mechanical calculations we have measured a high shear piezoelectricity (178 pm V-1) in the amino acid crystal beta (β) glycine, which is of similar magnitude to barium titanate or lead zirconate titanate. Our calculations show that the high piezoelectric coefficients originate from an efficient packing of the molecules along certain crystallographic planes and directions. The highest predicted piezoelectric voltage constant for β-glycine crystals is 8 V mN-1, which is an order of magnitude larger than the voltage generated by any currently used ceramic or polymer.

Control of piezoelectricity in amino acids by supramolecular packing.

PubMed

Guerin, Sarah; Stapleton, Aimee; Chovan, Drahomir; Mouras, Rabah; Gleeson, Matthew; McKeown, Cian; Noor, Mohamed Radzi; Silien, Christophe; Rhen, Fernando M F; Kholkin, Andrei L; Liu, Ning; Soulimane, Tewfik; Tofail, Syed A M; Thompson, Damien

2018-02-01

Piezoelectricity, the linear relationship between stress and induced electrical charge, has attracted recent interest due to its manifestation in biological molecules such as synthetic polypeptides or amino acid crystals, including gamma (γ) glycine. It has also been demonstrated in bone, collagen, elastin and the synthetic bone mineral hydroxyapatite. Piezoelectric coefficients exhibited by these biological materials are generally low, typically in the range of 0.1-10 pm V -1 , limiting technological applications. Guided by quantum mechanical calculations we have measured a high shear piezoelectricity (178 pm V -1 ) in the amino acid crystal beta (β) glycine, which is of similar magnitude to barium titanate or lead zirconate titanate. Our calculations show that the high piezoelectric coefficients originate from an efficient packing of the molecules along certain crystallographic planes and directions. The highest predicted piezoelectric voltage constant for β-glycine crystals is 8 V mN -1 , which is an order of magnitude larger than the voltage generated by any currently used ceramic or polymer.

Data on crystal organization in the structure of the Fab fragment from the NIST reference antibody, RM 8671.

PubMed

Gallagher, D T; Karageorgos, I; Hudgens, J W; Galvin, C V

2018-02-01

The reported data describe the crystallization, crystal packing, structure determination and twinning of the unliganded Fab (antigen-binding fragment) from the NISTmAb (standard reference material 8671). The raw atomic coordinates are available as Protein Data Bank structure 5K8A and biological aspects are described in the article, (Karageorgos et al., 2017) [1]. Crystal data show that the packing is unique, and show the basis for the crystal's twinned growth. Twinning is a common and often serious problem in protein structure determination by x-ray crystallography [2]. In the present case the twinning is due to a small deviation (about 0.3 nm) from 4-fold symmetry in the primary intermolecular interface. The deviation produces pseudosymmetry, generating slightly different conformations of the protein, and alternating strong and weak forms of key packing interfaces throughout the lattice.

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

Two-phase computerized planning of cryosurgery using bubble-packing and force-field analogy.

PubMed

Tanaka, Daigo; Shimada, Kenji; Rabin, Yoed

2006-02-01

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 paper, in an effort to improve the quality of cryosurgery. 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 element 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. As a proof-of-concept, results are demonstrated on a two-dimensional 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. This new method of planning has proven to reduce planning runtime from hours to minutes, making automated planning practical in a clinical time frame.

Generation of crystal structures using known crystal structures as analogues

PubMed Central

Cole, Jason C.; Groom, Colin R.; Read, Murray G.; Giangreco, Ilenia; McCabe, Patrick; Reilly, Anthony M.; Shields, Gregory P.

2016-01-01

This analysis attempts to answer the question of whether similar molecules crystallize in a similar manner. An analysis of structures in the Cambridge Structural Database shows that the answer is yes – sometimes they do, particularly for single-component structures. However, one does need to define what we mean by similar in both cases. Building on this observation we then demonstrate how this correlation between shape similarity and packing similarity can be used to generate potential lattices for molecules with no known crystal structure. Simple intermolecular interaction potentials can be used to minimize these potential lattices. Finally we discuss the many limitations of this approach. PMID:27484374

Liquid Crystals for Laser Applications

DTIC Science & Technology

1992-07-01

336. Zei’dovich, B . Ya. and Tabiryan, N. V., Induced light scattering in the mesophase of a nematic liquid crystal (NLC), JETP Lett., 30, 478- 482 ...and devices. ADVANCES IN MATERIALS I Ferroelectric LC’s Ferroelectricity in liquid crystals was first suggested in 1974 by R. B . Meyer2 3 who, by means...most recently, 2 4 the M* phase. These tilted chiral smectic phases are classified according to the nature of the intermolecular I I packing within

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.

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.

Atomic force microscopy study on crystal growth of Cu 2+-doped L-arginine phosphate monohydrate crystals

NASA Astrophysics Data System (ADS)

Geng, Y. L.; Xu, D.; Wang, Y. L.; Du, W.; Liu, H. Y.; Zhang, G. H.; Wang, X. Q.; Sun, D. L.

2005-01-01

Sub-steps and defects of the {1 0 0} planes of Cu 2+-doped L-arginine phosphate monohydrate (LAP) crystals are observed by atomic force microscopy. Formation of sub-steps is not due to the stacking faults but a result of single LAP: Cu 2+ molecule acting as growth unit. Two-dimensional (2D) nuclei with the same height as sub-steps occur on the step-edges. Impurities of Cu 2+ ions cause steps bunch and macrosteps formation. Liquid inclusions in the form of long channels form when the macrosteps lose their stability. Numerous small 3D growth hillocks are found in the channels. The extra stress induced by the 3D islands can result in dislocations and steps mismatches.

Fabrication and characterization of non-Brownian particle-based crystals.

PubMed

Lash, Melissa H; Fedorchak, Morgan V; Little, Steven R; McCarthy, Joseph J

2015-01-27

Particle-based crystals have been explored in the literature for applications in molecular electronics, photonics, sensors, and drug delivery. However, much of the research on these crystals has been focused on particles of nano- and submicrometer dimensions (so-called colloidal crystals) with limited attention directed toward building blocks with dimensions ranging from tens to hundreds of micrometers. This can be attributed, in part, to the fact that the underlying thermal effects in these larger systems typically cannot naturally overcome kinetic barriers at the meso- and macroscales so that many of the methods used for nanoscale particle assembly cannot be directly applied to larger components, as they become kinetically arrested in nonequilibrium states. In this work, ultrasonic agitation is being explored as a means of allowing large, non-Brownian microparticles (18-750 μm) to overcome the kinetic barriers to packing in the creation of close-packed, highly ordered, crystalline structures. In addition, we study how the energy input affects bulk particle behavior and describe several new ways to characterize particle-based crystals made from microparticles.

Using Depletion Force to synthesize PBG crystals

NASA Astrophysics Data System (ADS)

Sanyal, Subrata; Zhang, Jian; Lin, Keng-Hui; Work, William J.; Yodh, A. G.

2000-03-01

Using the pathway of depletion-mediated crystallization, we have undertaken an exhaustive set of experiments in order to synthesize materials with novel optical and rheological properties, e.g., photonic bandgap (PBG) crystals. With the primary use of miceller depletion, we grow crystals of submicron-sized model colloidal (e.g., aqueous suspensions of polyballs or silica) particles from the walls of our sample microchambers, used for optical microscopy. Furthermore, the order of such crystals can be controlled by patterning one of the cell walls(K. H. Lin et al.), Manuscript under preparation (1999)., and after the formation of crystals the particles can be ``locked'' in their positions using chemical techniques(G. Pan et al.), Phys. Rev. Lett., 78, 3860 (1997); P. V. Braun (private communication).. The locked arrangements of particles serve as templates to fabricate(B. T. Holland et al.), Science, 281, 538 (1998); J. E. G. J. Wijnhoven et al., Science, 281, 802 (1998). microporous PBG materials. Experiments are underway to synthesize solid microspheres of high dielectric constant materials, and hollow microspheres, that can be arranged on patterned surfaces.

An approach to crystallizing proteins by metal-mediated synthetic symmetrization

PubMed Central

Laganowsky, Arthur; Zhao, Minglei; Soriaga, Angela B; Sawaya, Michael R; Cascio, Duilio; Yeates, Todd O

2011-01-01

Combining the concepts of synthetic symmetrization with the approach of engineering metal-binding sites, we have developed a new crystallization methodology termed metal-mediated synthetic symmetrization. In this method, pairs of histidine or cysteine mutations are introduced on the surface of target proteins, generating crystal lattice contacts or oligomeric assemblies upon coordination with metal. Metal-mediated synthetic symmetrization greatly expands the packing and oligomeric assembly possibilities of target proteins, thereby increasing the chances of growing diffraction-quality crystals. To demonstrate this method, we designed various T4 lysozyme (T4L) and maltose-binding protein (MBP) mutants and cocrystallized them with one of three metal ions: copper (Cu2+), nickel (Ni2+), or zinc (Zn2+). The approach resulted in 16 new crystal structures—eight for T4L and eight for MBP—displaying a variety of oligomeric assemblies and packing modes, representing in total 13 new and distinct crystal forms for these proteins. We discuss the potential utility of the method for crystallizing target proteins of unknown structure by engineering in pairs of histidine or cysteine residues. As an alternate strategy, we propose that the varied crystallization-prone forms of T4L or MBP engineered in this work could be used as crystallization chaperones, by fusing them genetically to target proteins of interest. PMID:21898649

Packing of sidechains in low-resolution models for proteins.

PubMed

Keskin, O; Bahar, I

1998-01-01

Atomic level rotamer libraries for sidechains in proteins have been proposed by several groups. Conformations of side groups in coarse-grained models, on the other hand, have not yet been analyzed, although low resolution approaches are the only efficient way to explore global structural features. A residue-specific backbone-dependent library for sidechain isomers, compatible with a coarse-grained model, is proposed. The isomeric states are utilized in packing sidechains of known backbone structures. Sidechain positions are predicted with a root-mean-square deviation (r.m.s.d.) of 2.40 A with respect to crystal structure for 50 test proteins. The rmsd for core residues is 1.60 A and decreases to 1.35 A when conformational correlations and directional effects in inter-residue couplings are considered. An automated method for assigning sidechain positions in coarse-grained model proteins is proposed and made available on the internet; the method accounts satisfactorily for sidechain packing, particularly in the core.

Packing C60 in Boron Nitride Nanotubes

NASA Astrophysics Data System (ADS)

Mickelson, W.; Aloni, S.; Han, Wei-Qiang; Cumings, John; Zettl, A.

2003-04-01

We have created insulated C60 nanowire by packing C60 molecules into the interior of insulating boron nitride nanotubes (BNNTs). For small-diameter BNNTs, the wire consists of a linear chain of C60 molecules. With increasing BNNT inner diameter, unusual C60 stacking configurations are obtained (including helical, hollow core, and incommensurate) that are unknown for bulk or thin-film forms of C60. C60 in BNNTs thus presents a model system for studying the properties of dimensionally constrained ``silo'' crystal structures. For the linear-chain case, we have fused the C60 molecules to form a single-walled carbon nanotube inside the insulating BNNT.

Fabrication of Crack-Free Photonic Crystal Films on Superhydrophobic Nanopin Surface.

PubMed

Xia, Tian; Luo, Wenhao; Hu, Fan; Qiu, Wu; Zhang, Zhisen; Lin, Youhui; Liu, Xiang Yang

2017-07-05

On the basis of their superior optical performance, photonic crystals (PCs) have been investigated as excellent candidates for widespread applications including sensors, displays, separation processes, and catalysis. However, fabrication of structurally controllable large-area PC assemblies with no defects is still a tough task. Herein, we develop an effective strategy for preparing centimeter-scale crack-free photonic crystal films by the combined effects of soft assembly and superhydrophobic nanopin surfaces. Owing to its large contact angle and low-adhesive force on the superhydrophobic substrate, the colloidal suspension exhibits a continuous retraction of the three-phase (gas-liquid-solid) contact line (TCL) in the process of solvent (water molecules) evaporation. The constantly receding TCL can bring the colloidal spheres closer to each other, which could timely close the gaps due to the loss of water molecules. As a result, close-packed and well-ordered assembly structures can be easily obtained. We expect that this work may pave the way to utilize novel superhydrophobic materials for designing and developing high-quality PCs and to apply PCs in different fields.

Crystal growth, spectral, structural and optical studies of π-conjugated stilbazolium crystal: 4-bromobenzaldehyde-4'-N'-methylstilbazolium tosylate.

PubMed

Krishna Kumar, M; Sudhahar, S; Bhagavannarayana, G; Mohan Kumar, R

2014-05-05

Nonlinear optical (NLO) organic compound, 4-bromobenzaldehyde-4'-N'-methylstilbazolium tosylate was synthesized by reflux method. The formation of molecular complex was confirmed from (1)H NMR, FT-IR and FT-Raman spectral analyses. The single crystals were grown by slow evaporation solution growth method and the crystal structure and atomic packing of grown crystal was identified. The morphology and growth axis of grown crystal were determined. The crystal perfection was analyzed using high resolution X-ray diffraction study on (001) plane. Thermal stability, decomposition stages and melting point of the grown crystal were analyzed. The optical absorption coefficient (α) and energy band gap (E(g)) of the crystal were determined using UV-visible absorption studies. Second harmonic generation efficiency of the grown crystal was examined by Kurtz powder method with different particle size using 1064 nm laser. Laser induced damage threshold study was carried out for the grown crystal using Nd:YAG laser. Copyright © 2014 Elsevier B.V. All rights reserved.

Monte Carlo simulation of hard spheres near random closest packing using spherical boundary conditions

NASA Astrophysics Data System (ADS)

Tobochnik, Jan; Chapin, Phillip M.

1988-05-01

Monte Carlo simulations were performed for hard disks on the surface of an ordinary sphere and hard spheres on the surface of a four-dimensional hypersphere. Starting from the low density fluid the density was increased to obtain metastable amorphous states at densities higher than previously achieved. Above the freezing density the inverse pressure decreases linearly with density, reaching zero at packing fractions equal to 68% for hard spheres and 84% for hard disks. Using these new estimates for random closest packing and coefficients from the virial series we obtain an equation of state which fits all the data up to random closest packing. Usually, the radial distribution function showed the typical split second peak characteristic of amorphous solids and glasses. High density systems which lacked this split second peak and showed other sharp peaks were interpreted as signaling the onset of crystal nucleation.

Effect of local cooling on excitation-contraction coupling in myasthenic muscle: Another mechanism of ice-pack test in myasthenia gravis.

PubMed

Yamamoto, Daisuke; Imai, Tomihiro; Tsuda, Emiko; Hozuki, Takayoshi; Yamauchi, Rika; Hisahara, Shin; Kawamata, Jun; Shimohama, Shun

2017-11-01

The ice-pack test is a convenient diagnostic testing procedure for myasthenia gravis (MG). We investigated the underlying mechanism of the ice-pack test performed on bilateral masseters. We performed trigeminal repetitive nerve stimulation (RNS), excitation-contraction (E-C) coupling assessment (Imai's method) and bite force measurement before and after cooling of the masseters in MG patients and normal controls. After placing the ice-pack on the masseters for 3min, serial recordings of the three tests were performed at various time intervals during 10min after cooling. The bite force increased significantly after cooling in ice-pack-positive MG patients. The acceleration and acceleration ratio (acceleration at a given time to baseline acceleration) of jaw movement increased significantly after cooling of the masseters in ice-pack-positive MG patients compared to ice-pack-negative patients and normal controls. The prolonged effect of cooling continued until the end of recording even though decremental response to RNS had returned to baseline value. Cooling of myasthenic muscle may induce two effects. One is relatively short effect on electrical synaptic transmission at the endplate, and another is prolonged effect on E-C coupling in the muscle. The ice-pack test induces a prolonged effect of ameliorating impaired E-C coupling in MG. Copyright © 2017 International Federation of Clinical Neurophysiology. Published by Elsevier B.V. All rights reserved.

Exciton intrachain transport induced by interchain packing configurations in conjugated polymers.

PubMed

Meng, Ruixuan; Gao, Kun; Zhang, Gaiyan; Han, Shixuan; Yang, Fujiang; Li, Yuan; Xie, Shijie

2015-07-28

Based on a tight binding model combined with a nonadiabatic dynamics approach, we theoretically investigate the exciton intrachain transport in conjugated polymers with different interchain packing configurations. We construct two different interchain packing configurations, i.e. linear and exponential forms, and simulate the dynamical processes of the exciton transport in these systems. We find that, in both cases, there exists a distribution of driving force for exciton transport, which stems from the gradient of the exciton creation energy along the chains. This finding enriches the picture of exciton transport in polymers and provides a new idea to improve the exciton transport length in polymeric photovoltaic devices.

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

Crystal Growth Rate Dispersion: A Predictor of Crystal Quality in Microgravity?

NASA Technical Reports Server (NTRS)

Kephart, Richard D.; Judge, Russell A.; Snell, Edward H.; vanderWoerd, Mark J.

2003-01-01

In theory macromolecular crystals grow through a process involving at least two transport phenomena of solute to the crystal surface: diffusion and convection. In absence of standard gravitational forces, the ratio of these two phenomena can change and explain why crystal growth in microgravity is different from that on Earth. Experimental evidence clearly shows, however, that crystal growth of various systems is not equally sensitive to reduction in gravitational forces, leading to quality improvement in microgravity for some crystals but not for others. We hypothesize that the differences in final crystal quality are related to crystal growth rate dispersion. If growth rate dispersion exists on Earth, decreases in microgravity, and coincides with crystal quality improvements then this dispersion is a predictor for crystal quality improvement. In order to test this hypothesis, we will measure growth rate dispersion both in microgravity and on Earth and will correlate the data with previously established data on crystal quality differences for the two environments. We present here the first crystal growth rate measurement data for three proteins (lysozyme, xylose isomerase and human recombinant insulin), collected on Earth, using hardware identical to the hardware to be used in microgravity and show how these data correlate with crystal quality improvements established in microgravity.

Rheology of three-dimensional packings of aggregates: microstructure and effects of nonconvexity.

PubMed

Azéma, Emilien; Radjaï, Farhang; Saint-Cyr, Baptiste; Delenne, Jean-Yves; Sornay, Philippe

2013-05-01

We use three-dimensional contact dynamics simulations to analyze the rheological properties of granular materials composed of rigid aggregates. The aggregates are made from four overlapping spheres and described by a nonconvexity parameter depending on the relative positions of the spheres. The macroscopic and microstructural properties of several sheared packings are analyzed as a function of the degree of nonconvexity of the aggregates. We find that the internal angle of friction increases with the nonconvexity. In contrast, the packing fraction first increases to a maximum value but declines as the nonconvexity increases further. At a high level of nonconvexity, the packings are looser but show a higher shear strength. At the microscopic scale, the fabric and force anisotropy, as well as the friction mobilization, are enhanced by multiple contacts between aggregates and interlocking, thus revealings the mechanical and geometrical origins of shear strength.

The rheology of crystal-rich magmas (Kuno Award Lecture)

NASA Astrophysics Data System (ADS)

Huber, Christian; Aldin Faroughi, Salah; Degruyter, Wim

2016-04-01

The rheology of magmas controls not only eruption dynamics but also the rate of transport of magmas through the crust and to a large extent the rate of magma differentiation and degassing. Magma bodies stalled in the upper crust are known to spend most of their lifespan above the solidus at a high crystal content (Cooper and Kent, 2014; Huber et al., 2009), where the probability of melt extraction (crystal fractionation) is the greatest (Dufek and Bachmann, 2010). In this study, we explore a new theoretical framework to study the viscosity of crystal bearing magmas. Since the seminal work of A. Einstein and W. Sutherland in the early 20th century, it has been shown theoretically and tested experimentally that a simple self-similar behavior exist between the relative viscosity of dilute (low crystal content) suspensions and the particle volume fraction. The self-similar nature of that relationship is quickly lost as we consider crystal fractions beyond a few volume percent. We propose that the relative viscosity of crystal-bearing magmas can be fully described by two state variables, the intrinsic viscosity and the crowding factor (a measure of the packing threshold in the suspension). These two state variables can be measured experimentally under different conditions, which allows us to develop closure relationships in terms of the applied shear stress and the crystal shape and size distributions. We build these closure equations from the extensive literature on the rheology of synthetic suspensions, where the nature of the particle shape and size distributions is better constrained and apply the newly developed model to published experiments on crystal-bearing magmas. We find that we recover a self-similar behavior (unique rheology curve) up to the packing threshold and show that the commonly reported break in slope between the relative viscosity and crystal volume fraction around the expected packing threshold is most likely caused by a sudden change in the state

Controlling Chirality of Entropic Crystals

NASA Astrophysics Data System (ADS)

Damasceno, Pablo; Karas, Andrew; Schultz, Benjamin; Engel, Michael; Glotzer, Sharon

Colloidal crystal structures with complexity and diversity rivaling atomic and molecular crystals have been predicted and obtained for hard particles by entropy maximization. However, thus far homochiral colloidal crystals, which are candidates for photonic metamaterials, are absent. Using Monte Carlo simulations we show that chiral polyhedra exhibiting weak directional entropic forces self-assemble either an achiral crystal or a chiral crystal with limited control over the crystal handedness. Building blocks with stronger faceting exhibit higher selectivity and assemble a chiral crystal with handedness uniquely determined by the particle chirality. Tuning the strength of directional entropic forces by means of particle rounding or the use of depletants allows for reconfiguration between achiral and homochiral crystals. We rationalize our findings by quantifying the chirality strength of each particle, both from particle geometry and potential of mean force and torque diagrams. Work supported by the National Science Foundation, Division of Materials Research Award No. DMR 1120923, U.S. Army Research Office under Grant Award No. W911NF-10-1-0518, and also by the DOD/ASD (R&E) under Award No. N00244-09-1-0062.

Electric Field Tuning Molecular Packing and Electrical Properties of Solution-Shearing Coated Organic Semiconducting Thin Films

DOE PAGES

Molina-Lopez, Francisco; Yan, Hongping; Gu, Xiaodan; ...

2017-01-17

Recent improvements in solution-coated organic semiconductors (OSCs) evidence their high potential for cost-efficient organic electronics and sensors. Molecular packing structure determines the charge transport property of molecular solids. However, it remains challenging to control the molecular packing structure for a given OSC. Here, the application of alternating electric fields is reported to fine-tune the crystal packing of OSC solution-shearing coated at ambient conditions. First, a theoretical model based on dielectrophoresis is developed to guide the selection of the optimal conditions (frequency and amplitude) of the electric field applied through the solution-shearing blade during coating of OSC thin films. Next, electricmore » field-induced polymorphism is demonstrated for OSCs with both herringbone and 2D brick-wall packing motifs in 2,7-dioctyl[1]benzothieno[3,2-b][1]benzothiophene and 6,13-bis(triisopropylsilylethynyl) pentacene, respectively. Favorable molecular packing can be accessible in some cases, resulting in higher charge carrier mobilities. In conclusion, this work provides a new approach to tune the properties of solution-coated OSCs in functional devices for high-performance printed electronics.« less

Impact of interaction range and curvature on crystal growth of particles confined to spherical surfaces.

PubMed

Paquay, Stefan; Both, Gert-Jan; van der Schoot, Paul

2017-07-01

When colloidal particles form a crystal phase on a spherical template, their packing is governed by the effective interaction between them and the elastic strain of bending the growing crystal. For example, if growth commences under appropriate conditions, and the isotropic crystal that forms reaches a critical size, growth continues via the incorporation of defects to alleviate elastic strain. Recently, it was experimentally found that, if defect formation is somehow not possible, the crystal instead continues growing in ribbons that protrude from the original crystal. Here we report on computer simulations in which we observe both the formation of ribbons at short interaction ranges and packings that incorporate defects if the interaction is longer-ranged. The ribbons only form above some critical crystal size, below which the nucleus is disk-shaped. We find that the scaling of the critical crystal size differs slightly from the one proposed in the literature, and we argue that this is because the actual morphology transition is caused by the competition between line tension and elastic stress, rather than the competition between chemical potential and elastic stress.

Impact of interaction range and curvature on crystal growth of particles confined to spherical surfaces

NASA Astrophysics Data System (ADS)

Paquay, Stefan; Both, Gert-Jan; van der Schoot, Paul

2017-07-01

When colloidal particles form a crystal phase on a spherical template, their packing is governed by the effective interaction between them and the elastic strain of bending the growing crystal. For example, if growth commences under appropriate conditions, and the isotropic crystal that forms reaches a critical size, growth continues via the incorporation of defects to alleviate elastic strain. Recently, it was experimentally found that, if defect formation is somehow not possible, the crystal instead continues growing in ribbons that protrude from the original crystal. Here we report on computer simulations in which we observe both the formation of ribbons at short interaction ranges and packings that incorporate defects if the interaction is longer-ranged. The ribbons only form above some critical crystal size, below which the nucleus is disk-shaped. We find that the scaling of the critical crystal size differs slightly from the one proposed in the literature, and we argue that this is because the actual morphology transition is caused by the competition between line tension and elastic stress, rather than the competition between chemical potential and elastic stress.

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.

Molecular Packing of Amphiphilic Nanosheets Resolved by X-ray Scattering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harutyunyan, Boris; Dannenhoffer, Adam; Kewalramani, Sumit

2016-12-29

Molecular packing in light harvesting 2D assemblies of photocatalytic materials is a critical factor for solar-to-fuel conversion efficiency. However, structure–function correlations have yet to be fully established. This is partly due to the difficulties in extracting the molecular arrangements from the complex 3D powder averaged diffraction patterns of 2D lattices, obtained via in situ wide-angle X-ray scattering. Here, we develop a scattering theory formalism and couple it with a simple geometrical model for the molecular shape of chromophore 9-methoxy-N-(sodium hexanoate)perylene-3,4-dicarboximide (MeO-PMI) used in our study. This generally applicable method fully reproduces the measured diffraction pattern including the asymmetric line shapesmore » for the Bragg reflections and yields the molecular packing arrangement within a 2D crystal structure with a remarkable degree of detail. We find an approximate edge-centered herringbone structure for the PMI fused aromatic rings and ordering of the carboxypentyl chains above and below the nanosheets. Such a packing arrangement differs from the more symmetric face-to-face orientation of the unsubstituted PMI rings. This structural difference is correlated to our measurement of the reduced catalytic performance of MeO-PMI nanosheets as compared to the mesoscopically similar unsubstituted PMI assemblies.« less

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.

Ambipolar carrier transport properties and molecular packing structure of octahexyl-substituted copper phthalocyanine

NASA Astrophysics Data System (ADS)

Watanabe, Ken; Watanabe, Koichi; Tohnai, Norimitsu; Itani, Hiromichi; Shimizu, Yo; Fujii, Akihiko; Ozaki, Masanori

2018-04-01

The charge carrier mobility of a solution-processable low-molecular-weight organic semiconductor material, i.e., 1,4,8,11,15,18,22,25-octahexylphthalocyanine copper complex (C6PcCu), was investigated by the time-of-flight technique. The anomalous ambipolar carrier mobility was discussed from the viewpoint of the molecular packing structure, which was clarified by single-crystal X-ray structure analysis. In the comparison between the molecular packing structures of C6PcCu and its metal-free-type homologue, it was found that the difference in carrier mobility originates from the rotation of the molecule, which is caused by the steric hindrance due to the introduction of a center metal and the interpenetration of the nonperipheral alkyl chains.

Comparing the efficacy of mature mud pack and hot pack treatments for knee osteoarthritis.

PubMed

Sarsan, Ayşe; Akkaya, Nuray; Ozgen, Merih; Yildiz, Necmettin; Atalay, Nilgun Simsir; Ardic, Fusun

2012-01-01

The objective of this study is to compare the efficacy of mature mud pack and hot pack therapies on patients with knee osteoarthritis. This study was designed as a prospective, randomized-controlled, and single-blinded clinical trial. Twenty-seven patients with clinical and radiologic evidence of knee osteoarthritis were randomly assigned into two groups and were treated with mature mud packs (n 15) or hot packs (n=12). Patients were evaluated for pain [based on the visual analog scale (VAS)], function (WOMAC, 6 min walking distance), quality of life [Short Form-36 (SF-36)], and serum levels of tumor necrosis factor-alpha (TNF-α), interleukin-6 (IL-6), and insulin-like growth factor-1 (IGF-1) at baseline, post-treatment, and 3 and 6~months after treatment. The mud pack group shows a significant improvement in VAS, pain, stifness, and physical function domains of WOMAC. The difference between groups of pain and physical activity domains is significant at post-treatment in favor of mud pack. For a 6 min walking distance, mud pack shows significant improvement, and the difference is significant between groups in favor of mud pack at post-treatment and 3 and 6 months after treatment. Mud pack shows significant improvement in the pain subscale of SF-36 at the third month continuing until the sixth month after the treatment. Significant improvements are found for the social function, vitality/energy, physical role disability, and general health subscales of SF-36 in favor of the mud pack compared with the hot pack group at post-treatment. A significant increase is detected for IGF-1 in the mud pack group 3 months after treatment compared with the baseline, and the difference is significant between groups 3 months after the treatment. Mud pack is a favorable option compared with hotpack for pain relief and for the improvement of functional conditions in treating patients with knee osteoarthritis.

Granular Contact Forces: Proof of "Self-Ergodicity" by Generalizing Boltzmann's Stosszahlansatz and H Theorem

NASA Technical Reports Server (NTRS)

Metzger, Philip T.

2006-01-01

Ergodicity is proved for granular contact forces. To obtain this proof from first principles, this paper generalizes Boltzmann's stosszahlansatz (molecular chaos) so that it maintains the necessary correlations and symmetries of granular packing ensembles. Then it formally counts granular contact force states and thereby defines the proper analog of Boltzmann's H functional. This functional is used to prove that (essentially) all static granular packings must exist at maximum entropy with respect to their contact forces. Therefore, the propagation of granular contact forces through a packing is a truly ergodic process in the Boltzmannian sense, or better, it is self-ergodic. Self-ergodicity refers to the non-dynamic, internal relationships that exist between the layer-by-layer and column-by-column subspaces contained within the phase space locus of any particular granular packing microstate. The generalized H Theorem also produces a recursion equation that may be solved numerically to obtain the density of single particle states and hence the distribution of granular contact forces corresponding to the condition of self-ergodicity. The predictions of the theory are overwhelmingly validated by comparison to empirical data from discrete element modeling.

Column-to-column packing variation of disposable pre-packed columns for protein chromatography.

PubMed

Schweiger, Susanne; Hinterberger, Stephan; Jungbauer, Alois

2017-12-08

In the biopharmaceutical industry, pre-packed columns are the standard for process development, but they must be qualified before use in experimental studies to confirm the required performance of the packed bed. Column qualification is commonly done by pulse response experiments and depends highly on the experimental testing conditions. Additionally, the peak analysis method, the variation in the 3D packing structure of the bed, and the measurement precision of the workstation influence the outcome of qualification runs. While a full body of literature on these factors is available for HPLC columns, no comparable studies exist for preparative columns for protein chromatography. We quantified the influence of these parameters for commercially available pre-packed and self-packed columns of disposable and non-disposable design. Pulse response experiments were performed on 105 preparative chromatography columns with volumes of 0.2-20ml. The analyte acetone was studied at six different superficial velocities (30, 60, 100, 150, 250 and 500cm/h). The column-to-column packing variation between disposable pre-packed columns of different diameter-length combinations varied by 10-15%, which was acceptable for the intended use. The column-to-column variation cannot be explained by the packing density, but is interpreted as a difference in particle arrangement in the column. Since it was possible to determine differences in the column-to-column performance, we concluded that the columns were well-packed. The measurement precision of the chromatography workstation was independent of the column volume and was in a range of±0.01ml for the first peak moment and±0.007 ml 2 for the second moment. The measurement precision must be considered for small columns in the range of 2ml or less. The efficiency of disposable pre-packed columns was equal or better than that of self-packed columns. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

Computed crystal energy landscapes for understanding and predicting organic crystal structures and polymorphism.

PubMed

Price, Sarah Sally L

2009-01-20

The phenomenon of polymorphism, the ability of a molecule to adopt more than one crystal structure, is a well-established property of crystalline solids. The possible variations in physical properties between polymorphs make the reliable reproduction of a crystalline form essential for all research using organic materials, as well as quality control in manufacture. Thus, the last two decades have seen both an increase in interest in polymorphism and the availability of the computer power needed to make the computational prediction of organic crystal structures a practical possibility. In the past decade, researchers have made considerable improvements in the theoretical basis for calculating the sets of structures that are within the energy range of possible polymorphism, called crystal energy landscapes. It is common to find that a molecule has a wide variety of ways of packing with lattice energy within a few kilojoules per mole of the most stable structure. However, as we develop methods to search for and characterize "all" solid forms, it is also now usual for polymorphs and solvates to be found. Thus, the computed crystal energy landscape reflects and to an increasing extent "predicts" the emerging complexity of the solid state observed for many organic molecules. This Account will discuss the ways in which the calculation of the crystal energy landscape of a molecule can be used as a complementary technique to solid form screening for polymorphs. Current methods can predict the known crystal structure, even under "blind test" conditions, but such successes are generally restricted to those structures that are the most stable over a wide range of thermodynamic conditions. The other low-energy structures can be alternative polymorphs, which have sometimes been found in later experimental studies. Examining the computed structures reveals the various compromises between close packing, hydrogen bonding, and pi-pi stacking that can result in energetically feasible

Pseudoracemic amino acid complexes: blind predictions for flexible two-component crystals.

PubMed

Görbitz, Carl Henrik; Dalhus, Bjørn; Day, Graeme M

2010-08-14

Ab initio prediction of the crystal packing in complexes between two flexible molecules is a particularly challenging computational chemistry problem. In this work we present results of single crystal structure determinations as well as theoretical predictions for three 1 ratio 1 complexes between hydrophobic l- and d-amino acids (pseudoracemates), known from previous crystallographic work to form structures with one of two alternative hydrogen bonding arrangements. These are accurately reproduced in the theoretical predictions together with a series of patterns that have never been observed experimentally. In this bewildering forest of potential polymorphs, hydrogen bonding arrangements and molecular conformations, the theoretical predictions succeeded, for all three complexes, in finding the correct hydrogen bonding pattern. For two of the complexes, the calculations also reproduce the exact space group and side chain orientations in the best ranked predicted structure. This includes one complex for which the observed crystal packing clearly contradicted previous experience based on experimental data for a substantial number of related amino acid complexes. The results highlight the significant recent advances that have been made in computational methods for crystal structure prediction.

Machine learning for the structure-energy-property landscapes of molecular crystals.

PubMed

Musil, Félix; De, Sandip; Yang, Jack; Campbell, Joshua E; Day, Graeme M; Ceriotti, Michele

2018-02-07

Molecular crystals play an important role in several fields of science and technology. They frequently crystallize in different polymorphs with substantially different physical properties. To help guide the synthesis of candidate materials, atomic-scale modelling can be used to enumerate the stable polymorphs and to predict their properties, as well as to propose heuristic rules to rationalize the correlations between crystal structure and materials properties. Here we show how a recently-developed machine-learning (ML) framework can be used to achieve inexpensive and accurate predictions of the stability and properties of polymorphs, and a data-driven classification that is less biased and more flexible than typical heuristic rules. We discuss, as examples, the lattice energy and property landscapes of pentacene and two azapentacene isomers that are of interest as organic semiconductor materials. We show that we can estimate force field or DFT lattice energies with sub-kJ mol -1 accuracy, using only a few hundred reference configurations, and reduce by a factor of ten the computational effort needed to predict charge mobility in the crystal structures. The automatic structural classification of the polymorphs reveals a more detailed picture of molecular packing than that provided by conventional heuristics, and helps disentangle the role of hydrogen bonded and π-stacking interactions in determining molecular self-assembly. This observation demonstrates that ML is not just a black-box scheme to interpolate between reference calculations, but can also be used as a tool to gain intuitive insights into structure-property relations in molecular crystal engineering.

Supramolecular Packing Controls H 2 Photocatalysis in Chromophore Amphiphile Hydrogels

DOE PAGES

Weingarten, Adam S.; Kazantsev, Roman V.; Palmer, Liam C.; ...

2015-11-21

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. Here, we investigated 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 somemore » 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. Lastly, 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.« less

Supramolecular Packing Controls H 2 Photocatalysis in Chromophore Amphiphile Hydrogels

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weingarten, Adam S.; Kazantsev, Roman V.; Palmer, Liam C.

2015-11-21

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 somemore » 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.« less

Increase of hole-drilling speed by using packs of laser pulses

NASA Astrophysics Data System (ADS)

Gorny, Sergey G.; Grigoriev, A. M.; Lopota, Vitaliy A.; Turichin, Gleb A.

1999-09-01

For realization of the optimum mode of hole drilling the packs of laser pulses of high intensity were used, when average level of intensity of radiation is not too high, that reduces specific energy of destruction, and the peak intensity is reasonably great, that the pulse of pressure of effect at evaporation has completely deleted the liquid from the zone of processing. The high peak intensity of radiation permits in this case to place a target not in focus of a optical system, creating on its surface the image with the help of masks. It permits to receive in metal plates the holes of any section, to execute marking of surfaces and deep engraving of sample material with the help of laser. With the using of focused radiation the cutting of thin materials can be executed without a auxiliary gas. The condition of melt replacement is excess of power of recoil pressure above the power of viscous forces and forces of inertia. The decision of the hydrodynamic problem permits to evaluate the necessary parameters of laser radiation, frequency and longitude of packs of pulses which provide increases of process speed in several times. The conducted experiments confirm the indicated theoretical analysis of process of removing of the material under action of packs of pulses of laser radiation. The given process is realized in laser technological installations for holes drilling and marks of materials.

Odd-even chain packing, molecular and thermal models for some long chain sodium(I) n-alkanoates

NASA Astrophysics Data System (ADS)

Nelson, Peter N.; Ellis, Henry A.

2014-10-01

A homologous series of sodium(I) n-alkanoates, NaCnH2n-1O2, with chain lengths n = 8-18, inclusive, have been synthesized and their structural and thermal properties investigated via Fourier Transform Infrared and Solid State 13C NMR spectroscopies, X-ray powder diffraction, Thermogravimetry, Differential Scanning Calorimetry, Polarizing light microscopy and variable temperature Infrared spectroscopy. The measurements show that metal-carboxylate coordination is via asymmetric chelating bidentate bonding with extensive carboxyl group inter-molecular interactions in which four oxygen atoms are bonded tetrahedrally to a sodium atom. Furthermore, the compounds crystallize in a monoclinic crystal system with the hydrocarbon chains in the fully extended all-trans conformation, advancing along the c-axis. Moreover, the chains are packed as tilted (θ ∼ 63°), non-overlapping, tail-to-tail lamellar bilayers that are not in the same plane, within a lamellar. Though these compounds are nearly isostructural, there are subtle differences in the packing of the hydrocarbon chains in the crystal lattice, resulting in odd-even alternation in the terminal methyl group asymmetric stretching vibration and chemical shift. These differences arise from the relative vertical distances between hydrocarbon planes within the lamellar; such that, for odd-chain compounds, larger inter-planar distances result in less efficient packing in the crystal lattice and hence, lower inter-planar van der Waals interactions between hydrocarbon chains. Thermal traces, for all compounds, show several partially reversible solid-solid pre-melting transitions associated with different degrees of gauche conformers in the alkyl chains. The reversible gauche-trans isomerism, of the methylene groups, is kinetically controlled; hence, super-cooling of the melt and other transitions, are observed for all compounds. The kinetics of chain reversion follow the exponential law of nucleation, though complicated by

Crystal structure of alpha poly-p-xylylene.

NASA Technical Reports Server (NTRS)

Kubo, S.; Wunderlich, B.

1971-01-01

A crystal structure of alpha poly-p-xylylene is proposed with the help of data of oriented crystals grown during polymerization. The unit cell is monoclinic with the parameters a = 8.57 A, b = 10.62 A, c = 6.54 A (chain axis), and beta = 101.3 deg. Four repeating units per cell lead to a calculated density of 1.185 g/cu cm and a packing density of 0.71. The probable space group is P2 sub 1/m.

Crystal nucleation of colloidal hard dumbbells

NASA Astrophysics Data System (ADS)

Ni, Ran; Dijkstra, Marjolein

2011-01-01

Using computer simulations, we investigate the homogeneous crystal nucleation in suspensions of colloidal hard dumbbells. The free energy barriers are determined by Monte Carlo simulations using the umbrella sampling technique. We calculate the nucleation rates for the plastic crystal and the aperiodic crystal phase using the kinetic prefactor as determined from event driven molecular dynamics simulations. We find good agreement with the nucleation rates determined from spontaneous nucleation events observed in event driven molecular dynamics simulations within error bars of one order of magnitude. We study the effect of aspect ratio of the dumbbells on the nucleation of plastic and aperiodic crystal phases, and we also determine the structure of the critical nuclei. Moreover, we find that the nucleation of the aligned close-packed crystal structure is strongly suppressed by a high free energy barrier at low supersaturations and slow dynamics at high supersaturations.

Nematic Liquid-Crystal Colloids

PubMed Central

Muševič, Igor

2017-01-01

This article provides a concise review of a new state of colloidal matter called nematic liquid-crystal colloids. These colloids are obtained by dispersing microparticles of different shapes in a nematic liquid crystal that acts as a solvent for the dispersed particles. The microparticles induce a local deformation of the liquid crystal, which then generates topological defects and long-range forces between the neighboring particles. The colloidal forces in nematic colloids are much stronger than the forces in ordinary colloids in isotropic solvents, exceeding thousands of kBT per micrometer-sized particle. Of special interest are the topological defects in nematic colloids, which appear in many fascinating forms, such as singular points, closed loops, multitudes of interlinked and knotted loops or soliton-like structures. The richness of the topological phenomena and the possibility to design and control topological defects with laser tweezers make colloids in nematic liquid crystals an excellent playground for testing the basic theorems of topology. PMID:29295574

2D-crystallization of Rhodococcus 20S proteasome at the liquid-liquid interface

NASA Astrophysics Data System (ADS)

Aoyama, Kazuhiro

1996-10-01

The 2D-crystallization method using the liquid-liquid interface between a aqueous phase (protein solution) and a thin organic liquid (dehydroabietylamine) layer has been applied to the Rhodococcus 20S proteasome. The 20S proteasome is known to be the core complex of the 26S proteasome, which is the central protease of the ubiquitin-dependent pathway. Two types of ordered arrays were obtained, both large enough for high resolution analysis by electron crystallography. The first one had a four-fold symmetry, whereas the second one was found out to be a hexagonally close-packed array. By image analysis based on a real space correlation averaging (CAV) technique, the close-packed array was found to be hexagonally packed, but the molecules had presumably rotational freedom. The four-fold array was found to be a true crystal with p4 symmetry. Lattice constants were a = b = 20.0 nm and α = 90°. The unit cell of this crystal contained two molecules. The diffraction pattern computed from the original picture showed spots up to (4, 5) that corresponds to 3.1 nm resolution. After applying an unbending procedure, the diffraction pattern showed spots extending to 1.8 nm resolution.

Fresnel formulas for the forced electromagnetic pulses and their application for optical-to-terahertz conversion in nonlinear crystals.

PubMed

Bakunov, M I; Maslov, A V; Bodrov, S B

2007-11-16

We show that the usual Fresnel formulas for a free-propagating pulse are not applicable for a forced terahertz electromagnetic pulse supported by an optical pulse at the end of a nonlinear crystal. The correct linear reflection and transmission coefficients that we derive show that such pulses can experience a gain or loss at the boundary. This energy change depends on linear dielectric constants only. We also predict a regime where a complete disappearance of the forced pulse under oblique incidence occurs, an effect that has no counterpart for free-propagating pulses.

High-resolution of particle contacts via fluorophore exclusion in deep-imaging of jammed colloidal packings

NASA Astrophysics Data System (ADS)

Kyeyune-Nyombi, Eru; Morone, Flaviano; Liu, Wenwei; Li, Shuiqing; Gilchrist, M. Lane; Makse, Hernán A.

2018-01-01

Understanding the structural properties of random packings of jammed colloids requires an unprecedented high-resolution determination of the contact network providing mechanical stability to the packing. Here, we address the determination of the contact network by a novel strategy based on fluorophore signal exclusion of quantum dot nanoparticles from the contact points. We use fluorescence labeling schemes on particles inspired by biology and biointerface science in conjunction with fluorophore exclusion at the contact region. The method provides high-resolution contact network data that allows us to measure structural properties of the colloidal packing near marginal stability. We determine scaling laws of force distributions, soft modes, correlation functions, coordination number and free volume that define the universality class of jammed colloidal packings and can be compared with theoretical predictions. The contact detection method opens up further experimental testing at the interface of jamming and glass physics.

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.

Templated electrokinetic directed chemical assembly for the fabrication of close-packed plasmonic metamolecules

NASA Astrophysics Data System (ADS)

Thrift, W. J.; Darvishzadeh-Varcheie, M.; Capolino, F.; Ragan, R.

2017-08-01

Colloidal self-assembly combined with templated surfaces holds the promise of fabricating large area devices in a low cost facile manner. This directed assembly approach improves the complexity of assemblies that can be achieved with self-assembly while maintaining advantages of molecular scale control. In this work, electrokinetic driving forces, i.e., electrohydrodynamic flow, are paired with chemical crosslinking between colloidal particles to form close-packed plasmonic metamolecules. This method addresses challenges of obtaining uniformity in nanostructure geometry and nanometer scale gap spacings in structures. Electrohydrodynamic flows yield robust driving forces between the template and nanoparticles as well as between nanoparticles on the surface promoting the assembly of close-packed metamolecules. Here, electron beam lithography defined Au pillars are used as seed structures that generate electrohydrodynamic flows. Chemical crosslinking between Au surfaces enables molecular control over gap spacings between nanoparticles and Au pillars. An as-fabricated structure is analyzed via full wave electromagnetic simulations and shown to produce large magnetic field enhancements on the order of 3.5 at optical frequencies. This novel method for directed self-assembly demonstrates the synergy between colloidal driving forces and chemical crosslinking for the fabrication of plasmonic metamolecules with unique electromagnetic properties.

The growth of homogeneous semiconductor crystals in a centrifuge by the stabilizing influence of the Coriolis force

NASA Astrophysics Data System (ADS)

Müller, G.; Neumann, G.; Weber, W.

1992-04-01

Both experimental and numerical results on crystal growth and fluid flow studies carried out in a centrifuge are reported. It is shown that the formation of doping striations can be avoided in the vertical Bridgman and the horizontal zone melting growth of Te-doped InSb if the centrifugal acceleration is increased beyond a critical value depending on the thermal boundary conditions. Furthermore, the maximum rate for the growth of inclusion free GaSb crystals grown by the travelling heater method (THM) is increased by a factor of 10 if this method is carried out at an acceleration of 20 times earth gravity. Model experiments in the Bridgman configuration using a test cell with liquid Ga and a larger series of thermocouples are conducted by varying the thermal boundary conditions and the rotation rate of the centrifuge. A three-dimensional time dependent numerical simulation of the fluid flow under the experimental conditions was carried out using a finite difference numerical scheme. It follows clearly that the Coriolis force acting on the melt in the rotating centrifuge system significantly influences the buoyancy-driven convection with respect to the flow patterns as well as the stability. The Coriolis force causes two very different flow states (I and II), depending on whether the rotation sense of the flow is in the same or in the opposite direction to that of the centrifuge. Type I is very similar to that normally observed on earth. Type II is only observed on the centrifuge and has a very large stability range of steady convection which can be used to grow striation-free crystals. All results give excellent agreement between model experiments and numerical calculations, which finally leads to a fully satisfying explanation of the crystal growth results on our centrifuge.

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

PubMed

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

2016-12-19

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

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Altering DNA-Programmable Colloidal Crystallization Paths by Modulating Particle Repulsion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Mary X.; Brodin, Jeffrey D.; Millan, Jaime A.

Colloidal crystal engineering with DNA can be used to realize precise control over nanoparticle (NP) arrangement. Here, we investigate a case of DNA-based assembly where the properties of DNA as a polyelectrolyte brush are employed to alter a hybridization-driven NP crystallization pathway. Using the co-assembly of DNA-conjugated proteins and spherical gold 2 nanoparticles (AuNPs) as a model system, we explore how steric repulsion between non-complementary, neighboring DNA-NPs due to overlapping DNA shells can influence their ligand-directed behavior. Specifically, our experimental data coupled with coarse-grained molecular dynamics (MD) simulations reveal that by changing factors related to NP repulsion, two structurally distinctmore » outcomes can be achieved. When steric repulsion between DNA-AuNPs is significantly greater than that between DNA-proteins, a lower packing density crystal lattice is favored over the structure that is predicted by design rules based on DNA-hybridization considerations alone. This is enabled by the large difference in DNA density on AuNPs versus proteins and can be tuned by modulating the flexibility, and thus conformational entropy, of the DNA on the constituent particles. At intermediate ligand flexibility, the crystallization pathways are energetically similar and the structural outcome can be adjusted using the density of DNA duplexes on DNA-AuNPs and by screening the Coulomb potential between them. Such lattices are shown to undergo dynamic reorganization upon changing salt concentration. These data help elucidate the structural considerations necessary for understanding repulsive forces in DNA-assembly and lay the groundwork for using them to increase architectural diversity in engineering colloidal crystals.« less

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.

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.

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 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...

American Spirit Pack Descriptors and Perceptions of Harm: A Crowdsourced Comparison of Modified Packs.

PubMed

Pearson, Jennifer L; Richardson, Amanda; Feirman, Shari P; Villanti, Andrea C; Cantrell, Jennifer; Cohn, Amy; Tacelosky, Michael; Kirchner, Thomas R

2016-08-01

In 2015, the Food and Drug Administration issued warnings to three tobacco manufacturers who label their cigarettes as "additive-free" and/or "natural" on the grounds that they make unauthorized reduced risk claims. The goal of this study was to examine US adults' perceptions of three American Spirit (AS) pack descriptors ("Made with Organic Tobacco," "100% Additive-Free," and "100% US Grown Tobacco") to assess if they communicate reduced risk. In September 2012, three cross-sectional surveys were posted on Amazon Mechanical Turk. Adult participants evaluated the relative harm of a Marlboro Red pack versus three different AS packs with the descriptors "Made with Organic Tobacco," "100% Additive-Free," or "100% US Grown Tobacco" (Survey 1; n = 461); a Marlboro Red pack versus these AS packs modified to exclude descriptors (Survey 2; n = 857); and unmodified versus modified AS pack images (Survey 3; n = 1001). The majority of Survey 1 participants rated the unmodified AS packs as less harmful than the Marlboro Red pack; 35.4%-58.8% of Survey 2 participants also rated the modified (no claims) packs as less harmful than Marlboro Red. In these surveys, prior use of AS cigarettes was associated with reduced perceptions of risk (adjusted odds ratio [AOR] 1.59-2.40). "Made with Organic Tobacco" and "100% Additive-Free" were associated with reduced perceptions of risk when comparing the modified versus the unmodified AS packs (Survey 3). Data suggest that these AS pack descriptors communicate reduced harm messages to consumers. Findings have implications for regulatory actions related to product labeling and packaging. These findings provide additional evidence that the "Made with Organic Tobacco," "100% Additive-Free," and "100% US Grown" descriptors, as well as other aspects of the AS pack design, communicate reduced harm to non-, current, and former smokers. Additionally, they provide support for the importance of FDA's 2015 warning to Santa Fe Natural Tobacco Company on

Failures of fractional crystallization: ordered co-crystals of isomers and near isomers.

PubMed

Kelley, Steven P; Fábián, László; Brock, Carolyn Pratt

2011-02-01

A list of 270 structures of ordered co-crystals of isomers, near isomers and molecules that are almost the same has been compiled. Searches for structures containing isomers could be automated by the use of IUPAC International Chemical Identifier (InChI™) strings but searches for co-crystals of very similar molecules were more labor intensive. Compounds in which the heteromolecular A···B interactions are clearly better than the average of the homomolecular A···A and B···B interactions were excluded. The two largest structural classes found include co-crystals of configurational diastereomers and of quasienantiomers (or quasiracemates). These two groups overlap. There are 114 co-crystals of diastereomers and the same number of quasiracemates, with 71 structures being counted in both groups; together the groups account for 157 structures or 58% of the total. The large number of quasiracemates is strong evidence for inversion symmetry being very favorable for crystal packing. Co-crystallization of two diastereomers is especially likely if a 1,1 switch of a methyl group and an H atom, or of an inversion of a [2.2.1] or [2.2.2] cage, in one of the diastereomers would make the two molecules enantiomers.

The Elegance of Disordered Granular Packings: A Validation of Edwards' Hypothesis

NASA Technical Reports Server (NTRS)

Metzger, Philip T.; Donahue, Carly M.

2004-01-01

We have found a way to analyze Edwards' density of states for static granular packings in the special case of round, rigid, frictionless grains assuming constant coordination number. It obtains the most entropic density of single grain states, which predicts several observables including the distribution of contact forces. We compare these results against empirical data obtained in dynamic simulations of granular packings. The agreement between theory and the empirics is quite good, helping validate the use of statistical mechanics methods in granular physics. The differences between theory and empirics are mainly due to the variable coordination number, and when the empirical data are sorted by that number we obtain several insights that suggest an underlying elegance in the density of states

Computational study of packing a collagen-like molecule: quasi-hexagonal vs "Smith" collagen microfibril model.

PubMed

Lee, J; Scheraga, H A; Rackovsky, S

1996-01-01

The lateral packing of a collagen-like molecule, CH3CO-(Gly-L-Pro-L-Pro)4-NHCH3, has been examined by energy minimization with the ECEPP/3 force field. Two current packing models, the Smith collagen microfibril twisted equilateral pentagonal model and the quasi-hexagonal packing model, have been extensively investigated. In treating the Smith microfibril model, energy minimization was carried out on various conformations including those with the symmetry of equivalent packing, i.e., in which the triple helices were arranged equivalently with respect to each other. Both models are based on the experimental observation of the characteristic axial periodicity, D = 67 nm, of light and dark bands, indicating that, if any superstructure exists, it should consist of five triple helices. The quasi-hexagonal packing structure is found to be energetically more favorable than the Smith microfibril model by as much as 31.2 kcal/mol of five triple helices. This is because the quasi-hexagonal packing geometry provides more nonbonded interaction possibilities between triple helices than does the Smith microfibril geometry. Our results are consistent with recent x-ray studies with synthetic collagen-like molecules and rat tail tendon, in which the data were interpreted as being consistent with either a quasi-hexagonal or a square-triangular structure.

PCR detection of psychrophilic Clostridium spp. causing 'blown pack' spoilage of vacuum-packed chilled meats.

PubMed

Broda, D M; Boerema, J A; Bell, R G

2003-01-01

To develop a practical molecular procedure that directly, without isolation, and specifically detects the presence of clostridia which cause 'blown pack' spoilage of vacuum-packed meat. Primer sets and PCR amplification procedures were developed that detect the presence of 16S rDNA gene and/or 16S-23S rDNA internal transcribed spacer fragments of 'blown pack' causing clostridia in meat. The specificity of the developed procedures was evaluated with DNA obtained from close phylogenetic neighbours of 'blown pack' causing clostridia, food clostridia and common meat spoilage microorganisms. The sensitivity of detection was assessed in non-enriched and low-temperature-enriched beef mince inoculated with serially diluted pure cultures of Clostridium estertheticum DSMZ 8809T and Cl. gasigenes DB1AT. The efficacy of detection procedures was evaluated for naturally contaminated vacuum-packed meat samples. Three primer sets, 16SE, 16SDB and EISR, produced amplicons of the expected size with DNA templates from target clostridia, but failed to yield PCR products with DNAs from any other microorganisms tested. With 16SE and 16SDB primers, minimum levels of detection were 104 CFU g(-1) for non-enriched, and 102 CFU g(-1) for enriched meat samples. Based on the established specificity of these primers, as well as DNA sequencing of amplicons, Cl. gasigenes was confirmed as the causative agent of 'blown pack' spoilage in two packs, and Cl. estertheticum as the causative agent in the third. The developed method can be used for rapid detection of 'blown pack' causing clostridia in commercial blown packs, or following low temperature enrichment, for detection of these microorganisms in meat containing as few as 100 clostridial cells per gram. The paper reports practical procedures that can be used for rapid confirmation of the causative agents of clostridial 'blown pack' spoilage in commercial spoiled packs, or for detection of psychrophilic clostridia in epidemiological trace back of

Crystallization of Deformable Spherical Colloids

NASA Astrophysics Data System (ADS)

Batista, Vera M. O.; Miller, Mark A.

2010-08-01

We introduce and characterize a first-order model for a generic class of colloidal particles that have a preferred spherical shape but can undergo deformations while always maintaining hard-body interactions. The model consists of hard spheres that can continuously change shape at fixed volume into prolate or oblate ellipsoids of revolution, subject to an energetic penalty. The severity of this penalty is specified by a single parameter that determines the flexibility of the particles. The deformable hard spheres crystallize at higher packing fractions than rigid hard spheres, have a narrower solid-fluid coexistence region and can reach high densities by a second transition to an orientationally ordered crystal.

An alternative cooling system to enhance the safety of Li-ion battery packs

NASA Astrophysics Data System (ADS)

Kizilel, Riza; Sabbah, Rami; Selman, J. Robert; Al-Hallaj, Said

A passive thermal management system is evaluated for high-power Li-ion packs under stressful or abusive conditions, and compared with a purely air-cooling mode under normal and abuse conditions. A compact and properly designed passive thermal management system utilizing phase change material (PCM) provides faster heat dissipation than active cooling during high pulse power discharges while preserving sufficiently uniform cell temperature to ensure the desirable cycle life for the pack. This study investigates how passive cooling with PCM contributes to preventing the propagation of thermal runaway in a single cell or adjacent cells due to a cell catastrophic failure. Its effectiveness is compared with that of active cooling by forced air flow or natural convection using the same compact module and pack configuration corresponding to the PCM matrix technology. The effects of nickel tabs and spacing between the cells were also studied.

Kinetics of pack aluminization of nickel

NASA Technical Reports Server (NTRS)

Seigle, L. L.; Gupta, B. K.; Shankar, R.; Sarkhel, A. K.

1978-01-01

The kinetics of pack aluminization of unalloyed nickel in packs of varying aluminum activity with various halide activators were studied. Surface compositions of the coatings as functions of time, temperature, and pack composition were obtained in order to establish the boundary conditions for diffusion in the system. The structure of the packs was also examined in order to clarify the mechanism of aluminum transport. The results indicate that the kinetics of pack aluminization are controlled jointly by gas diffusion in the pack and solid diffusion in the coating. Levine and Caves' model for gas diffusion was combined with calculations of rates of diffusion in the solid to formulate a more complete theory for the kinetics of pack aluminization.

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

DOE PAGES

Arul Kumar, Mariyappan; Beyerlein, Irene Jane; McCabe, Rodney James; ...

2016-12-19

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

Βiocolloid and colloid transport through water-saturated columns packed with glass beads: Effect of gravity

NASA Astrophysics Data System (ADS)

Chrysikopoulos, C. V.; Syngouna, V. I.

2013-12-01

The role of gravitational force on biocolloid and colloid transport in water-saturated columns packed with glass beads was investigated. Transport experiments were performed with biocolloids (bacteriophages: ΦΧ174, MS2) and colloids (clays: kaolinite KGa-1b, montmorillonite STx-1b). The packed columns were placed in various orientations (horizontal, vertical, and diagonal) and a steady flow rate of Q=1.5 mL/min was applied in both up-flow and down-flow modes. All experiments were conducted under electrostatically unfavorable conditions. The experimental data were fitted with a newly developed, analytical, one dimensional, colloid transport model, accounting for gravity effects. The results revealed that flow direction has a significant influence on particle deposition. The rate of particle deposition was shown to be greater for up-flow than for down-flow direction, suggesting that gravity was a significant driving force for biocolloid and colloid deposition. Schematic illustration of a packed column with up-flow velocity having orientation (-i) with respect to gravity. The gravity vector components are: g(i)= g(-z) sinβ i, and g(-j)= -g(-z) cosβ j. Experimental setup showing the various column arrangements: (a) horizontal, (b) diagonal, and (c) vertical.

Career Action Pack.

ERIC Educational Resources Information Center

Blum, Robert E.; Raymond, Carolyn D.

One of five McDonald's Action Packs, these instructional materials for ninth and tenth graders (and more able sixth and seventh graders) have incorporated ideas around three career development goals--subject relevance, career awareness, and self-awareness. The action pack contains six units--three units each in the subject areas of language arts…

Crystallization of phycoerythrocyanin from the cyanobacterium Mastigocladus laminosus and preliminary characterization of two crystal forms.

PubMed

Rümbeli, R; Schirmer, T; Bode, W; Sidler, W; Zuber, H

1985-11-05

The light-harvesting protein phycoerythrocyanin from the cyanobacterium Mastigocladus laminosus Cohn has been crystallized in two different crystal forms by vapour diffusion. In 5% (w/v) polyethylene glycol at pH 8.5, hexagonal crystals of space group P63 with cell constants a = b = 158 A, c = 40.6 A were obtained, which turned out to be almost isomorphous with the hexagonal crystals of C-phycocyanin from the same organism. Consequently, the conformation of both phycobiliproteins must be very similar. From 1.5 M-ammonium sulfate (pH 8.5), orthorhombic crystals of space group P2221 with cell constants a = 60.5 A, b = 105 A, c = 188 A could be grown. Density measurements of these crystals indicate that the unit cell contains 18 (alpha beta)-units. A detailed packing scheme is proposed that is consistent with the observed pseudo-hexagonal X-ray intensity pattern and with the known size and shape of (alpha beta)3-trimers of C-phycocyanin. Accordingly, disc-like (alpha beta)3-trimers are associated face-to-face and stacked one upon another in rods with a period of 60.5 A, corresponding to the cell dimension a.

Fully Dynamic Bin Packing

NASA Astrophysics Data System (ADS)

Ivković, Zoran; Lloyd, Errol L.

Classic bin packing seeks to pack a given set of items of possibly varying sizes into a minimum number of identical sized bins. A number of approximation algorithms have been proposed for this NP-hard problem for both the on-line and off-line cases. In this chapter we discuss fully dynamic bin packing, where items may arrive (Insert) and depart (Delete) dynamically. In accordance with standard practice for fully dynamic algorithms, it is assumed that the packing may be arbitrarily rearranged to accommodate arriving and departing items. The goal is to maintain an approximately optimal solution of provably high quality in a total amount of time comparable to that used by an off-line algorithm delivering a solution of the same quality.

Modeling the Growth Rates of Tetragonal Lysozyme Crystal Faces

NASA Technical Reports Server (NTRS)

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

1998-01-01

The measured macroscopic growth rates of the (110) and (101) faces of tetragonal lysozyme show an unexpectedly complex dependence on the supersaturation. The growth rates decay asymptotically to zero when the supersaturation is lowered to zero and increase rapidly when the supersaturation is increased. When supersaturations are increased still further the growth rates attain a maximum before starting to decrease. However, growth of these crystals is known to proceed by the classical dislocation and 2D nucleation growth mechanisms. This anomaly can be explained if growth is assumed to occur not by monomer units but by lysozyme aggregates. Analysis of the molecular packing of these crystals revealed that they were constructed of strongly bonded 4(sub 3) helices, while weaker bonds were responsible for binding the helices to each other. It follows that during crystal growth the stronger bonds are formed before the weaker ones. Thus, the growth of these crystals could be viewed as a two step process: aggregate growth units corresponding to the 4(sub 3) helix are first formed in the bulk solution by stronger intermolecular bonds and then attached to the crystal face by weaker bonds on dislocation hillocks or 2D islands. This will lead to a distribution of aggregates in the solution with monomers and lower order aggregates being predominant at low supersaturations and higher order aggregates being predominant at high supersaturations. If the crystal grows mostly by higher order aggregates, such as tetramers and octamers, it would explain the anomalous dependence of the growth rates on the supersaturation. Besides the analysis of molecular packing, a comprehensive analysis of the measured (110) and (101) growth rates was also undertaken in this study. The distribution of aggregates in lysozyme nutrient solutions at various solution conditions were determined from reversible aggregation reactions at equilibrium. The supersaturation was defined for each aggregate species

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.

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

PubMed

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

2017-10-01

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

Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling.

PubMed

Arnautova, Yelena A; Abagyan, Ruben A; Totrov, Maxim

2011-02-01

We report the development of internal coordinate mechanics force field (ICMFF), new force field parameterized using a combination of experimental data for crystals of small molecules and quantum mechanics calculations. The main features of ICMFF include: (a) parameterization for the dielectric constant relevant to the condensed state (ε = 2) instead of vacuum, (b) an improved description of hydrogen-bond interactions using duplicate sets of van der Waals parameters for heavy atom-hydrogen interactions, and (c) improved backbone covalent geometry and energetics achieved using novel backbone torsional potentials and inclusion of the bond angles at the C(α) atoms into the internal variable set. The performance of ICMFF was evaluated through loop modeling simulations for 4-13 residue loops. ICMFF was combined with a solvent-accessible surface area solvation model optimized using a large set of loop decoys. Conformational sampling was carried out using the biased probability Monte Carlo method. Average/median backbone root-mean-square deviations of the lowest energy conformations from the native structures were 0.25/0.21 Å for four residues loops, 0.84/0.46 Å for eight residue loops, and 1.16/0.73 Å for 12 residue loops. To our knowledge, these results are significantly better than or comparable with those reported to date for any loop modeling method that does not take crystal packing into account. Moreover, the accuracy of our method is on par with the best previously reported results obtained considering the crystal environment. We attribute this success to the high accuracy of the new ICM force field achieved by meticulous parameterization, to the optimized solvent model, and the efficiency of the search method. © 2010 Wiley-Liss, Inc.

Electrocauterization and no packing may be comparable with nasal packing for postoperative hemorrhage after endoscopic sinus surgery.

PubMed

Kim, Dong-Kyu; Rhee, Chae Seo; Kim, Jeong-Whun

2016-05-01

Nasal packing is commonly performed after functional endoscopic sinus surgery (FESS). However, nasal packing is associated with higher cost (owing to the cost of packing materials), patient discomfort, delayed wound healing, and concern about toxic shock syndrome. Some surgeons have been performing FESS without packing, but there are few studies that show its safety. The purpose of this study was to evaluate the safety of electrocauterization and no packing. A total of 490 patients who underwent bilateral FESS for chronic rhinosinusitis were included in this retrospective study, 242 in the nasal packing group and 248 in the electrocauterization and no-packing group. Electrocauterization was performed by using a suction coagulator. Rates of immediate (first 24 hours after surgery) and delayed postoperative bleeding were compared. Patient characteristics, including concomitant disease and medication history, and Lund-Mackay computed tomography score were also assessed Results: There were no significant differences in age; sex; Lund-Mackay score; use of anticoagulant drugs; or prevalence of hypertension, diabetes, or asthma between the two groups. In the electrocauterization and no-packing group, there were fewer patients with allergic rhinitis and more smokers. Primary bleeding did not occur in the nasal packing group, but 11 patients (4.4%) had delayed bleeding. Primary bleeding occurred in four patients (1.7%) in the electrocauterization and no-packing group, and five patients (2.1%) had delayed bleeding. There were no significant differences in primary (p = 0.058) and secondary bleeding (p = 0.142) between the two groups. All bleeding was minor and easily controlled. Multivariate logistic regression analysis ruled out significant correlation between no packing and postoperative bleeding. This study provided evidence that, in terms of postoperative hemorrhage, the safety of the electrocauterization and no-packing technique after FESS was comparable with that of

Apparatus for mounting crystal

DOEpatents

Longeway, Paul A.

1985-01-01

A thickness monitor useful in deposition or etching reactor systems comprising a crystal-controlled oscillator in which the crystal is deposited or etched to change the frequency of the oscillator. The crystal rests within a thermally conductive metallic housing and arranged to be temperature controlled. Electrode contacts are made to the surface primarily by gravity force such that the crystal is substantially free of stress otherwise induced by high temperature.

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...

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...

Clot contraction: compression of erythrocytes into tightly packed polyhedra and redistribution of platelets and fibrin

PubMed Central

Cines, Douglas B.; Lebedeva, Tatiana; Nagaswami, Chandrasekaran; Hayes, Vincent; Massefski, Walter; Litvinov, Rustem I.; Rauova, Lubica; Lowery, Thomas J.

2014-01-01

Contraction of blood clots is necessary for hemostasis and wound healing and to restore flow past obstructive thrombi, but little is known about the structure of contracted clots or the role of erythrocytes in contraction. We found that contracted blood clots develop a remarkable structure, with a meshwork of fibrin and platelet aggregates on the exterior of the clot and a close-packed, tessellated array of compressed polyhedral erythrocytes within. The same results were obtained after initiation of clotting with various activators and also with clots from reconstituted human blood and mouse blood. Such close-packed arrays of polyhedral erythrocytes, or polyhedrocytes, were also observed in human arterial thrombi taken from patients. The mechanical nature of this shape change was confirmed by polyhedrocyte formation from the forces of centrifugation of blood without clotting. Platelets (with their cytoskeletal motility proteins) and fibrin(ogen) (as the substrate bridging platelets for contraction) are required to generate the forces necessary to segregate platelets/fibrin from erythrocytes and to compress erythrocytes into a tightly packed array. These results demonstrate how contracted clots form an impermeable barrier important for hemostasis and wound healing and help explain how fibrinolysis is greatly retarded as clots contract. PMID:24335500

Gravity-independent constant force resistive exercise unit

NASA Technical Reports Server (NTRS)

Colosky, Jr., Paul E. (Inventor); Ruttley, Tara M. (Inventor)

2004-01-01

This invention describes a novel gravity-independent exercise unit designed for use in microgravity, or on the ground, as a means by which to counter muscle atrophy and bone degradation due to disuse or underuse. Modular resistive packs comprising constant torque springs provide constant force opposing the withdrawal of an exercise cable from the device. In addition to uses within the space program, the compact resistive packs of the CFREU allow the unit to be small enough for easy use as a home gym for personal use, or as a supplement for rehabilitation programs. Resistive packs may be changed conveniently out of the CFREU according to the desired exercise regimen. Thus, the resistive packs replace the need for expensive, heavy, and bulky traditional weight plates. The CFREU may be employed by hospitals, rehabilitation and physical therapy clinics, and other related professional businesses.

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...

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

Molecular structures of the inclusion complexes beta-cyclodextrin-1,2-bis(4-aminophenyl)ethane and beta-cyclodextrin-4,4'-diaminobiphenyl; packing of dimeric beta-cyclodextrin inclusion complexes.

PubMed

Giastas, Petros; Yannakopoulou, Konstantina; Mavridis, Irene M

2003-04-01

The present investigation is part of an ongoing study on the influence of the long end-functonalized guest molecules DBA and BNZ in the crystal packing of beta-cyclodextrin (betaCD) dimeric complexes. The title compounds are 2:2 host:guest complexes showing limited host-guest hydrogen bonding at the primary faces of the betaCD dimers. Within the betaCD cavity the guests exhibit mutual pi...pi interactions and between betaCD dimers perpendicular NH...pi interactions. The DBA guest molecule exhibits one extended and two bent conformations in the complex. The BNZ guest molecule is not planar inside betaCD, in contrast to the structure of BNZ itself, which indicates that the cavity isolates the molecules and forbids the pi...pi stacking of the aromatic rings. NMR spectroscopy studies show that in aqueous solution both DBA and BNZ form strong complexes that have 1:1 stoichiometry and structures similar to the solid state ones. The relative packing of the dimers is the same in both complexes. The axes of two adjacent dimers form an angle close to 20 degrees and have a lateral displacement approximately 2.45 A, both of which characterize the screw-channel mode of packing. Although the betaCD/BNZ complex indeed crystallizes in a space group characterizing the latter mode, the betaCD/DBA complex crystallizes in a space group with novel dimensions not resembling any of the packing modes reported so far. The new lattice is attributed to the three conformations exhibited by the guest in the crystals. However, this lattice can be transformed into another, which is isostructural to that of the betaCD/BNZ inclusion complex, if the conformation of the guest is not taken into account.

Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins.

PubMed

Gaines, J C; Acebes, S; Virrueta, A; Butler, M; Regan, L; O'Hern, C S

2018-05-01

We compare side chain prediction and packing of core and non-core regions of soluble proteins, protein-protein interfaces, and transmembrane proteins. We first identified or created comparable databases of high-resolution crystal structures of these 3 protein classes. We show that the solvent-inaccessible cores of the 3 classes of proteins are equally densely packed. As a result, the side chains of core residues at protein-protein interfaces and in the membrane-exposed regions of transmembrane proteins can be predicted by the hard-sphere plus stereochemical constraint model with the same high prediction accuracies (>90%) as core residues in soluble proteins. We also find that for all 3 classes of proteins, as one moves away from the solvent-inaccessible core, the packing fraction decreases as the solvent accessibility increases. However, the side chain predictability remains high (80% within 30°) up to a relative solvent accessibility, rSASA≲0.3, for all 3 protein classes. Our results show that ≈40% of the interface regions in protein complexes are "core", that is, densely packed with side chain conformations that can be accurately predicted using the hard-sphere model. We propose packing fraction as a metric that can be used to distinguish real protein-protein interactions from designed, non-binding, decoys. Our results also show that cores of membrane proteins are the same as cores of soluble proteins. Thus, the computational methods we are developing for the analysis of the effect of hydrophobic core mutations in soluble proteins will be equally applicable to analyses of mutations in membrane proteins. © 2018 Wiley Periodicals, Inc.

Phase behavior and crystal structure of 3-(1-naphthyloxy)- and 3-(4-indolyloxy)-propane-1,2-diol, synthetic precursors of chiral drugs propranolol and pindolol

NASA Astrophysics Data System (ADS)

Bredikhin, Alexander A.; Gubaidullin, Aidar T.; Bredikhina, Zemfira A.; Fayzullin, Robert R.; Samigullina, Aida I.; Zakharychev, Dmitry V.

2013-08-01

Valuable precursors of popular chiral drugs propranolol and pindolol, 3-(1-naphthyloxy)-propane-1,2-diol 3 and 3-(4-indolyloxy)-propane-1,2-diol 4 were investigated by IR spectroscopy, DSC, and X-ray diffraction methods. Both compounds, crystallizing from enantiopure feed material, form "guaifenesin-like" crystal packing in which the classic H-bonded bilayers, framed in both sides by hydrophobic fragments of the molecules, acts as the basic crystal-forming motif. Diol 4 prone to spontaneous resolution and conserves its packing pattern crystallizing from racemate. Under the same conditions, diol 3 forms weakly stable solid racemic compound. Some reasons for such a behavior are identified and discussed.

Disappearance of the force-free current configuration at the first order vortex lattice phase transition in YBa 2Cu 3O 7-δ single crystals

NASA Astrophysics Data System (ADS)

van der Beek, C. J.; Indenbom, M. V.; Berseth, V.; Benoit, W.; Erb, A.; Flükiger, R.

1997-08-01

The anisotropy in the transverse AC susceptibility of YBa2Cu3O7-δ single crystals, induced by the periodic appearance of a force-free current configuration upon rotation of a superimposed DC field in the crystal plane, disappears at the vortex phase transition, indicating the loss of the vortex lines' stability against mutual cutting.

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,…

Conical wave propagation and diffraction in two-dimensional hexagonally packed granular lattices

DOE PAGES

Chong, C.; Kevrekidis, P. G.; Ablowitz, M. J.; ...

2016-01-25

We explore linear and nonlinear mechanisms for conical wave propagation in two-dimensional lattices in the realm of phononic crystals. As a prototypical example, a statically compressed granular lattice of spherical particles arranged in a hexagonal packing configuration is analyzed. Upon identifying the dispersion relation of the underlying linear problem, the resulting diffraction properties are considered. Analysis both via a heuristic argument for the linear propagation of a wave packet and via asymptotic analysis leading to the derivation of a Dirac system suggests the occurrence of conical diffraction. This analysis is valid for strong precompression, i.e., near the linear regime. Formore » weak precompression, conical wave propagation is still possible, but the resulting expanding circular wave front is of a nonoscillatory nature, resulting from the complex interplay among the discreteness, nonlinearity, and geometry of the packing. Lastly, the transition between these two types of propagation is explored.« less

The Strength of Binary Junctions in Hexagonal Close-Packed Crystals

DTIC Science & Technology

2014-03-01

equilib- rium, on either slip plane, the dislocation on that plane intersects both triple points at the same angle with the junc- tion line, regardless...electronic properties of threading dislocations in wide band-gap gallium nitride (a wurtzite crystal structure consisting of two interpenetrating hcp...yield surface was composed of individual points , it pro- vided insight on the resistance of the lock to breaking as a result of the applied stresses. Via

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

PubMed

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

2015-11-01

A novel opal closest-packing (OCP) photonic crystal (PC) was prepared by the introduction of molecular imprinting technique into the OCP PC. This molecular imprinted (MI)-OCP PC was fabricated via a vertical convective self-assembly method using 17β-estradiol (E2) as template molecules for monitoring E2 in aqueous solution. Morphology characterization showed that the MI-OCP PC possessed a highly ordered three-dimensional (3D) periodically-ordered structure, showing the desired structural color. The proposed PC material displayed a reduced reflection intensity when detecting E2 in water environment, because the molecular imprinting recognition events make the optical characteristics of PC change. The Bragg diffraction intensity decreased by 19.864 a.u. with the increase of E2 concentration from 1.5 ng mL(-1) to 364.5 ng mL(-1) within 6 min, whereas there were no obvious peak intensity changes for estriol, estrone, cholesterol, testosterone and diethylstilbestrol, indicating that the MI-OCP PC had selective and rapid response for E2 molecules. The adsorption results showed that the OCP structure and homogeneous layers were created in the MI-OCP PC with higher adsorption capacity. Thus, it was learned the MI-OCP PC is a simple prepared, sensitive, selective, and easy operative material, which shows promising use in routine supervision for residue detection in food and environment. Copyright © 2015 Elsevier B.V. All rights reserved.

Crystal structure and conformational analysis of s-cis-(acetylacetonato)(ethylenediamine-N,N'-diacetato)-chromium(III): development of vibrationally optimized force field (VOFF).

PubMed

Choi, Jong-Ha; Niketić, Svetozar R; Djordjević, Ivana; Clegg, William; Harrington, Ross W

2012-05-01

The crystal structure of [Cr(edda)(acac)] (edda = ethylediamine-N,N'-diacetate; acac = acetylacetonato) has been determined by a single crystal X-ray diffraction study at 150 K. The chromium ion is in a distorted octahedral environment coordinated by two N and two O atoms of chelating edda and two O atoms of acac, resulting in s-cis configuration. The complex crystallizes in the space group P2(1)/c of the monoclinic system in a cell of dimensions a = 10.2588(9), b = 15.801(3), c = 8.7015(11) Å, β =101.201(9)° and Z = 4. The mean Cr-N(edda), Cr-O(edda) and Cr-O(acac) bond distances are 2.0829(14), 1.9678(11) and 1.9477(11) Å while the angles O-Cr-O of edda and O-Cr-O of acac are 171.47(5) and 92.72(5)°, respectively. The crystal structure is stabilized by N-H···O hydrogen bonds linking [Cr(edda)(acac)] molecules in distinct linear strands. The visible electronic and IR spectroscopic properties are also discussed. An improved, physically more realistic force field, Vibrationally Optimized Force Field (VOFF), capable of reproducing structural and vibrational properties of [Cr(edda)(acac)] was developed and its transferability demonstrated on selected chromium(III) complexes with similar ligands.

William Barlow and the Determination of Atomic Arrangement in Crystals.

PubMed

Mauskopf, Seymour H

2015-04-01

William Barlow (1845-1934) was an important if unconventional scientist, known for having developed the 'closest-packing' atomic models of crystal structure. He resumed an early nineteenth-century tradition of utilizing crystallographical and chemical data to determine atomic arrangements in crystals. This essay recounts Barlow's career and scientific activity in three parts: (a) His place in the tradition of determining atomic arrangement in context of this earlier tradition and of contemporaneous developments of crystallography and chemistry, (b) his unconventional career, and (c) the 'success' of his program to determine atomic arrangements in crystals and its influence on the work of William Lawrence Bragg.

Nonlinear coherent structures in granular crystals

NASA Astrophysics Data System (ADS)

Chong, C.; Porter, Mason A.; Kevrekidis, P. G.; Daraio, C.

2017-10-01

The study of granular crystals, which are nonlinear metamaterials that consist of closely packed arrays of particles that interact elastically, is a vibrant area of research that combines ideas from disciplines such as materials science, nonlinear dynamics, and condensed-matter physics. Granular crystals exploit geometrical nonlinearities in their constitutive microstructure to produce properties (such as tunability and energy localization) that are not conventional to engineering materials and linear devices. In this topical review, we focus on recent experimental, computational, and theoretical results on nonlinear coherent structures in granular crystals. Such structures—which include traveling solitary waves, dispersive shock waves, and discrete breathers—have fascinating dynamics, including a diversity of both transient features and robust, long-lived patterns that emerge from broad classes of initial data. In our review, we primarily discuss phenomena in one-dimensional crystals, as most research to date has focused on such scenarios, but we also present some extensions to two-dimensional settings. Throughout the review, we highlight open problems and discuss a variety of potential engineering applications that arise from the rich dynamic response of granular crystals.

Anisotropic Strain Relaxation of Graphene by Corrugation on Copper Crystal Surfaces.

PubMed

Deng, Bing; Wu, Juanxia; Zhang, Shishu; Qi, Yue; Zheng, Liming; Yang, Hao; Tang, Jilin; Tong, Lianming; Zhang, Jin; Liu, Zhongfan; Peng, Hailin

2018-05-01

Corrugation is a ubiquitous phenomenon for graphene grown on metal substrates by chemical vapor deposition, which greatly affects the electrical, mechanical, and chemical properties. Recent years have witnessed great progress in controlled growth of large graphene single crystals; however, the issue of surface roughness is far from being addressed. Here, the corrugation at the interface of copper (Cu) and graphene, including Cu step bunches (CuSB) and graphene wrinkles, are investigated and ascribed to the anisotropic strain relaxation. It is found that the corrugation is strongly dependent on Cu crystallographic orientations, specifically, the packed density and anisotropic atomic configuration. Dense Cu step bunches are prone to form on loose packed faces due to the instability of surface dynamics. On an anisotropic Cu crystal surface, Cu step bunches and graphene wrinkles are formed in two perpendicular directions to release the anisotropic interfacial stress, as revealed by morphology imaging and vibrational analysis. Cu(111) is a suitable crystal face for growth of ultraflat graphene with roughness as low as 0.20 nm. It is believed the findings will contribute to clarifying the interplay between graphene and Cu crystal faces, and reducing surface roughness of graphene by engineering the crystallographic orientation of Cu substrates. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Computerized Planning of Cryosurgery Using Bubble Packing: An Experimental Validation on a Phantom Material

PubMed Central

Rossi, Michael R.; Tanaka, Daigo; Shimada, Kenji; Rabin, Yoed

2009-01-01

The current study focuses on experimentally validating a planning scheme based on the so-called bubble-packing method. This study is a part of an ongoing effort to develop computerized planning tools for cryosurgery, where bubble packing has been previously developed as a means to find an initial, uniform distribution of cryoprobes within a given domain; the so-called force-field analogy was then used to move cryoprobes to their optimum layout. However, due to the high quality of the cryoprobes’ distribution, suggested by bubble packing and its low computational cost, it has been argued that a planning scheme based solely on bubble packing may be more clinically relevant. To test this argument, an experimental validation is performed on a simulated cross-section of the prostate, using gelatin solution as a phantom material, proprietary liquid-nitrogen based cryoprobes, and a cryoheater to simulate urethral warming. Experimental results are compared with numerically simulated temperature histories resulting from planning. Results indicate an average disagreement of 0.8 mm in identifying the freezing front location, which is an acceptable level of uncertainty in the context of prostate cryosurgery imaging. PMID:19885373

Fine-Tuning Nanoparticle Packing at Water-Oil Interfaces Using Ionic Strength.

PubMed

Chai, Yu; Lukito, Alysia; Jiang, Yufeng; Ashby, Paul D; Russell, Thomas P

2017-10-11

Nanoparticle-surfactants (NPSs) assembled at water-oil interfaces can significantly lower the interfacial tension and can be used to stabilize liquids. Knowing the formation and assembly and actively tuning the packing of these NPSs is of significant fundamental interest for the interfacial behavior of nanoparticles and of interest for water purification, drug encapsulation, enhanced oil recovery, and innovative energy transduction applications. Here, we demonstrate by means of interfacial tension measurements the high ionic strength helps the adsorption of NPSs to the water-oil interface leading to a denser packing of NPSs at the interface. With the reduction of interfacial area, the phase transitions from a "gas"-like to "liquid" to "solid" states of NPSs in two dimensions are observed. Finally, we provide the first in situ real-space imaging of NPSs at the water-oil interface by atomic force microcopy.

Adhesive loose packings of small dry particles.

PubMed

Liu, Wenwei; Li, Shuiqing; Baule, Adrian; Makse, Hernán A

2015-08-28

We explore adhesive loose packings of small dry spherical particles of micrometer size using 3D discrete-element simulations with adhesive contact mechanics and statistical ensemble theory. A dimensionless adhesion parameter (Ad) successfully combines the effects of particle velocities, sizes and the work of adhesion, identifying a universal regime of adhesive packings for Ad > 1. The structural properties of the packings in this regime are well described by an ensemble approach based on a coarse-grained volume function that includes the correlation between bulk and contact spheres. Our theoretical and numerical results predict: (i) an equation of state for adhesive loose packings that appear as a continuation from the frictionless random close packing (RCP) point in the jamming phase diagram and (ii) the existence of an asymptotic adhesive loose packing point at a coordination number Z = 2 and a packing fraction ϕ = 1/2(3). Our results highlight that adhesion leads to a universal packing regime at packing fractions much smaller than the random loose packing (RLP), which can be described within a statistical mechanical framework. We present a general phase diagram of jammed matter comprising frictionless, frictional, adhesive as well as non-spherical particles, providing a classification of packings in terms of their continuation from the spherical frictionless RCP.

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. Copyright © 2016 Elsevier Inc. All rights reserved.

5 Reasons to Pack Your Lunch

MedlinePlus

... Staying Safe Videos for Educators Search English Español 5 Reasons to Pack Your Lunch KidsHealth / For Teens / 5 Reasons to Pack Your Lunch Print 5 Reasons to Pack Your Lunch Most schools are ...

Interplay of electrostatics and lipid packing determines the binding of charged polymer coated nanoparticles to model membranes.

PubMed

Biswas, Nupur; Bhattacharya, Rupak; Saha, Arindam; Jana, Nikhil R; Basu, Jaydeep K

2015-10-07

Understanding of nanoparticle-membrane interactions is useful for various applications of nanoparticles like drug delivery and imaging. Here we report on the studies of interaction between hydrophilic charged polymer coated semiconductor quantum dot nanoparticles with model lipid membranes. Atomic force microscopy and X-ray reflectivity measurements suggest that cationic nanoparticles bind and penetrate bilayers of zwitterionic lipids. Penetration and binding depend on the extent of lipid packing and result in the disruption of the lipid bilayer accompanied by enhanced lipid diffusion. On the other hand, anionic nanoparticles show minimal membrane binding although, curiously, their interaction leads to reduction in lipid diffusivity. It is suggested that the enhanced binding of cationic QDs at higher lipid packing can be understood in terms of the effective surface potential of the bilayers which is tunable through membrane lipid packing. Our results bring forth the subtle interplay of membrane lipid packing and electrostatics which determine nanoparticle binding and penetration of model membranes with further implications for real cell membranes.

Berkeley Screen: a set of 96 solutions for general macromolecular crystallization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pereira, Jose H.; McAndrew, Ryan P.; Tomaleri, Giovani P.

Using statistical analysis of the Biological Macromolecular Crystallization Database, combined with previous knowledge about crystallization reagents, a crystallization screen called the Berkeley Screen has been created. Correlating crystallization conditions and high-resolution protein structures, it is possible to better understand the influence that a particular solution has on protein crystal formation. Ions and small molecules such as buffers and precipitants used in crystallization experiments were identified in electron density maps, highlighting the role of these chemicals in protein crystal packing. The Berkeley Screen has been extensively used to crystallize target proteins from the Joint BioEnergy Institute and the Collaborative Crystallography programmore » at the Berkeley Center for Structural Biology, contributing to several Protein Data Bank entries and related publications. The Berkeley Screen provides the crystallographic community with an efficient set of solutions for general macromolecular crystallization trials, offering a valuable alternative to the existing commercially available screens. The Berkeley Screen provides an efficient set of solutions for general macromolecular crystallization trials.« less

Berkeley Screen: a set of 96 solutions for general macromolecular crystallization

DOE PAGES

Pereira, Jose H.; McAndrew, Ryan P.; Tomaleri, Giovani P.; ...

2017-09-05

Using statistical analysis of the Biological Macromolecular Crystallization Database, combined with previous knowledge about crystallization reagents, a crystallization screen called the Berkeley Screen has been created. Correlating crystallization conditions and high-resolution protein structures, it is possible to better understand the influence that a particular solution has on protein crystal formation. Ions and small molecules such as buffers and precipitants used in crystallization experiments were identified in electron density maps, highlighting the role of these chemicals in protein crystal packing. The Berkeley Screen has been extensively used to crystallize target proteins from the Joint BioEnergy Institute and the Collaborative Crystallography programmore » at the Berkeley Center for Structural Biology, contributing to several Protein Data Bank entries and related publications. The Berkeley Screen provides the crystallographic community with an efficient set of solutions for general macromolecular crystallization trials, offering a valuable alternative to the existing commercially available screens. The Berkeley Screen provides an efficient set of solutions for general macromolecular crystallization trials.« less

Facile synthesis of gold nanomaterials with unusual crystal structures.

PubMed

Fan, Zhanxi; Huang, Xiao; Chen, Ye; Huang, Wei; Zhang, Hua

2017-11-01

Gold (Au) nanomaterials have attracted wide research attention, owing to their high chemical stability, promising catalytic properties, excellent biocompatibility, unique electronic structure and outstanding localized surface plasmon resonance (LSPR) absorption properties; all of which are closely related to their size and shape. Recently, crystal-phase-controlled synthesis of noble metal nanomaterials has emerged as a promising strategy to tune their physicochemical properties. This protocol describes the detailed experimental procedures for the crystal-phase-controlled syntheses of Au nanomaterials with unusual crystal structures under mild conditions. Briefly, pure hexagonal close-packed (hcp) Au square sheets (AuSSs) with a thickness of ∼2.4 nm are synthesized using a graphene-oxide-assisted method in which HAuCl 4 is reduced by oleylamine in a mixture of hexane and ethanol. By using pure hexane as the solvent, well-dispersed ultrathin hcp/face-centered cubic (fcc) Au nanowires with a diameter of ∼1.6 nm on graphene oxide can be obtained. Meanwhile, hcp/fcc Au square-like plates with a side length of 200-400 nm are prepared via the secondary growth of Au on the hcp AuSSs. Remarkably, hexagonal (4H) Au nanoribbons with a thickness of 2.0-6.0 nm can be synthesized with a one-pot colloidal method in which HAuCl 4 is reduced by oleylamine in a mixed solvent of hexane and 1,2-dichloropropane. It takes 17-37 h for the synthesis of these Au nanomaterials with unusual crystal structures. Transmission electron microscopy (TEM) and atomic force microscopy (AFM) are used to characterize the resultant Au nanomaterials, which could have many promising applications, such as biosensing, near-IR photothermal therapy, catalysis and surface-enhanced Raman scattering (SERS).

Pack Density Limitations of Hybrid Parachutes

NASA Technical Reports Server (NTRS)

Zwicker, Matthew L.; Sinclair, Robert J.

2013-01-01

The development and testing of the Orion crew capsule parachute system has provided a unique opportunity to study dense parachute packing techniques and limits, in order to establish a new baseline for future programs. The density of parachute packs has a significant influence on vibration loads, retention system stresses, and parachute mortar performance. Material compositions and pack densities of existing designs for space capsule recovery were compared, using the pack density of the Apollo main parachutes as the current baseline. The composition of parachutes has changed since Apollo, incorporating new materials such as Kevlar , Vectran , Teflon and Spectra . These materials have different specific densities than Nylon, so the densities of hybrid parachute packs cannot be directly compared to Nylon parachutes for determination of feasibility or volume allocation. Six parachute packs were evaluated in terms of weighted average solid density in order to achieve a non-dimensional comparison of packing density. Means of mitigating damage due to packing pressure and mortar firing were examined in light of the Capsule Parachute Assembly System (CPAS) and Apollo experience. Parachute design improvements including incorporation of modern materials and manufacturing processes serves to make CPAS the new knowledge base on which future spacecraft parachute systems will be built.

Visualization and quantification of two-phase flow in transparent miniature packed beds

NASA Astrophysics Data System (ADS)

Zhu, Peixi; Papadopoulos, Kyriakos D.

2012-10-01

Optical microscopy was used to visualize the flow of two phases [British Petroleum (BP) oil and an aqueous surfactant phase] in confined space, three-dimensional, transparent, natural porous media. The porous media consisted of water-wet cryolite grains packed inside cylindrical, glass microchannels, thus producing microscopic packed beds. Primary drainage of BP oil displacing an aqueous surfactant phase was studied at capillary numbers that varied between 10-6 and 10-2. The confinement space had a significant effect on the flow behavior. Phenomena of burst motion and capillary fingering were observed for low capillary numbers due to the domination of capillary forces. It was discovered that breakthrough time and capillary number bear a log-log scale linear relationship, based on which a generalized correlation between oil travel distance x and time t was found empirically.

Visualization and quantification of two-phase flow in transparent miniature packed beds.

PubMed

Zhu, Peixi; Papadopoulos, Kyriakos D

2012-10-01

Optical microscopy was used to visualize the flow of two phases [British Petroleum (BP) oil and an aqueous surfactant phase] in confined space, three-dimensional, transparent, natural porous media. The porous media consisted of water-wet cryolite grains packed inside cylindrical, glass microchannels, thus producing microscopic packed beds. Primary drainage of BP oil displacing an aqueous surfactant phase was studied at capillary numbers that varied between 10(-6) and 10(-2). The confinement space had a significant effect on the flow behavior. Phenomena of burst motion and capillary fingering were observed for low capillary numbers due to the domination of capillary forces. It was discovered that breakthrough time and capillary number bear a log-log scale linear relationship, based on which a generalized correlation between oil travel distance x and time t was found empirically.

Soft Pneumatic Actuator Fascicles for High Force and Reliability

PubMed Central

Robertson, Matthew A.; Sadeghi, Hamed; Florez, Juan Manuel

2017-01-01

Abstract Soft pneumatic actuators (SPAs) are found in mobile robots, assistive wearable devices, and rehabilitative technologies. While soft actuators have been one of the most crucial elements of technology leading the development of the soft robotics field, they fall short of force output and bandwidth requirements for many tasks. In addition, other general problems remain open, including robustness, controllability, and repeatability. The SPA-pack architecture presented here aims to satisfy these standards of reliability crucial to the field of soft robotics, while also improving the basic performance capabilities of SPAs by borrowing advantages leveraged ubiquitously in biology; namely, the structured parallel arrangement of lower power actuators to form the basis of a larger and more powerful actuator module. An SPA-pack module consisting of a number of smaller SPAs will be studied using an analytical model and physical prototype. Experimental measurements show an SPA pack to generate over 112 N linear force, while the model indicates the benefit of parallel actuator grouping over a geometrically equivalent single SPA scale as an increasing function of the number of individual actuators in the group. For a module of four actuators, a 23% increase in force production over a volumetrically equivalent single SPA is predicted and validated, while further gains appear possible up to 50%. These findings affirm the advantage of utilizing a fascicle structure for high-performance soft robotic applications over existing monolithic SPA designs. An example of high-performance soft robotic platform will be presented to demonstrate the capability of SPA-pack modules in a complete and functional system. PMID:28289573

Soft Pneumatic Actuator Fascicles for High Force and Reliability.

PubMed

Robertson, Matthew A; Sadeghi, Hamed; Florez, Juan Manuel; Paik, Jamie

2017-03-01

Soft pneumatic actuators (SPAs) are found in mobile robots, assistive wearable devices, and rehabilitative technologies. While soft actuators have been one of the most crucial elements of technology leading the development of the soft robotics field, they fall short of force output and bandwidth requirements for many tasks. In addition, other general problems remain open, including robustness, controllability, and repeatability. The SPA-pack architecture presented here aims to satisfy these standards of reliability crucial to the field of soft robotics, while also improving the basic performance capabilities of SPAs by borrowing advantages leveraged ubiquitously in biology; namely, the structured parallel arrangement of lower power actuators to form the basis of a larger and more powerful actuator module. An SPA-pack module consisting of a number of smaller SPAs will be studied using an analytical model and physical prototype. Experimental measurements show an SPA pack to generate over 112 N linear force, while the model indicates the benefit of parallel actuator grouping over a geometrically equivalent single SPA scale as an increasing function of the number of individual actuators in the group. For a module of four actuators, a 23% increase in force production over a volumetrically equivalent single SPA is predicted and validated, while further gains appear possible up to 50%. These findings affirm the advantage of utilizing a fascicle structure for high-performance soft robotic applications over existing monolithic SPA designs. An example of high-performance soft robotic platform will be presented to demonstrate the capability of SPA-pack modules in a complete and functional system.

Imaging and engineering the nanoscale-domain structure of a Sr0.61Ba0.39Nb2O6 crystal using a scanning force microscope

NASA Astrophysics Data System (ADS)

Terabe, K.; Takekawa, S.; Nakamura, M.; Kitamura, K.; Higuchi, S.; Gotoh, Y.; Gruverman, A.

2002-09-01

We have investigated the ferroelectric domain structure formed in a Sr0.61Ba0.39Nb2O6 single crystal by cooling the crystal through the Curie point. Imaging the etched surface structure using a scanning force microscope (SFM) in both the topographic mode and the piezoresponse mode revealed that a multidomain structure of nanoscale islandlike domains was formed. The islandlike domains could be inverted by applying an appropriate voltage using a conductive SFM tip. Furthermore, a nanoscale periodically inverted-domain structure was artificially fabricated using the crystal which underwent poling treatment.

Stabilizing the hexagonal close packed structure of hard spheres with polymers: Phase diagram, structure, and dynamics

NASA Astrophysics Data System (ADS)

Edison, John R.; Dasgupta, Tonnishtha; Dijkstra, Marjolein

2016-08-01

We study the phase behaviour of a binary mixture of colloidal hard spheres and freely jointed chains of beads using Monte Carlo simulations. Recently Panagiotopoulos and co-workers predicted [Nat. Commun. 5, 4472 (2014)] that the hexagonal close packed (HCP) structure of hard spheres can be stabilized in such a mixture due to the interplay between polymer and the void structure in the crystal phase. Their predictions were based on estimates of the free-energy penalty for adding a single hard polymer chain in the HCP and the competing face centered cubic (FCC) phase. Here we calculate the phase diagram using free-energy calculations of the full binary mixture and find a broad fluid-solid coexistence region and a metastable gas-liquid coexistence region. For the colloid-monomer size ratio considered in this work, we find that the HCP phase is only stable in a small window at relatively high polymer reservoir packing fractions, where the coexisting HCP phase is nearly close packed. Additionally we investigate the structure and dynamic behaviour of these mixtures.

On the kinetics of pack aluminization

NASA Technical Reports Server (NTRS)

Gupta, B. K.; Sarkhel, A. K.; Seigle, L. L.

1975-01-01

A theory of pack aluminization has been formulated by combining gaseous and solid-state diffusion rates. This theory relates the surface composition of the coating and therefore, in principle, the phase morphology and the growth rate of the coating, to pack operating parameters such as pack aluminum density, type of activator, temperature and others. Experimental data on the aluminization of unalloyed nickel in pure aluminum packs obtained to date are in good agreement with the predictions of the theory.

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.

Rhombohedral crystals of 2-dehydro-3-deoxygalactarate aldolase from Escherichia coli.

PubMed

Blackwell, N C; Cullis, P M; Cooper, R A; Izard, T

1999-07-01

2-Dehydro-3-deoxygalactarate (DDG) aldolase (E.C. 4.1.2.20) catalyzes the reversible aldol cleavage of DDG and 2-dehydro-3-deoxyglucarate to pyruvate and tartronic semialdehyde. Rhombohedral crystals of recombinant DDG aldolase from Escherichia coli K-12 were obtained. The crystals belong to space group R32 with unit-cell parameters a = 93 A, alpha = 85 degrees. The crystals diffract to beyond 1.8 A resolution on a Cu Kalpha rotating-anode generator. The asymmetric unit is likely to contain two molecules, corresponding to a packing density of 1.34 A3 Da-1.

Monitoring structural transformations in crystals. 7. 1-Chloroanthracene and its photodimer.

PubMed

Turowska-Tyrk, Ilona; Grześniak, Karolina

2004-02-01

Crystals of the 1-chloroanthracene photodimer, viz. trans-bi(1-chloro-9,10-dihydro-9,10-anthracenediyl), C(28)H(18)Cl(2), were obtained from the solid-state [4+4]-photodimerization of the monomer, C(14)H(9)Cl, followed by recrystallization. The symmetry of the product molecules is defined by the orientation of the reactant molecules in the crystal. The mutual orientation parameters calculated for adjacent monomers explain the reactivity of the compound. The molecules in the crystal of the monomer and the recrystallized photodimer pack differently and the photodimer has crystallographically imposed inversion symmetry.

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

PubMed

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

2014-05-01

The abiotic deterioration of three conventional organic packing materials used in biofiltration (compost, wood bark and Macadamia nutshells) caused by their interaction with toluene (used as a model volatile organic compound) was here studied. The deterioration of the materials was evaluated in terms of structural damage, release of co-substrates and increase of the packing biodegradability. After 21 days of exposure to toluene, all packing materials released co-substrates able to support microbial growth, which were not released by the control materials not exposed to toluene. Likewise, the exposure to toluene increased the packing material biodegradability by 26% in wood bark, 20% in compost and 17% in Macadamia nutshells. Finally, scanning electron microscopy analysis confirmed the deterioration in the structure of the packing materials evaluated due to the exposure to toluene, Macadamia nutshells being the material with the highest resistance to volatile organic compound attack. Copyright © 2014 Elsevier Ltd. All rights reserved.

Zinc oxide crystal whiskers as a novel sorbent for solid-phase extraction of flavonoids.

PubMed

Wang, Licheng; Shangguan, Yangnan; Hou, Xiudan; Jia, Yong; Liu, Shujuan; Sun, Yingxin; Guo, Yong

2017-08-15

As a novel solid-phase extraction material, zinc oxide crystal whiskers were used to extract flavonoid compounds and showed good extraction abilities. X-ray diffraction, scanning electron microscopy with energy dispersive X-ray spectroscopy and surface area/pore volume characterized the sorbent. The zinc oxide was packed into a solid-phase extraction micro-column and its extraction ability was evaluated by four model flavonoid compounds. The sample loading and elution parameters were optimized and the zinc oxide based analytical method for flavonoids was established. It showed that the method has wide linearities from 1 to 150μg/L and low limits of detection at 0.25μg/L. The relative standard deviations of a single column repeatability and column to column reproducibility were less than 6.8% and 10.6%. Several real samples were analyzed by the established method and satisfactory results were obtained. The interactions between flavonoids and zinc oxide were calculated and proved to be from the Van der Waals' forces between the 4p and 5d orbitals from zinc atom and the neighboring π orbitals from flavonoid phenyl groups. Moreover, the zinc oxide crystal whiskers showed good stability and could be reused more than 50 times under the operation conditions. This work proves that the zinc oxide crystal whiskers are a good candidate for flavonoids enrichment. Copyright © 2017. Published by Elsevier B.V.

Confined disordered strictly jammed binary sphere packings

NASA Astrophysics Data System (ADS)

Chen, D.; Torquato, S.

2015-12-01

Disordered jammed packings under confinement have received considerably less attention than their bulk counterparts and yet arise in a variety of practical situations. In this work, we study binary sphere packings that are confined between two parallel hard planes and generalize the Torquato-Jiao (TJ) sequential linear programming algorithm [Phys. Rev. E 82, 061302 (2010), 10.1103/PhysRevE.82.061302] to obtain putative maximally random jammed (MRJ) packings that are exactly isostatic with high fidelity over a large range of plane separation distances H , small to large sphere radius ratio α , and small sphere relative concentration x . We find that packing characteristics can be substantially different from their bulk analogs, which is due to what we term "confinement frustration." Rattlers in confined packings are generally more prevalent than those in their bulk counterparts. We observe that packing fraction, rattler fraction, and degree of disorder of MRJ packings generally increase with H , though exceptions exist. Discontinuities in the packing characteristics as H varies in the vicinity of certain values of H are due to associated discontinuous transitions between different jammed states. When the plane separation distance is on the order of two large-sphere diameters or less, the packings exhibit salient two-dimensional features; when the plane separation distance exceeds about 30 large-sphere diameters, the packings approach three-dimensional bulk packings. As the size contrast increases (as α decreases), the rattler fraction dramatically increases due to what we call "size-disparity" frustration. We find that at intermediate α and when x is about 0.5 (50-50 mixture), the disorder of packings is maximized, as measured by an order metric ψ that is based on the number density fluctuations in the direction perpendicular to the hard walls. We also apply the local volume-fraction variance στ2(R ) to characterize confined packings and find that these

Structure of force networks in tapped particulate systems of disks and pentagons. I. Clusters and loops.

PubMed

Pugnaloni, Luis A; Carlevaro, C Manuel; Kramár, M; Mischaikow, K; Kondic, L

2016-06-01

The force network of a granular assembly, defined by the contact network and the corresponding contact forces, carries valuable information about the state of the packing. Simple analysis of these networks based on the distribution of force strengths is rather insensitive to the changes in preparation protocols or to the types of particles. In this and the companion paper [Kondic et al., Phys. Rev. E 93, 062903 (2016)10.1103/PhysRevE.93.062903], we consider two-dimensional simulations of tapped systems built from frictional disks and pentagons, and study the structure of the force networks of granular packings by considering network's topology as force thresholds are varied. We show that the number of clusters and loops observed in the force networks as a function of the force threshold are markedly different for disks and pentagons if the tangential contact forces are considered, whereas they are surprisingly similar for the network defined by the normal forces. In particular, the results indicate that, overall, the force network is more heterogeneous for disks than for pentagons. Such differences in network properties are expected to lead to different macroscale response of the considered systems, despite the fact that averaged measures (such as force probability density function) do not show any obvious differences. Additionally, we show that the states obtained by tapping with different intensities that display similar packing fraction are difficult to distinguish based on simple topological invariants.

Unusual Crystallization Behavior Close to the Glass Transition

NASA Astrophysics Data System (ADS)

Desgranges, Caroline; Delhommelle, Jerome

2018-03-01

Using molecular simulations, we shed light on the mechanism underlying crystal nucleation in metal alloys and unravel the interplay between crystal nucleation and glass transition, as the conditions of crystallization lie close to this transition. While decreasing the temperature of crystallization usually results in a lower free energy barrier, we find an unexpected reversal of behavior for glass-forming alloys as the temperature of crystallization approaches the glass transition. For this purpose, we simulate the crystallization process in two glass-forming Copper alloys, Ag6 Cu4 , which has a positive heat of mixing, and CuZr, characterized by a large negative heat of mixing. Our results allow us to identify this unusual behavior as directly correlated with a nonmonotonic temperature dependence for the formation energy of connected icosahedral structures, which are incompatible with crystalline order and impede the development of the crystal nucleus, leading to an unexpectedly larger free energy barrier at low temperature. This, in turn, promotes the formation of a predominantly closed-packed critical nucleus, with fewer defects, thereby suggesting a new way to control the structure of the crystal nucleus, which is of key importance in catalysis.

Rational Design of Charge-Transfer Interactions in Halogen-Bonded Co-crystals toward Versatile Solid-State Optoelectronics.

PubMed

Zhu, Weigang; Zheng, Renhui; Zhen, Yonggang; Yu, Zhenyi; Dong, Huanli; Fu, Hongbing; Shi, Qiang; Hu, Wenping

2015-09-02

Charge-transfer (CT) interactions between donor (D) and acceptor (A) groups, as well as CT exciton dynamics, play important roles in optoelectronic devices, such as organic solar cells, photodetectors, and light-emitting sources, which are not yet well understood. In this contribution, the self-assembly behavior, molecular stacking structure, CT interactions, density functional theory (DFT) calculations, and corresponding physicochemical properties of two similar halogen-bonded co-crystals are comprehensively investigated and compared, to construct an "assembly-structure-CT-property" relationship. Bpe-IFB wire-like crystals (where Bpe = 1,2-bis(4-pyridyl)ethylene and IFB = 1,3,5-trifluoro-2,4,6-triiodobenzene), packed in a segregated stacking form with CT ground and excited states, are measured to be quasi-one-dimensional (1D) semiconductors and show strong violet-blue photoluminescence (PL) from the lowest CT1 excitons (ΦPL = 26.1%), which can be confined and propagate oppositely along the 1D axial direction. In comparison, Bpe-F4DIB block-like crystals (F4DIB = 1,4-diiodotetrafluorobenzene), packed in a mixed stacking form without CT interactions, are determined to be insulators and exhibit unique white light emission and two-dimensional optical waveguide property. Surprisingly, it seems that the intrinsic spectroscopic states of Bpe and F4DIB do not change after co-crystallization, which is also confirmed by theoretical calculations, thus offering a new design principle for white light emitting materials. More importantly, we show that the CT interactions in co-crystals are related to their molecular packing and can be triggered or suppressed by crystal engineering, which eventually leads to distinct optoelectronic properties. These results help us to rationally control the CT interactions in organic D-A systems by tuning the molecular stacking, toward the development of a fantastic "optoelectronic world".

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. Copyright © 2016 Elsevier Inc. All rights reserved.

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

7 CFR 51.310 - Packing requirements.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 2 2010-01-01 2010-01-01 false Packing requirements. 51.310 Section 51.310... MARKETING ACT OF 1946 FRESH FRUITS, VEGETABLES AND OTHER PRODUCTS 1,2 (INSPECTION, CERTIFICATION, AND.... (a) Apples tray packed or cell packed in cartons shall be arranged according to approved and...

Crystal Model Kits for Use in the General Chemistry Laboratory.

ERIC Educational Resources Information Center

Kildahl, Nicholas J.; And Others

1986-01-01

Dynamic crystal model kits are described. Laboratory experiments in which students use these kits to build models have been extremely successful in providing them with an understanding of the three-dimensional structures of the common cubic unit cells as well as hexagonal and cubic closest-packing of spheres. (JN)

Crystals of Janus colloids at various interaction ranges

DOE Office of Scientific and Technical Information (OSTI.GOV)

Preisler, Z.; Soft Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht; Vissers, T.

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

Microstructure and phase behavior in colloids and liquid crystals

NASA Astrophysics Data System (ADS)

Lohr, Matthew Alan

This thesis describes our investigation of microstructure and phase behavior in colloids and liquid crystals. The first set of experiments explores the phase behavior of helical packings of thermoresponsive microspheres inside glass capillaries as a function of volume fraction. Stable helical packings are observed with long-range orientational order. Some of these packings evolve abruptly to disordered states as the volume fraction is reduced. We quantify these transitions using correlation functions and susceptibilities of an orientational order parameter. The emergence of coexisting metastable packings, as well as coexisting ordered and disordered states, is also observed. These findings support the notion of phase-transition-like behavior in quasi-one-dimensional systems. The second set of experiments investigates cross-over behavior from glasses with attractive interactions to sparse gel-like states. In particular, the vibrational modes of quasi-two-dimensional disordered colloidal packings of hard colloidal spheres with short-range attractions are measured as a function of packing fraction. A crossover from glassy to sparse gel-like states is indicated by an excess of low-frequency phonon modes. This change in vibrational mode distribution appears to arise from highly localized vibrations that tend to involve individual and/or small clusters of particles with few local bonds. These mode behaviors and corresponding structural insights may serve as a useful signature for glass-gel transitions in wider classes of attractive packings. A third set of experiments explores the director structures of aqueous lyotropic chromonic liquid crystal (LCLC) films created on square lattice cylindrical-micropost substrates. The structures are manipulated by modulating of the concentration-dependent elastic properties of LCLC s via drying. Nematic LCLC films exhibit preferred bistable alignment along the diagonals of the micropost lattice. Columnar LCLC films form two distinct

The Pressure induced by salt crystallization in confinement.

PubMed

Desarnaud, J; Bonn, D; Shahidzadeh, N

2016-08-05

Salt crystallization is a major cause of weathering of rocks, artworks and monuments. Damage can only occur if crystals continue to grow in confinement, i.e. within the pore space of these materials, thus generating mechanical stress. We report the direct measurement, at the microscale, of the force exerted by growing alkali halide salt crystals while visualizing their spontaneous nucleation and growth. The experiments reveal the crucial role of the wetting films between the growing crystal and the confining walls for the development of the pressure. Our results suggest that the measured force originates from repulsion between the similarly charged confining wall and the salt crystal separated by a ~1.5 nm liquid film. Indeed, if the walls are made hydrophobic, no film is observed and no repulsive forces are detected. We also show that the magnitude of the induced pressure is system specific explaining why different salts lead to different amounts of damage to porous materials.

Systematic Approach to Electrostatically Induced 2D Crystallization of Nanoparticles at Liquid Interfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fukuto, M.; Kewalramani, S.; Wang, S.

2011-02-07

We report an experimental demonstration of a strategy for inducing two-dimensional (2D) crystallization of charged nanoparticles on oppositely charged fluid interfaces. This strategy aims to maximize the interfacial adsorption of nanoparticles, and hence their lateral packing density, by utilizing a combination of weakly charged particles and a high surface charge density on the planar interface. In order to test this approach, we investigated the assembly of cowpea mosaic virus (CPMV) on positively charged lipid monolayers at the aqueous solution surface, by means of in situ X-ray scattering measurements at the liquid-vapor interface. The assembly was studied as a function ofmore » the solution pH, which was used to vary the charge on CPMV, and of the mole fraction of the cationic lipid in the binary lipid monolayer, which set the interface charge density. The 2D crystallization of CPMV occurred in a narrow pH range just above the particle's isoelectric point, where the particle charge was weakly negative, and only when the cationic-lipid fraction in the monolayer exceeded a threshold. The observed 2D crystals exhibited nearly the same packing density as the densest lattice plane within the known 3D crystals of CPMV. The above electrostatic approach of maximizing interfacial adsorption may provide an efficient route to the crystallization of nanoparticles at aqueous interfaces.« less

Liquid Crystals of Dendron-Like Pt Complexes Processable Into Nanofilms Dendrimers. Phase 2. Cholesteric Liquid Crystal Glass Platinum Acetylides

DTIC Science & Technology

2014-08-01

Std. Z39.18 Final Report Liquid Crystals of Dendron-Like Pt Complexes Processable Into Nanofilms. Dendrimers Eduardo Arias...to pack and also the presence of a polar group. Figure 4. Summary of phase behavior. DENDRIMERS New Denrimers. The synthesis...purification and some spectral characteristics of the new dendrimers shown in Fig 5 were reported in AFOSR FA9550-11-1-0169, May, 2013. Further

An expanded model and application of the combined effect of crystal-size distribution and crystal shape on the relative viscosity of magmas

NASA Astrophysics Data System (ADS)

Klein, Johannes; Mueller, Sebastian P.; Helo, Christoph; Schweitzer, Silja; Gurioli, Lucia; Castro, Jonathan M.

2018-05-01

This study examines the combined effect of crystal-size distributions (CSD) and crystal shape on the rheology of vesicle free magmatic suspensions and provides the first practical application of an empirical model to estimate the relative effect of crystal content and CSD's on the viscosity of magma directly from textural image analysis of natural rock samples in the form of a user-friendly texture-rheology spreadsheet calculator. We extend and apply established relationships between the maximum packing fraction ϕm of a crystal bearing suspension and both its rheological properties and the polydispersity γ of a CSD. By using analogue rotational rheometric experiments with glass fibres and glass flakes in silicone oil acting as magma equivalent, this study also provides new insights in the relationship between ϕm and the aspect ratio rp of suspended particles.

Straight-Chain Alkyl Isocyanides Open the Distal Histidine Gate in Crystal Structures of Myoglobin†

PubMed Central

Smith, Rober D.; Blouin, George C.; Johnson, Kenneth A.; Phillips, George N.; Olson, John S.

2014-01-01

Crystal structures of methyl, ethyl, propyl and butyl isocyanide bound to sperm whale myoglobin (Mb) reveal two major conformations. In the in conformer, His(E7) is in a “closed” position, forcing the ligand alkyl chain to point inward. In the out conformer, His(E7) is in an “open” position, allowing the ligand side chain to point outward. A progressive increase in the population of the out conformer is observed with increasing ligand length in P21 crystals of native Mb at pH 7.0. This switch from in to out with increasing ligand size also occurs in solution as measured by the decrease in the relative intensity of the low (~2075 cm 1) versus high frequency (~2125 cm 1) isocyano bands. In contrast, all four isocyanides in P6 crystals of wild type recombinant Mb occupy the in conformation. However, mutating either His64 to Ala, creating a “hole” to solvent, or Phe46 to Val, freeing rotation of His64, causes bound butyl isocyanide to point completely outward in P6 crystals. Thus, the unfavorable hindrance caused with crowding a large alkyl side chain into the distal pocket appears to be roughly equal to that for pushing open the His(E7) gate and is easily affected by crystal packing. This structural conclusion supports the “side path” kinetic mechanism for O2 release, in which the dissociated ligand first moves toward the protein interior and then encounters steric resistance, which is roughly equal to that for escaping to solvent through the His(E7) channel. PMID:20481504

REVIEW: Optics of globular photonic crystals

NASA Astrophysics Data System (ADS)

Gorelik, V. S.

2007-05-01

The results of experimental and theoretical studies of the optical properties of globular photonic crystals - new physical objects having a crystal structure with the lattice period exceeding considerably the atomic size, are presented. As globular photonic crystals, artificial opal matrices consisting of close-packed silica globules of diameter ~200 nm were used. The reflection spectra of these objects characterising the parameters of photonic bands existing in these crystals in the visible spectral region are presented. The idealised models of the energy band structure of photonic crystals investigated in the review give analytic dispersion dependences for the group velocity and the effective photon mass in a globular photonic crystal. The characteristics of secondary emission excited in globular photonic crystals by monochromatic and broadband radiation are presented. The results of investigations of single-photon-excited delayed scattering of light observed in globular photonic crystals exposed to cw UV radiation and radiation from a repetitively pulsed copper vapour laser are presented. The possibilities of using globular photonic crystals as active media for lasing in different spectral regions are considered. It is proposed to use globular photonic crystals as sensitive sensors in optoelectronic devices for molecular analysis of organic and inorganic materials by the modern methods of laser spectroscopy. The results of experimental studies of spontaneous and stimulated globular scattering of light are discussed. The conditions for observing resonance and two-photon-excited delayed scattering of light are found. The possibility of accumulation and localisation of the laser radiation energy inside a globular photonic crystal is reported.

Paediatric oncology information pack for general practitioners

PubMed Central

James, J A; Harris, D J; Mott, M G; Oakhill, A

1988-01-01

An information pack covering important aspects of paediatric oncology has been developed for general practitioners. Sixty general practitioners who received the information pack found that it helped them in managing children with neoplastic disease and their families. The pack has also improved communications between the oncology unit and general practitioners. Similar packs could be produced by paediatricians working in other specialties. PMID:3122972

Polyhedra and packings from hyperbolic honeycombs.

PubMed

Pedersen, Martin Cramer; Hyde, Stephen T

2018-06-20

We derive more than 80 embeddings of 2D hyperbolic honeycombs in Euclidean 3 space, forming 3-periodic infinite polyhedra with cubic symmetry. All embeddings are "minimally frustrated," formed by removing just enough isometries of the (regular, but unphysical) 2D hyperbolic honeycombs [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], and [Formula: see text] to allow embeddings in Euclidean 3 space. Nearly all of these triangulated "simplicial polyhedra" have symmetrically identical vertices, and most are chiral. The most symmetric examples include 10 infinite "deltahedra," with equilateral triangular faces, 6 of which were previously unknown and some of which can be described as packings of Platonic deltahedra. We describe also related cubic crystalline packings of equal hyperbolic discs in 3 space that are frustrated analogues of optimally dense hyperbolic disc packings. The 10-coordinated packings are the least "loosened" Euclidean embeddings, although frustration swells all of the hyperbolic disc packings to give less dense arrays than the flat penny-packing even though their unfrustrated analogues in [Formula: see text] are denser.

Effect of counter-ion on packing and crystal density of 5,5'-(3,3'-bi[1,2,4-oxadiazole]-5,5'-diyl)bis(1 H -tetrazol-1-olate) with five different cations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Giles, Ian D.; DeHope, Alan J.; Zuckerman, Nathaniel B.

In energetic materials, the crystal density is an important parameter that affects the performance of the material. When making ionic energetic materials, the choice of counter-ion can have detrimental or beneficial effects on the packing, and therefore the density, of the resulting energetic crystal. Presented herein are a series of five ionic energetic crystals, all containing the dianion 5,5′-(3,3′-bi[1,2,4-oxadiazole]-5,5′-diyl)bis(1 H -tetrazol-1-olate), with the following cations: hydrazinium ( 1 ) (2N 2 H 5 + ·C 6 N 12 O 4 2− ), hydroxylammonium ( 2 ) 2NH 4 O + ·C 6 N 12 O 4 2− [Pagoria et al..more » (2017). Chem. Heterocycl. Compd , 53 , 760–778; included for comparison], dimethylammonium ( 3 ) (2C 2 H 8 N + ·C 6 N 12 O 4 2− ), 5-amino-1 H -tetrazol-4-ium ( 4 ) (2CH 4 N 5 + ·C 6 N 12 O 4 2− ·4H 2 O), and aminoguanidinium ( 5 ) (2CH 7 N 4 + ·C 6 N 12 O 4 2− ). Both the supramolecular interactions and the sterics of the cation play a role in the density of the resulting crystals, which range from 1.544 to 1.873 Mg m −1 . In 5 , the tetrazolate ring is disordered over two positions [occupancy ratio 0.907 (5):0.093 (5)] due to a 180° rotation in the terminal tetrazole rings.« less

Effect of counter-ion on packing and crystal density of 5,5'-(3,3'-bi[1,2,4-oxadiazole]-5,5'-diyl)bis(1 H -tetrazol-1-olate) with five different cations

DOE PAGES

Giles, Ian D.; DeHope, Alan J.; Zuckerman, Nathaniel B.; ...

2018-03-09

In energetic materials, the crystal density is an important parameter that affects the performance of the material. When making ionic energetic materials, the choice of counter-ion can have detrimental or beneficial effects on the packing, and therefore the density, of the resulting energetic crystal. Presented herein are a series of five ionic energetic crystals, all containing the dianion 5,5′-(3,3′-bi[1,2,4-oxadiazole]-5,5′-diyl)bis(1 H -tetrazol-1-olate), with the following cations: hydrazinium ( 1 ) (2N 2 H 5 + ·C 6 N 12 O 4 2− ), hydroxylammonium ( 2 ) 2NH 4 O + ·C 6 N 12 O 4 2− [Pagoria et al..more » (2017). Chem. Heterocycl. Compd , 53 , 760–778; included for comparison], dimethylammonium ( 3 ) (2C 2 H 8 N + ·C 6 N 12 O 4 2− ), 5-amino-1 H -tetrazol-4-ium ( 4 ) (2CH 4 N 5 + ·C 6 N 12 O 4 2− ·4H 2 O), and aminoguanidinium ( 5 ) (2CH 7 N 4 + ·C 6 N 12 O 4 2− ). Both the supramolecular interactions and the sterics of the cation play a role in the density of the resulting crystals, which range from 1.544 to 1.873 Mg m −1 . In 5 , the tetrazolate ring is disordered over two positions [occupancy ratio 0.907 (5):0.093 (5)] due to a 180° rotation in the terminal tetrazole rings.« less

7 CFR 51.1527 - Standard pack.

Code of Federal Regulations, 2011 CFR

2011-01-01

... peach boxes, lug boxes and small consumer packages. In layer-packed California peach boxes or lug boxes... package. The number of plums or prunes in California peach boxes or lug boxes shall not vary more than 4... container. (ii) Face and fill packs in cartons and lug boxes. In face and fill packs in cartons and lug...

7 CFR 51.1527 - Standard pack.

Code of Federal Regulations, 2012 CFR

2012-01-01

... peach boxes, lug boxes and small consumer packages. In layer-packed California peach boxes or lug boxes... package. The number of plums or prunes in California peach boxes or lug boxes shall not vary more than 4... container. (ii) Face and fill packs in cartons and lug boxes. In face and fill packs in cartons and lug...

Modular vaccine packaging increases packing efficiency

PubMed Central

Norman, Bryan A.; Rajgopal, Jayant; Lim, Jung; Gorham, Katrin; Haidari, Leila; Brown, Shawn T.; Lee, Bruce Y.

2015-01-01

Background Within a typical vaccine supply chain, vaccines are packaged into individual cylindrical vials (each containing one or more doses) that are bundled together in rectangular “inner packs” for transport via even larger groupings such as cold boxes and vaccine carriers. The variability of vaccine inner pack and vial size may hinder efficient vaccine distribution because it constrains packing of cold boxes and vaccine carriers to quantities that are often inappropriate or suboptimal in the context of country-specific vaccination guidelines. Methods We developed in Microsoft Excel (Microsoft Corp., Redmond, WA) a spreadsheet model that evaluated the impact of different packing schemes for the Benin routine regimen plus the introduction of the Rotarix vaccine. Specifically, we used the model to compare the current packing scheme to that of a proposed modular packing scheme. Results Conventional packing of a Dometic RCW25 that aims to maximize fully-immunized children (FICs) results in 123 FICs and a packing efficiency of 81.93% compared to a maximum of 155 FICs and 94.1% efficiency for an alternative modular packaging system. Conclusions Our analysis suggests that modular packaging systems could offer significant advantages over conventional vaccine packaging systems with respect to space efficiency and potential FICs, when they are stored in standard vaccine carrying devices. This allows for more vaccines to be stored within the same volume while also simplifying the procedures used by field workers to pack storage devices. Ultimately, modular packaging systems could be a simple way to help increase vaccine coverage worldwide. PMID:25957666

Cluster and constraint analysis in tetrahedron packings

NASA Astrophysics Data System (ADS)

Jin, Weiwei; Lu, Peng; Liu, Lufeng; Li, Shuixiang

2015-04-01

The disordered packings of tetrahedra often show no obvious macroscopic orientational or positional order for a wide range of packing densities, and it has been found that the local order in particle clusters is the main order form of tetrahedron packings. Therefore, a cluster analysis is carried out to investigate the local structures and properties of tetrahedron packings in this work. We obtain a cluster distribution of differently sized clusters, and peaks are observed at two special clusters, i.e., dimer and wagon wheel. We then calculate the amounts of dimers and wagon wheels, which are observed to have linear or approximate linear correlations with packing density. Following our previous work, the amount of particles participating in dimers is used as an order metric to evaluate the order degree of the hierarchical packing structure of tetrahedra, and an order map is consequently depicted. Furthermore, a constraint analysis is performed to determine the isostatic or hyperstatic region in the order map. We employ a Monte Carlo algorithm to test jamming and then suggest a new maximally random jammed packing of hard tetrahedra from the order map with a packing density of 0.6337.

Virtual modeling of polycrystalline structures of materials using particle packing algorithms and Laguerre cells

NASA Astrophysics Data System (ADS)

Morfa, Carlos Recarey; Farias, Márcio Muniz de; Morales, Irvin Pablo Pérez; Navarra, Eugenio Oñate Ibañez de; Valera, Roberto Roselló

2018-04-01

The influence of the microstructural heterogeneities is an important topic in the study of materials. In the context of computational mechanics, it is therefore necessary to generate virtual materials that are statistically equivalent to the microstructure under study, and to connect that geometrical description to the different numerical methods. Herein, the authors present a procedure to model continuous solid polycrystalline materials, such as rocks and metals, preserving their representative statistical grain size distribution. The first phase of the procedure consists of segmenting an image of the material into adjacent polyhedral grains representing the individual crystals. This segmentation allows estimating the grain size distribution, which is used as the input for an advancing front sphere packing algorithm. Finally, Laguerre diagrams are calculated from the obtained sphere packings. The centers of the spheres give the centers of the Laguerre cells, and their radii determine the cells' weights. The cell sizes in the obtained Laguerre diagrams have a distribution similar to that of the grains obtained from the image segmentation. That is why those diagrams are a convenient model of the original crystalline structure. The above-outlined procedure has been used to model real polycrystalline metallic materials. The main difference with previously existing methods lies in the use of a better particle packing algorithm.

Roles of bond orientational ordering in glass transition and crystallization.

PubMed

Tanaka, Hajime

2011-07-20

It is widely believed that crystallization in three dimensions is primarily controlled by positional ordering, and not by bond orientational ordering. In other words, bond orientational ordering is usually considered to be merely a consequence of positional ordering and thus has often been ignored. This one-order-parameter (density) description may be reasonable when we consider an equilibrium liquid-solid transition, but may not be enough to describe a metastable state and the kinetics of the transition. Here we propose that bond orientational ordering can play a key role in (i) crystallization, (ii) the ordering to quasi-crystal and (iii) vitrification, which occurs under rather weak frustration against crystallization. In a metastable supercooled state before crystallization, a system generally tends to have bond orientational order at least locally as a result of a constraint of dense packing. For a system interacting with hard-core repulsions, the constraint is intrinsically of geometrical origin and thus the basic physics is the same as nematic ordering of rod-like particles upon densification. Furthermore, positional ordering is easily destroyed even by weak frustration such as polydispersity and anisotropic interactions which favour a symmetry not consistent with that of the equilibrium crystal. Thus we may say that vitrification can be achieved by disturbing and prohibiting long-range positional ordering. Even in such a situation, bond orientational ordering still survives, accompanying its critical-like fluctuations, which are the origin of dynamic heterogeneity for this case. This scenario naturally explains both the absence of positional order and the development of bond orientational order upon cooling in a supercooled state. Although our argument is speculative in nature, we emphasize that this physical picture can coherently explain crystallization, vitrification, quasi-crystallization and their relationship in a natural manner. For a strongly

An overview of inverted colloidal crystal systems for tissue engineering.

PubMed

João, Carlos Filipe C; Vasconcelos, Joana Marta; Silva, Jorge Carvalho; Borges, João Paulo

2014-10-01

Scaffolding is at the heart of tissue engineering but the number of techniques available for turning biomaterials into scaffolds displaying the features required for a tissue engineering application is somewhat limited. Inverted colloidal crystals (ICCs) are inverse replicas of an ordered array of monodisperse colloidal particles, which organize themselves in packed long-range crystals. The literature on ICC systems has grown enormously in the past 20 years, driven by the need to find organized macroporous structures. Although replicating the structure of packed colloidal crystals (CCs) into solid structures has produced a wide range of advanced materials (e.g., photonic crystals, catalysts, and membranes) only in recent years have ICCs been evaluated as devices for medical/pharmaceutical and tissue engineering applications. The geometry, size, pore density, and interconnectivity are features of the scaffold that strongly affect the cell environment with consequences on cell adhesion, proliferation, and differentiation. ICC scaffolds are highly geometrically ordered structures with increased porosity and connectivity, which enhances oxygen and nutrient diffusion, providing optimum cellular development. In comparison to other types of scaffolds, ICCs have three major unique features: the isotropic three-dimensional environment, comprising highly uniform and size-controllable pores, and the presence of windows connecting adjacent pores. Thus far, this is the only technique that guarantees these features with a long-range order, between a few nanometers and thousands of micrometers. In this review, we present the current development status of ICC scaffolds for tissue engineering applications.

An automated parallel crystallisation search for predicted crystal structures and packing motifs of carbamazepine.

PubMed

Florence, Alastair J; Johnston, Andrea; Price, Sarah L; Nowell, Harriott; Kennedy, Alan R; Shankland, Norman

2006-09-01

An automated parallel crystallisation search for physical forms of carbamazepine, covering 66 solvents and five crystallisation protocols, identified three anhydrous polymorphs (forms I-III), one hydrate and eight organic solvates, including the single-crystal structures of three previously unreported solvates (N,N-dimethylformamide (1:1); hemi-furfural; hemi-1,4-dioxane). Correlation of physical form outcome with the crystallisation conditions demonstrated that the solvent adopts a relatively nonspecific role in determining which polymorph is obtained, and that the previously reported effect of a polymer template facilitating the formation of form IV could not be reproduced by solvent crystallisation alone. In the accompanying computational search, approximately half of the energetically feasible predicted crystal structures exhibit the C=O...H--N R2(2)(8)dimer motif that is observed in the known polymorphs, with the most stable correctly corresponding to form III. Most of the other energetically feasible structures, including the global minimum, have a C=O...H--N C(4) chain hydrogen bond motif. No such chain structures were observed in this or any other previously published work, suggesting that kinetic, rather than thermodynamic, factors determine which of the energetically feasible crystal structures are observed experimentally, with the kinetics apparently favouring nucleation of crystal structures based on the CBZ-CBZ R2(2)(8) motif. (c) 2006 Wiley-Liss, Inc. and the American Pharmacists Association.

Coalescence preference in densely packed microbubbles

DOE PAGES

Kim, Yeseul; Lim, Su Jin; Gim, Bopil; ...

2015-01-13

A bubble merged from two parent bubbles with different size tends to be placed closer to the larger parent. This phenomenon is known as the coalescence preference. Here we demonstrate that the coalescence preference can be blocked inside a densely packed cluster of bubbles. We utilized high-speed high-resolution X-ray microscopy to clearly visualize individual coalescence events inside densely packed microbubbles with a local packing fraction of ~40%. Thus, the surface energy release theory predicts an exponent of 5 in a relation between the relative coalescence position and the parent size ratio, whereas our observation for coalescence in densely packed microbubblesmore » shows a different exponent of 2. We believe that this result would be important to understand the reality of coalescence dynamics in a variety of packing situations of soft matter.« less

Coalescence preference in densely packed microbubbles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Yeseul; Lim, Su Jin; Gim, Bopil

A bubble merged from two parent bubbles with different size tends to be placed closer to the larger parent. This phenomenon is known as the coalescence preference. Here we demonstrate that the coalescence preference can be blocked inside a densely packed cluster of bubbles. We utilized high-speed high-resolution X-ray microscopy to clearly visualize individual coalescence events inside densely packed microbubbles with a local packing fraction of ~40%. Thus, the surface energy release theory predicts an exponent of 5 in a relation between the relative coalescence position and the parent size ratio, whereas our observation for coalescence in densely packed microbubblesmore » shows a different exponent of 2. We believe that this result would be important to understand the reality of coalescence dynamics in a variety of packing situations of soft matter.« less

Packing loops into annular cavities.

PubMed

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.

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.

Eating less from bigger packs: Preventing the pack size effect with diet primes.

PubMed

Versluis, Iris; Papies, Esther K

2016-05-01

An increase in the package size of food has been shown to lead to an increase in energy intake from this food, the so-called pack size effect. Previous research has shown that providing diet-concerned individuals with a reminder, or prime, of their dieting goal can help them control their consumption. Here, we investigated if providing such a prime is also effective for reducing the magnitude of the pack size effect. We conducted two experiments in which the cover of a dieting magazine (Experiment 1) and diet-related commercials (Experiment 2) served as diet goal primes. Both experiments had a 2 (pack size: small vs. large) × 2 (prime: diet vs. control) × 2 (dietary restraint: high vs. low) between participants design. We measured expected consumption of four snack foods in Experiment 1 (N = 477), and actual consumption of M&M's in Experiment 2 (N = 224). Results showed that the diet prime reduced the pack size effect for both restrained and unrestrained eaters in Experiment 1 and for restrained eaters only in Experiment 2. Although effect sizes were small, these findings suggest that a diet prime motivates restrained eaters to limit their consumption, and as a result the pack size has less influence on the amount consumed. We discuss limitations of this research as well as potential avenues for further research and theoretical and practical implications. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effect of gravity on colloid transport through water-saturated columns packed with glass beads: modeling and experiments.

PubMed

Chrysikopoulos, Constantinos V; Syngouna, Vasiliki I

2014-06-17

The role of gravitational force on colloid transport in water-saturated columns packed with glass beads was investigated. Transport experiments were performed with colloids (clays: kaolinite KGa-1b, montmorillonite STx-1b). The packed columns were placed in various orientations (horizontal, vertical, and diagonal) and a steady flow rate of Q = 1.5 mL/min was applied in both up-flow and down-flow modes. All experiments were conducted under electrostatically unfavorable conditions. The experimental data were fitted with a newly developed, analytical, one-dimensional, colloid transport model. The effect of gravity is incorporated in the mathematical model by combining the interstitial velocity (advection) with the settling velocity (gravity effect). The results revealed that flow direction influences colloid transport in porous media. The rate of particle deposition was shown to be greater for up-flow than for down-flow direction, suggesting that gravity was a significant driving force for colloid deposition.

Ex situ investigation of the step bunching on crystal surfaces by atomic force microscopy

NASA Astrophysics Data System (ADS)

Krasinski, Mariusz J.

1997-07-01

We are describing ex situ observation of step bunching on the surfaces of solution grown potassium dihydrogen phosphate (KDP) and sodium chlorate monocrystals. The measurements have been done with the use of atomic force microscope. The use of this equipment allowed us to see directly the structure of macrosteps. Observation confirmed the existence of step pinning which is one of the proposed mechanisms of step bunching. Despite the very high resolution of AFM it was not possible to determine the nature of pinning point. The monatomic steps on KDP and sodium chlorate crystal surfaces are mainly one unit cell high what seems to be the result of the steps pairing. The origin of observed step pattern is discussed in frames of existing theories.

Combined centrifugal force/gravity gas/liquid separator system

NASA Astrophysics Data System (ADS)

Lema, Luis E.

1993-04-01

A gas/liquid separator system has an outer enclosing tank filled with a demisting packing material. The tank has a gas outlet port and a liquid outlet port located at its top and bottom, respectively. At least one cylindrical, centrifugal force gas/liquid separator is vertically aligned and centrally located within the tank and is surrounded by the packing material. The cylindrical separator receives a gas/liquid mixture, separates the mixture into respective substantially gas and substantially liquid components, and allows the substantially gas components to exit its gas escape port. It also allows the substantially liquid components to exit its liquid escape port. The packing material in the tank further separates the substantially gas and liquid components as they rise and fall, respectively, through the packing material. An inflow line introduces the mixture into the cylindrical separator. The inflow line is upwardly inclined in a direction of flow of the mixture at a point where the inflow line communicates with the cylindrical separator.

Random close packing of polydisperse jammed emulsions

NASA Astrophysics Data System (ADS)

Brujic, Jasna

2010-03-01

Packing problems are everywhere, ranging from oil extraction through porous rocks to grain storage in silos and the compaction of pharmaceutical powders into tablets. At a given density, particulate systems pack into a mechanically stable and amorphous jammed state. Theoretical frameworks have proposed a connection between this jammed state and the glass transition, a thermodynamics of jamming, as well as geometric modeling of random packings. Nevertheless, a simple underlying mechanism for the random assembly of athermal particles, analogous to crystalline ordering, remains unknown. Here we use 3D measurements of polydisperse packings of emulsion droplets to build a simple statistical model in which the complexity of the global packing is distilled into a local stochastic process. From the perspective of a single particle the packing problem is reduced to the random formation of nearest neighbors, followed by a choice of contacts among them. The two key parameters in the model, the available space around a particle and the ratio of contacts to neighbors, are directly obtained from experiments. Remarkably, we demonstrate that this ``granocentric'' view captures the properties of the polydisperse emulsion packing, ranging from the microscopic distributions of nearest neighbors and contacts to local density fluctuations and all the way to the global packing density. Further applications to monodisperse and bidisperse systems quantitatively agree with previously measured trends in global density. This model therefore reveals a general principle of organization for random packing and lays the foundations for a theory of jammed matter.

Respiratory complications from nasal packing: systematic review.

PubMed

Rotenberg, Brian; Tam, Samantha

2010-10-01

Patients with posterior nasal packing are thought to be at high risk for the development of respiratory complications. Controversy exists regarding the evidence in that regard; consequently, the level of vital sign monitoring required for these patients is unclear. The objective of this article is to systematically review the literature describing respiratory complications from nasal packing. Literature published before July 2009 on Medline and Embase was eligible for inclusion. Original research and review articles whose major topic was nasal packing for epistaxis were included. Nonhuman studies and studies not published in English were excluded. Studies were evaluated for quality using a modified Downs and Black scale. Data regarding respiratory complications of nasal packing were extracted and summarized. Of the 262 studies retrieved, 14 met inclusion criteria (7 case series, 3 cohort studies, and 4 reviews). Six studies discussed pulmonary mechanics, three discussed sleep apnea, two reviews described complications of nasal packing, and three articles focused on the treatment of posterior epistaxis. There was a lack of high-quality literature describing adverse respiratory events following posterior packing. The literature regarding development of respiratory complications from posterior packing is mostly based on expert opinion or case series. There is some suggestion that sleep apnea may develop after placement posterior nasal packing, but the severity appears to be mild. Evidence is lacking to support the contention that all patients with posterior packing are at risk for developing adverse respiratory events or require admission to a monitored setting.

Entanglement Theories: Packing vs. Percolation

NASA Astrophysics Data System (ADS)

Wool, Richard

2007-03-01

There are two emergent theories of polymer entanglements, the Packing Model (Fetters, Lohse, Graessley, Milner, Whitten, ˜'98) and the Percolation Model (Wool ˜'93). The Packing model suggests that the entanglement molecular weight Me is determined by Me = K p^3, where the packing length parameter p = V/R^2 in which V is the volume of the chain (V=M/ρNa), R is the end-to end vector of the chain, and K 357 ρNa, is an empirical constant. The Percolation model states that an entanglement network develops when the number of chains per unit area σ, intersecting any load bearing plane, is equal to 3 times the number of chain segments (1/a cross-section), such that when 3aσ =1 at the percolation threshold, Me 31 MjC∞, in which Mj is the step molecular weight and C∞ is the characteristic ratio. There are no fitting parameters in the Percolation model. The Packing model predicts that Me decreases rapidly with chain stiffness, as Me˜1/C∞^3, while the Percolation model predicts that Me increases with C∞, as Me˜C∞. The Percolation model was found to be the correct model based on computer simulations (M. Bulacu et al) and a re-analysis of the Packing model experimental data. The Packing model can be derived from the Percolation model, but not visa versa, and reveals a surprising accidental relation between C∞ and Mj in the front factor K. This result significantly impacts the interpretation of the dynamics of rheology and fracture of entangled polymers.

Tuning jammed frictionless disk packings from isostatic to hyperstatic.

PubMed

Schreck, Carl F; O'Hern, Corey S; Silbert, Leonardo E

2011-07-01

We perform extensive computational studies of two-dimensional static bidisperse disk packings using two distinct packing-generation protocols. The first involves thermally quenching equilibrated liquid configurations to zero temperature over a range of thermal quench rates r and initial packing fractions followed by compression and decompression in small steps to reach packing fractions φ(J) at jamming onset. For the second, we seed the system with initial configurations that promote micro- and macrophase-separated packings followed by compression and decompression to φ(J). Using these protocols, we generate more than 10(4) static packings over a wide range of packing fraction, contact number, and compositional and positional order. We find that disordered, isostatic packings exist over a finite range of packing fractions in the large-system limit. In agreement with previous calculations, the most dilute mechanically stable packings with φ min ≈ 0.84 are obtained for r > r*, where r* is the rate above which φ(J) is insensitive to rate. We further compare the structural and mechanical properties of isostatic versus hyperstatic packings. The structural characterizations include the contact number, several order parameters, and mixing ratios of the large and small particles. We find that the isostatic packings are positionally and compositionally disordered (with only small changes in a number of order parameters), whereas bond-orientational and compositional order increase strongly with contact number for hyperstatic packings. In addition, we calculate the static shear modulus and normal mode frequencies (in the harmonic approximation) of the static packings to understand the extent to which the mechanical properties of disordered, isostatic packings differ from partially ordered packings. We find that the mechanical properties of the packings change continuously as the contact number increases from isostatic to hyperstatic.

Random sphere packing model of heterogeneous propellants

NASA Astrophysics Data System (ADS)

Kochevets, Sergei Victorovich

It is well recognized that combustion of heterogeneous propellants is strongly dependent on the propellant morphology. Recent developments in computing systems make it possible to start three-dimensional modeling of heterogeneous propellant combustion. A key component of such large scale computations is a realistic model of industrial propellants which retains the true morphology---a goal never achieved before. The research presented develops the Random Sphere Packing Model of heterogeneous propellants and generates numerical samples of actual industrial propellants. This is done by developing a sphere packing algorithm which randomly packs a large number of spheres with a polydisperse size distribution within a rectangular domain. First, the packing code is developed, optimized for performance, and parallelized using the OpenMP shared memory architecture. Second, the morphology and packing fraction of two simple cases of unimodal and bimodal packs are investigated computationally and analytically. It is shown that both the Loose Random Packing and Dense Random Packing limits are not well defined and the growth rate of the spheres is identified as the key parameter controlling the efficiency of the packing. For a properly chosen growth rate, computational results are found to be in excellent agreement with experimental data. Third, two strategies are developed to define numerical samples of polydisperse heterogeneous propellants: the Deterministic Strategy and the Random Selection Strategy. Using these strategies, numerical samples of industrial propellants are generated. The packing fraction is investigated and it is shown that the experimental values of the packing fraction can be achieved computationally. It is strongly believed that this Random Sphere Packing Model of propellants is a major step forward in the realistic computational modeling of heterogeneous propellant of combustion. In addition, a method of analysis of the morphology of heterogeneous

On the kinetics of the pack - Aluminization process

NASA Technical Reports Server (NTRS)

Sivakumar, R.; Seigle, L. L.

1976-01-01

An investigation has been made of the aluminization of unalloyed Ni in fluoride-activated packs of varying Al activity. In packs of low Al activity, in which the ratio of Al to Ni was less than 50 at. pct, the specimen surface quickly came to equilibrium with the pack and remained close to equilibrium for the duration of normal coating runs. In these packs the kinetics of aluminization was controlled by diffusion in the solid. In packs of higher Al activity the surface of the specimen did not come to equilibrium with the pack and the kinetics of the process was governed by a combination of solid and gas diffusion rates. Under most conditions however, the surface composition was time-invariant and a steady-state appeared to exist at the pack-coating interface. By combining Levine and Caves' model for gaseous diffusion in pure-Al packs with calculations of solid diffusion rates some success has been achieved in explaining the results.

A new crystal form of a hyperthermophilic endocellulase

PubMed Central

Kataoka, Misumi; Ishikawa, Kazuhiko

2014-01-01

The hyperthermophilic glycoside hydrolase family endocellulase 12 from the archaeon Pyrococcus furiosus (EGPf; Gene ID PF0854; EC 3.2.1.4) catalyzes the hydrolytic cleavage of the β-1,4-glucosidic linkage in β-glucan in lignocellulose biomass. A crystal of EGPf was previously prepared at pH 9.0 and its structure was determined at an atomic resolution of 1.07 Å. This article reports the crystallization of EGPf at the more physiologically relevant pH of 5.5. Structure determination showed that this new crystal form has the symmetry of space group C2. Two molecules of the enzyme are observed in the asymmetric unit. Crystal packing is weak at pH 5.5 owing to two flexible interfaces between symmetry-related molecules. Comparison of the EGPf structures obtained at pH 9.0 and pH 5.5 reveals a significant conformational difference at the active centre and in the surface loops. The interfaces in the vicinity of the flexible surface loops impact the quality of the EGPf crystal. PMID:25005081

7 CFR 982.11 - Pack.

Code of Federal Regulations, 2010 CFR

2010-01-01

... according to size, internal quality, and external appearance and condition of hazelnuts packed in accordance... 7 Agriculture 8 2010-01-01 2010-01-01 false Pack. 982.11 Section 982.11 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Marketing Agreements and...

From Global Stresses to Local Cell Packing During Development

NASA Astrophysics Data System (ADS)

Lubensky, David

2011-03-01

To perform their functions, cells in epithelial tissues must often adopt highly regular packings. It is still not fully understood how these ordered arrangements of cells arise from disordered, proliferative epithelia during development. I will use experimental and theoretical studies on an attractive model system, the cone cell mosaic in fish retina, to illustrate some ways that mechanical forces and cell signaling can interact to produce this transformation. Experiments examining the response to surgical lesions suggest that the correct mechanical environment at the tissue scale is essential to induce cone cells to rearrange into a rectangular lattice. Starting from this observation, I will argue that large-scale mechanical stresses naturally couple to and orient cell polarization and that this coupling can lead cells to line up in regular rows, as observed in the fish retina. This model predicts that cells in the rows will adopt characteristic trapezoidal shapes and that fragments of rows will persist even in tissue where the mosaic pattern is disrupted by lesions; these predictions are borne out by an analysis of cell packings at the level of the zonula occludens in wildtype and lesioned retinas. Supported by NSF grant IOS-0952873.

7 CFR 51.2840 - Export packing requirements.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 2 2010-01-01 2010-01-01 false Export packing requirements. 51.2840 Section 51.2840 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards...) Export Packing Requirements § 51.2840 Export packing requirements. Onions specified as meeting Export...

Hard sphere packings within cylinders.

PubMed

Fu, Lin; Steinhardt, William; Zhao, Hao; Socolar, Joshua E S; Charbonneau, Patrick

2016-03-07

Arrangements of identical hard spheres confined to a cylinder with hard walls have been used to model experimental systems, such as fullerenes in nanotubes and colloidal wire assembly. Finding the densest configurations, called close packings, of hard spheres of diameter σ in a cylinder of diameter D is a purely geometric problem that grows increasingly complex as D/σ increases, and little is thus known about the regime for D > 2.873σ. In this work, we extend the identification of close packings up to D = 4.00σ by adapting Torquato-Jiao's adaptive-shrinking-cell formulation and sequential-linear-programming (SLP) technique. We identify 17 new structures, almost all of them chiral. Beyond D ≈ 2.85σ, most of the structures consist of an outer shell and an inner core that compete for being close packed. In some cases, the shell adopts its own maximum density configuration, and the stacking of core spheres within it is quasiperiodic. In other cases, an interplay between the two components is observed, which may result in simple periodic structures. In yet other cases, the very distinction between the core and shell vanishes, resulting in more exotic packing geometries, including some that are three-dimensional extensions of structures obtained from packing hard disks in a circle.

Liquid Crystals: The Phase of the Future.

ERIC Educational Resources Information Center

Ondris-Crawford, Renate; And Others

1992-01-01

Liquid crystal displays are currently utilized to convey information via graphic displays. Presents experiments and explanations that employ the concept of liquid crystals to learn concepts related to the various states of matter, electric and magnetic forces, refraction of light, and optics. Discusses applications of liquid crystal technology.…

Mechanisms for pressure-induced crystal-crystal transition, amorphization, and devitrification of Snl 4

DOE PAGES

Liu, Hanyu; Tse, John S.; Hu, Michael Y.; ...

2015-10-27

The pressure-induced amorphization and subsequent recrystallization of SnI 4 have been investigated using first principles molecular dynamics calculations together with high-pressure 119Sn nuclear resonant inelastic x-ray scattering measurements. Above ~8 GPa, we observe a transformation from an ambient crystalline phase to an intermediate crystal structure and a subsequent recrystallization into a cubic phase at ~64 GPa. The crystalline-to-amorphous transition was identified on the basis of elastic compatibility criteria. The measured tin vibrational density of states shows large amplitude librations of SnI 4 under ambient conditions. Although high pressure structures of SnI 4 were thought to be determined by random packingmore » of equal-sized spheres, we detected electron charge transfer in each phase. As a result, this charge transfer results in a crystal structure packing determined by larger than expected iodine atoms. (C) 2015 AIP Publishing LLC.« less

Comparative study of crystallization process in metallic melts using ab initio molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Debela, Tekalign T.; Wang, X. D.; Cao, Q. P.; Zhang, D. X.; Jiang, J. Z.

2017-05-01

The crystallization process of liquid metals is studied using ab initio molecular dynamics simulations. The evolution of short-range order during quenching in Pb and Zn liquids is compared with body-centered cubic (bcc) Nb and V, and hexagonal closed-packed (hcp) Mg. We found that the fraction and type of the short-range order depends on the system under consideration, in which the icosahedral symmetry seems to dominate in the body-centered cubic metals. Although the local atomic structures in stable liquids are similar, liquid hcp-like Zn, bcc-like Nb and V can be deeply supercooled far below its melting point before crystallization while the supercooled temperature range in liquid Pb is limited. Further investigations into the nucleation process reveal the process of polymorph selection. In the body-centered cubic systems, the polymorph selection occurs in the supercooled state before the nucleation is initiated, while in the closed-packed systems it starts at the time of onset of crystallization. Atoms with bcc-like lattices in all studied supercooled liquids are always detected before the polymorph selection. It is also found that the bond orientational ordering is strongly correlated with the crystallization process in supercooled Zn and Pb liquids.

Optical Investigation of Nanoconfined Crystal Growth

NASA Astrophysics Data System (ADS)

Kohler, F.; Dysthe, D. K.

2015-12-01

Crystals growing in a confined space exert forces on their surroundings. This crystallization force causes deformation of solids and is therefore particularly relevant for the comprehension of geological processes such as replacement and weathering [1]. In addition, these forces are relevant for the understanding of damages in porous building materials caused by crystallization, which is of great economical importance and fundamental for methods that can help to preserve our cultural heritage [2,3]. However, the exact behavior of the growth and the dissolution process in close contact to an interface are still not known in detail. The crystallization, the dissolution and the transport of material is mediated by a nanoconfined water film. We observe brittle NaClO3 crystals growing against a glass surface by optical methods such as reflective interference contrast microscopy (RICM) [4]. In order to carefully control the supersaturation of the fluid close to the crystal interface, a temperature regulated microfluidic system is used (fig. A). The interference based precision of RICM enables to resolve distance variations down to the sub nanometer range without any unwanted disturbances by the measuring method. The combination of RICM with a sensitive camera allows us to observe phenomena such as periodic, wavelike growth of atomic layers. These waves are particularly obvious when observing the difference between two consecutive images (fig. B). In contradiction to some theoretical results, which predict a smooth interface, some recent experiments have shown that the nanoconfined growth surfaces are rough. In combination with theoretical studies and Kinetic Monte Carlo simulations we aim at providing more realistic descriptions of surface energies and energy barriers which are able to explain the discrepancies between experiments and current theory. References:[1] Maliva, Diagenetic replacement controlled by force of crystallization, Geology, August (1988), v. 16 [2] G

Bidispersed Sphere Packing on Spherical Surfaces

NASA Astrophysics Data System (ADS)

Atherton, Timothy; Mascioli, Andrew; Burke, Christopher

Packing problems on spherical surfaces have a long history, originating in the classic Thompson problem of finding the ground state configuration of charges on a sphere. Such packings contain a minimal number of defects needed to accommodate the curvature; this is predictable using the Gauss-Bonnet theorem from knowledge of the topology of the surface and the local symmetry of the ordering. Famously, the packing of spherical particles on a sphere contains a 'scar' transition, where additional defects over those required by topology appear above a certain critical number of particles and self-organize into chains or scars. In this work, we study the packing of bidispersed packings on a sphere, and hence determine the interaction of bidispersity and curvature. The resultant configurations are nearly crystalline for low values of bidispersity and retain scar-like structures; these rapidly become disordered for intermediate values and approach a so-called Appollonian limit at the point where smaller particles can be entirely accommodated within the voids left by the larger particles. We connect our results with studies of bidispersed packings in the bulk and on flat surfaces from the literature on glassy systems and jamming. Supported by a Cottrell Award from the Research Corporation for Science Advancement.

Drag and lift forces in granular media

NASA Astrophysics Data System (ADS)

Guillard, F.; Forterre, Y.; Pouliquen, O.

2013-09-01

Forces exerted on obstacles moving in granular media are studied. The experiment consists in a horizontal cylinder rotating around the vertical axis in a granular medium. Both drag forces and lift forces experienced by the cylinder are measured. The first striking result is obtained during the first half rotation, before the cylinder crosses its wake. Despite the symmetry of the object, a strong lift force is measured, about 20 times the buoyancy. The scaling of this force is studied experimentally. The second remarkable observation is made after several rotations. The drag force dramatically drops and becomes independent of depth, showing that it no longer scales with the hydrostatic pressure. The rotation of the cylinder induces a structure in the packing, which screens the weight of the grains above

Crystal pathologies in macromolecular crystallography.

PubMed

Dauter, Zbigniew; Jaskólski, Mariusz

Macromolecules, such as proteins or nucleic acids, form crystals with a large volume fraction of water, ~50% on average. Apart from typical physical defects and rather trivial poor quality problems, macromolecular crystals, as essentially any crystals, can also suffer from several kinds of pathologies, in which everything seems to be perfect, except that from the structural point of view the interpretation may be very difficult, sometimes even impossible. A frequent nuisance is pseudosymmetry, or non-crystallographic symmetry (NCS), which is particularly nasty when it has translational character. Lattice-translocation defects, also called order-disorder twinning (OD-twinning), occur when molecules are packed regularly in layers but the layers are stacked (without rotation) in two (or more) discrete modes, with a unique translocation vector. Crystal twinning arises when twin domains have different orientations, incompatible with the symmetry of the crystal structure. There are also crystals in which the periodic (lattice) order is broken or absent altogether. When the strict short-range translational order from one unit cell to the next is lost but the long-range order is restored by a periodic modulation, we have a modulated crystal structure. In quasicrystals (not observed for macromolecules yet), the periodic order (in 3D space) is lost completely and the diffraction pattern (which is still discrete) cannot be even indexed using three hkl indices. In addition, there are other physical defects and phenomena (such as high mosaicity, diffraction anisotropy, diffuse scattering, etc.) which make diffraction data processing and structure solution difficult or even impossible.

Prediction of EPR Spectra of Lyotropic Liquid Crystals using a Combination of Molecular Dynamics Simulations and the Model-Free Approach.

PubMed

Prior, Christopher; Oganesyan, Vasily S

2017-09-21

We report the first application of fully atomistic molecular dynamics (MD) simulations to the prediction of the motional electron paramagnetic resonance (EPR) spectra of lyotropic liquid crystals in different aggregation states doped with a paramagnetic spin probe. The purpose of this study is twofold. First, given that EPR spectra are highly sensitive to the motions and order of the spin probes doped within lyotropic aggregates, simulation of EPR line shapes from the results of MD modelling provides an ultimate test bed for the force fields currently employed to model such systems. Second, the EPR line shapes are simulated using the motional parameters extracted from MD trajectories using the Model-Free (MF) approach. Thus a combined MD-EPR methodology allowed us to test directly the validity of the application of the MF approach to systems with multi-component molecular motions. All-atom MD simulations using the General AMBER Force Field (GAFF) have been performed on sodium dodecyl sulfate (SDS) and dodecyltrimethylammonium chloride (DTAC) liquid crystals. The resulting MD trajectories were used to predict and interpret the EPR spectra of pre-micellar, micellar, rod and lamellar aggregates. The predicted EPR spectra demonstrate good agreement with most of experimental line shapes thus confirming the validity of both the force fields employed and the MF approach for the studied systems. At the same time simulation results confirm that GAFF tends to overestimate the packing and the order of the carbonyl chains of the surfactant molecules. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Force Measurements in Magnetic Suspension and Balance System

NASA Technical Reports Server (NTRS)

Kuzin, Alexander; Shapovalov, George; Prohorov, Nikolay

1996-01-01

The description of an infrared telemetry system for measurement of drag forces in Magnetic Suspension and Balance Systems (MSBS) is presented. This system includes a drag force sensor, electronic pack and transmitter placed in the model which is of special construction, and receiver with a microprocessor-based measuring device, placed outside of the test section. Piezosensitive resonators as sensitive elements and non-magnetic steel as the material for the force sensor are used. The main features of the proposed system for load measurements are discussed and the main characteristics are presented.

Battery Pack Thermal Design

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pesaran, Ahmad

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 themore » 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.« less

Growth of potassium sulfate crystals in the presence of organic dyes: in situ characterization by atomic force microscopy

NASA Astrophysics Data System (ADS)

Mauri, Andrea; Moret, Massimo

2000-01-01

In situ atomic force microscopy (AFM) has been used to observe potassium sulfate crystals growing in the presence of acid fuchsin and pyranine. These polysulfonated dyes are well known for their ability to adsorb onto the {1 1 0} and {0 1 0} (pyranine only) crystal faces. Using AFM, we analyzed the changes in surface micromorphology induced by the additives on advancing steps for the {1 1 0} and {0 1 0} surfaces. In situ AFM showed that layers grow by step flow at pre-existing steps by the addition of growth units at the step edges. It has been found that dye concentrations as low as ˜2×10 -6 M for pyranine and ˜4×10 -4 M for acid fuchsin produce significant changes in the step morphology and growth rates. The additive molecules attach to the terraces and pin the growing front. As a consequence, the edges of the growing steps become jagged as the dye molecules are adsorbed onto the crystal surface. At critical dye concentrations crystal growth is heavily hampered or even stopped along certain crystallographic directions producing, on a macroscopic scale, strong habit modifications. The formation of dye inclusions by means of macrosteps overgrowing the poisoned surface was also imaged. Interestingly, comparison of the in situ AFM experiments with previous habit modification studies showed acid fuchsin is also able to enter the {0 1 0} surfaces, a previously unnoticed phenomenon.

Effect of co-crystallization on singlet fission efficiency in pentacene derivatives

NASA Astrophysics Data System (ADS)

Wang, Xiaopeng; Sanders, Samuel; Campos, Luis; Sfeir, Matthew; Marom, Noa

Singlet fission (SF), the conversion of one singlet exciton into two triplet excitons, may lead to a twofold increase in the efficiency of organic photovoltaics. Since SF has been observed in crystalline pentacene, this material has drawn interest both experimentally and theoretically. Recently, it has been shown that SF efficiency in rubrene may be improved by modifying the crystal packing. Here, we study the effect of co-crystallization with small molecule H-bond donors on SF efficiency in pentacene derivatives. Five co-crystals are synthetized and their photoluminescence (PL) and absorption spectra are measured. First-principles calculations based on many-body perturbation theory (MBPT) are then employed to study their excitonic properties. By combining experiment and theory, we demonsrate that excitonic properties, including singlet-triplet gaps, exciton binding energies, and exciton localization, are significantly modulated in pentacene co-crystals. Consequently, co-crystallization becomes an effective strategy for improving SF efficiency in molecular crystals of organic semiconductors.

Impact of molecular packing on electronic polarization in organic crystals: the case of pentacene vs TIPS-pentacene.

PubMed

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

2014-04-30

Polarization energy corresponds to the stabilization of the cation or anion state of an atom or molecule when going from the gas phase to the solid state. The decrease in ionization energy and increase in electron affinity in the solid state are related to the (electronic and nuclear) polarization of the surrounding atoms and molecules in the presence of a charged entity. Here, through a combination of molecular mechanics and quantum mechanics calculations, we evaluate the polarization energies in two prototypical organic semiconductors, pentacene and 6,13-bis(2-(tri-isopropylsilyl)ethynyl)pentacene (TIPS-pentacene). Comparison of the results for the two systems reveals the critical role played by the molecular packing configurations in the determination of the polarization energies and provides physical insight into the experimental data reported by Lichtenberger and co-workers (J. Amer. Chem. Soc. 2010, 132, 580; J. Phys. Chem. C 2010, 114, 13838). Our results underline that the impact of packing configurations, well established in the case of the charge-transport properties, also extends to the polarization properties of π-conjugated materials.

Crystallization of a Keplerate-type polyoxometalate into a superposed kagome-lattice with huge channels.

PubMed

Saito, Masaki; Ozeki, Tomoji

2012-09-07

Crystal structures of two Sr(2+) salts of the Keplerate-type polyoxometalate, [Mo(VI)(72)Mo(V)(60)O(372)(CH(3)COO)(30)(H(2)O)(72)](42-), have been determined by single crystal X-ray diffraction. One compound exhibits a superposed kagome-lattice with huge channels whose diameters measure approximately 3.0 nm, while the arrangement of the Keplerate anions in the other compound approximates to a distorted cubic close packing.

Exploring contribution of intermolecular interactions in supramolecular layered assembly of naphthyridine co-crystals: Insights from Hirshfeld surface analysis of their crystalline states

NASA Astrophysics Data System (ADS)

Seth, Saikat Kumar; Das, Nirmal Kumar; Aich, Krishnendu; Sen, Debabrata; Fun, Hoong-Kun; Goswami, Shyamaprasad

2013-09-01

Co-crystals of 1a and 1b have been prepared by slow evaporation of the solutions of mixtures of 2,7-dimethyl-1,8-naphthyridine (1), urea (a) and thiourea (b). The structures of the complexes are determined by the single crystal X-ray diffraction and a detailed investigation of the crystal packing and classification of intermolecular interactions is presented by means of Hirshfeld surface analysis which is of considerable current interest in crystal engineering. The X-ray study reveals that the co-crystal formers are envisioned to produce N-H⋯N hydrogen bond as well as N-H⋯O/N-H⋯S pair-wise hydrogen bonds and also the weaker aromatic π⋯π interactions which cooperatively take part in the crystal packing. The recurring feature of the self-assembly in the compounds is the appearance of the molecular ribbon through multiple hydrogen bonding which are further stacked into molecular layers by π⋯π stacking interactions. Hirshfeld surface analysis for visually analyzing intermolecular interactions in crystal structures employing molecular surface contours and 2D Fingerprint plots have been used to examine molecular shapes. Crystal structure analysis supported with the Hirshfeld surface and fingerprint plots enabled the identification of the significant intermolecular interactions.

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

PubMed

Allen, Frank H; Motherwell, W D Samuel

2002-06-01

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

48 CFR 552.211-87 - Export packing.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 48 Federal Acquisition Regulations System 4 2010-10-01 2010-10-01 false Export packing. 552.211-87... FORMS SOLICITATION PROVISIONS AND CONTRACT CLAUSES Text of Provisions and Clauses 552.211-87 Export packing. As prescribed in 511.204(b)(7), insert the following clause: Export Packing (JAN 2010) (a...

Crystallization and preliminary X-ray diffraction analysis of West Nile virus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaufmann, Barbel; Plevka, Pavel; Kuhn, Richard J.

2010-05-25

West Nile virus, a human pathogen, is closely related to other medically important flaviviruses of global impact such as dengue virus. The infectious virus was purified from cell culture using polyethylene glycol (PEG) precipitation and density-gradient centrifugation. Thin amorphously shaped crystals of the lipid-enveloped virus were grown in quartz capillaries equilibrated by vapor diffusion. Crystal diffraction extended at best to a resolution of about 25 {angstrom} using synchrotron radiation. A preliminary analysis of the diffraction images indicated that the crystals had unit-cell parameters a {approx_equal} b {approx_equal} 480 {angstrom}, {gamma} = 120{sup o}, suggesting a tight hexagonal packing of onemore » virus particle per unit cell.« less

Trace fluorescent labeling for protein crystallization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pusey, Marc, E-mail: marc.pusey@ixpressgenes.com; Barcena, Jorge; Morris, Michelle

2015-06-27

The presence of a covalently bound fluorescent probe at a concentration of <0.5% does not affect the outcome of macromolecule crystallization screening experiments. Additionally, the fluorescence can be used to determine new, not immediately apparent, lead crystallization conditions. Fluorescence can be a powerful tool to aid in the crystallization of proteins. In the trace-labeling approach, the protein is covalently derivatized with a high-quantum-yield visible-wavelength fluorescent probe. The final probe concentration typically labels ≤0.20% of the protein molecules, which has been shown to not affect the crystal nucleation or diffraction quality. The labeled protein is then used in a plate-screening experimentmore » in the usual manner. As the most densely packed state of the protein is the crystalline form, then crystals show as the brightest objects in the well under fluorescent illumination. A study has been carried out on the effects of trace fluorescent labeling on the screening results obtained compared with nonlabeled protein, and it was found that considering the stochastic nature of the crystal nucleation process the presence of the probe did not affect the outcomes obtained. Other effects are realised when using fluorescence. Crystals are clearly seen even when buried in precipitate. This approach also finds ‘hidden’ leads, in the form of bright spots, with ∼30% of the leads found being optimized to crystals in a single-pass optimization trial. The use of visible fluorescence also enables the selection of colors that bypass interfering substances, and the screening materials do not have to be UV-transparent.« less

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…

New investigations of the guanine trichloro cuprate(II) complex crystal

NASA Astrophysics Data System (ADS)

Fabijanić, Ivana; Matković-Čalogović, Dubravka; Pilepić, Viktor; Ivanišević, Irena; Mohaček-Grošev, Vlasta; Sanković, Krešimir

2017-01-01

Crystals of the guanine trichloro cuprate(II) complex, (HGua)2[Cu2Cl6]·2H2O (HGua = protonated guanine), were prepared and analysed by spectroscopic (IR, Raman) and computational methods. A new single-crystal X-ray diffraction analysis was conducted to obtain data with lower standard uncertainties than those in the previously published structure. Raman and IR spectroscopy and quantum-mechanical analysis gave us new insight into the vibrational states of the (HGua)2[Cu2Cl6]·2H2O crystal. The vibrational spectra of the crystal were assigned by performing a normal coordinate analysis for a free dimer with a centre of inversion as the only symmetry element. The stretching vibration observed at 279 cm-1 in the infrared spectrum corresponds to the N-Cu bond. The noncovalent interaction (NCI) plots and quantum theory of atoms in molecules (QTAIM) analysis of the electron density obtained from periodic DFT calculations elucidated the interactions that exist within the crystal structure. Closed-shell ionic attractions, as well as weak and medium strength hydrogen bonds, prevailed in the crystal packing.

Robust 2-Qubit Gates in a Linear Ion Crystal Using a Frequency-Modulated Driving Force

NASA Astrophysics Data System (ADS)

Leung, Pak Hong; Landsman, Kevin A.; Figgatt, Caroline; Linke, Norbert M.; Monroe, Christopher; Brown, Kenneth R.

2018-01-01

In an ion trap quantum computer, collective motional modes are used to entangle two or more qubits in order to execute multiqubit logical gates. Any residual entanglement between the internal and motional states of the ions results in loss of fidelity, especially when there are many spectator ions in the crystal. We propose using a frequency-modulated driving force to minimize such errors. In simulation, we obtained an optimized frequency-modulated 2-qubit gate that can suppress errors to less than 0.01% and is robust against frequency drifts over ±1 kHz . Experimentally, we have obtained a 2-qubit gate fidelity of 98.3(4)%, a state-of-the-art result for 2-qubit gates with five ions.

Packing of flexible 2D materials in vesicles

NASA Astrophysics Data System (ADS)

Zou, Guijin; Yi, Xin; Zhu, Wenpeng; Gao, Huajian

2018-06-01

To understand the mechanics of cellular packing of two-dimensional (2D) materials, we perform systematic molecular dynamics simulations and theoretical analysis to investigate the packing of a flexible circular sheet in a spherical vesicle and the 2D packing problem of a strip in a cylindrical vesicle. Depending on the system dimensions and the bending rigidity ratio between the confined sheet and the vesicle membrane, a variety of packing morphologies are observed, including a conical shape, a shape of three-fold symmetry, a cylindrically curved shape, an axisymmetrically buckled shape, as well as the initial circular shape. A set of buckling analyses lead to phase diagrams of the packing morphologies of the encapsulated sheets. These results may have important implications on the mechanism of intracellular packing and toxicity of 2D materials.

Relationship Between Equilibrium Forms of Lysozyme Crystals and Precipitant Anions

NASA Technical Reports Server (NTRS)

Nadarajah, Arunan

1996-01-01

Molecular forces, such as electrostatic, hydrophobic, van der Waals and steric forces, are known to be important in determining protein interactions. These forces are affected by the solution conditions and changing the pH, temperature or the ionic strength of the solution can sharply affect protein interactions. Several investigations of protein crystallization have shown that this process is also strongly dependent on solution conditions. As the ionic strength of the solution is increased, the initially soluble protein may either crystallize or form an amorphous precipitate at high ionic strengths. Studies done on the model protein hen egg white lysozyme have shown that different crystal forms can be easily and reproducibly obtained, depending primarily on the anion used to desolubilize the protein. In this study we employ pyranine to probe the effect of various anions on the water structure. Additionally, lysozyme crystallization was carried out at these conditions and the crystal form was determined by X-ray crystallography. The goal of the study was to understand the physico-chemical basis for the effect of changing the anion concentration on the equilibrium form of lysozyme crystals. It will also verify the hypothesis that the anions, by altering the bulk water structure in the crystallizing solutions, alter the surface energy of the between the crystal faces and the solution and, consequently, the equilibrium form of the crystals.

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.

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. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

The effect of nanoparticle packing on capacitive electrode performance.

PubMed

Lee, Younghee; Noh, Seonmyeong; Kim, Min-Sik; Kong, Hye Jeong; Im, Kyungun; Kwon, Oh Seok; Kim, Sungmin; Yoon, Hyeonseok

2016-06-09

Nanoparticles pack together to form macro-scale electrodes in various types of devices, and thus, optimization of the nanoparticle packing is a prerequisite for the realization of a desirable device performance. In this work, we provide in-depth insight into the effect of nanoparticle packing on the performance of nanoparticle-based electrodes by combining experimental and computational findings. As a model system, polypyrrole nanospheres of three different diameters were used to construct pseudocapacitive electrodes, and the performance of the electrodes was examined at various nanosphere diameter ratios and mixed weight fractions. Two numerical algorithms are proposed to simulate the random packing of the nanospheres on the electrode. The binary nanospheres exhibited diverse, complicated packing behaviors compared with the monophasic packing of each nanosphere species. The packing of the two nanosphere species with lower diameter ratios at an optimized composition could lead to more dense packing of the nanospheres, which in turn could contribute to better device performance. The dense packing of the nanospheres would provide more efficient transport pathways for ions because of the reduced inter-nanosphere pore size and enlarged surface area for charge storage. Ultimately, it is anticipated that our approach can be widely used to define the concept of "the best nanoparticle packing" for desirable device performance.

Solution-processed, Self-organized Organic Single Crystal Arrays with Controlled Crystal Orientation

PubMed Central

Kumatani, Akichika; Liu, Chuan; Li, Yun; Darmawan, Peter; Takimiya, Kazuo; Minari, Takeo; Tsukagoshi, Kazuhito

2012-01-01

A facile solution process for the fabrication of organic single crystal semiconductor devices which meets the demand for low-cost and large-area fabrication of high performance electronic devices is demonstrated. In this paper, we develop a bottom-up method which enables direct formation of organic semiconductor single crystals at selected locations with desired orientations. Here oriented growth of one-dimensional organic crystals is achieved by using self-assembly of organic molecules as the driving force to align these crystals in patterned regions. Based upon the self-organized organic single crystals, we fabricate organic field effect transistor arrays which exhibit an average field-effect mobility of 1.1 cm2V−1s−1. This method can be carried out under ambient atmosphere at room temperature, thus particularly promising for production of future plastic electronics. PMID:22563523

Leadership in wolf, Canis lupus, packs

USGS Publications Warehouse

Mech, L. David

2000-01-01

I examine leadership in Wolf (Canis lupus) packs based on published observations and data gathered during summers from 1986 to 1998 studying a free-ranging pack of Wolves on Ellesmere Island that were habituated to my presence. The breeding male tended to initiate activities associated with foraging and travel, and the breeding female to initiate, and predominate in, pup care and protection. However, there was considerable overlap and interaction during these activities such that leadership could be considered a joint function. In packs with multiple breeders, quantitative information about leadership is needed.

Physical reconstruction of packed beds and their morphological analysis: core-shell packings as an example.

PubMed

Bruns, Stefan; Tallarek, Ulrich

2011-04-08

We report a fast, nondestructive, and quantitative approach to characterize the morphology of packed beds of fine particles by their three-dimensional reconstruction from confocal laser scanning microscopy images, exemplarily shown for a 100μm i.d. fused-silica capillary packed with 2.6μm-sized core-shell particles. The presented method is generally applicable to silica-based capillary columns, monolithic or particulate, and comprises column pretreatment, image acquisition, image processing, and statistical analysis of the image data. It defines a unique platform for fundamental comparisons of particulate and monolithic supports using the statistical measures derived from their reconstructions. Received morphological data are column cross-sectional porosity profiles and chord length distributions from the interparticle macropore space, which are a descriptor of local density and can be characterized by a simplified k-gamma distribution. This distribution function provides a parameter of location and a parameter of dispersion which can be correlated to individual chromatographic band broadening processes (i.e., to transchannel and short-range interchannel contributions to eddy dispersion, respectively). Together with the transcolumn porosity profile the presented approach allows to analyze and quantify the packing microstructure from pore to column scale and therefore holds great promise in a comparative study of packing conditions and particle properties, particularly for characterizing and minimizing the packing process-specific heterogeneities in the final bed structure. Copyright © 2011 Elsevier B.V. All rights reserved.

Nonuniversality of density and disorder in jammed sphere packings

NASA Astrophysics Data System (ADS)

Jiao, Yang; Stillinger, Frank H.; Torquato, Salvatore

2011-01-01

We show for the first time that collectively jammed disordered packings of three-dimensional monodisperse frictionless hard spheres can be produced and tuned using a novel numerical protocol with packing density ϕ as low as 0.6. This is well below the value of 0.64 associated with the maximally random jammed state and entirely unrelated to the ill-defined "random loose packing" state density. Specifically, collectively jammed packings are generated with a very narrow distribution centered at any density ϕ over a wide density range ϕ ɛ(0.6,0.740 48…) with variable disorder. Our results support the view that there is no universal jamming point that is distinguishable based on the packing density and frequency of occurrence. Our jammed packings are mapped onto a density-order-metric plane, which provides a broader characterization of packings than density alone. Other packing characteristics, such as the pair correlation function, average contact number, and fraction of rattlers are quantified and discussed.

In situ observation of containerless protein crystallization by magnetically levitating crystal growth

NASA Astrophysics Data System (ADS)

Maki, Syou; Tanimoto, Yoshifumi; Udagawa, Chikako; Morimoto, Shotaro; Hagiwara, Masayuki

2016-03-01

We report on the results of the crystal growth of hen-egg lysozyme by magnetically levitating crystals in a small amount of buffer solution. The concentrations of lysozyme and the precipitating agent (gadolinium chloride) were 6.53 wt % and 0.362 mol/kg, respectively. Gadolinium chloride, which induces the magneto-Archimedes effect, was utilized to levitate the crystals with Bz · (dBz/dz) = 22.46 T2/m, where Bz is the vertical (z) component of the magnetic flux density vector. Although the collected crystals were small, we succeeded in maintaining the levitation of the crystals into a specific place in the liquid phase from the beginning of nucleation. In situ observation revealed that a state of pseudo-weightlessness was generated in the vicinity of the magnet bore edge, and small crystals were concentrated inside the domain moving along an hourglass-shaped surface. We found by numerical computations that the formation of the hourglass-shaped domain is attributable to the radial component of the magnetic force.

Sixty years from discovery to solution: crystal structure of bovine liver catalase form III

DOE Office of Scientific and Technical Information (OSTI.GOV)

Foroughi, Leila M.; Kang, You-Na; Matzger, Adam J.

2012-03-27

The crystallization and structural characterization of bovine liver catalase (BLC) has been intensively studied for decades. Forms I and II of BLC have previously been fully characterized using single-crystal X-ray diffraction. Form III has previously been analyzed by electron microscopy, but owing to the thinness of this crystal form an X-ray crystal structure had not been determined. Here, the crystal structure of form III of BLC is presented in space group P212121, with unit-cell parameters a = 68.7, b = 173.7, c = 186.3 {angstrom}. The asymmetric unit is composed of the biological tetramer, which is packed in a tetrahedronmore » motif with three other BLC tetramers. This higher resolution structure has allowed an assessment of the previously published electron-microscopy studies.« less

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%H 2 O 2 ; Group III- 35%H 2 O 2 + artificial saliva; Group IV- 35%H 2 O 2 + catalase+ artificial saliva; Group V- 35%H 2 O 2 + 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. H 2 O 2 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.

Motion of packings of frictional grains.

PubMed

Halsey, Thomas C

2009-07-01

Friction plays a key role in controlling the rheology of dense granular flows. Counting the number of constraints vs the number of variables indicates that critical coordination numbers Zc=3 (in D=2) and Zc=4 (in D=3) are special, in that states in which all contacts roll without frictional sliding are naively possible at and below these average coordination numbers. We construct an explicit example of such a state in D=2 based on a honeycomb lattice. This state has surprisingly large values for the typical angular velocities of the particles. Solving for the forces in such a state, we conclude that organized shear can exist in this state only on scales lforces between a significant fraction of the grains. Moving to disordered lattices, we observe that rolling regions in such lattices are characterized by an antiferromagnetic short-range ordering of the particle rotations; the frustration of this ordering links the shearing states of the grain packing to low-energy spin-glass states on the same lattice. Random lattice states are also expected to exhibit large values for the typical angular velocities and to also have regions of coherent shear limited to be smaller than l.

An Amino Acid Code for β-sheet Packing Structure

PubMed Central

Joo, Hyun; Tsai, Jerry

2014-01-01

To understand the relationship between protein sequence and structure, this work extends the knob-socket model in an investigation of β-sheet packing. Over a comprehensive set of β-sheet folds, the contacts between residues were used to identify packing cliques: sets of residues that all contact each other. These packing cliques were then classified based on size and contact order. From this analysis, the 2 types of 4 residue packing cliques necessary to describe β-sheet packing were characterized. Both occur between 2 adjacent hydrogen bonded β-strands. First, defining the secondary structure packing within β-sheets, the combined socket or XY:HG pocket consists of 4 residues i,i+2 on one strand and j,j+2 on the other. Second, characterizing the tertiary packing between β-sheets, the knob-socket XY:H+B consists of a 3 residue XY:H socket (i,i+2 on one strand and j on the other) packed against a knob B residue (residue k distant in sequence). Depending on the packing depth of the knob B residue, 2 types of knob-sockets are found: side-chain and main-chain sockets. The amino acid composition of the pockets and knob-sockets reveal the sequence specificity of β-sheet packing. For β-sheet formation, the XY:HG pocket clearly shows sequence specificity of amino acids. For tertiary packing, the XY:H+B side-chain and main-chain sockets exhibit distinct amino acid preferences at each position. These relationships define an amino acid code for β-sheet structure and provide an intuitive topological mapping of β-sheet packing. PMID:24668690

[Research progress on the management of no packing after septoplasty].

PubMed

Lu, Sheng; Zhang, Longcheng; Li, Jieen

2016-01-01

Packing the nose after septoplasty is common practice. The use of postoperative packing has been proposed to reduce the dead space between the subperichondrial flaps and minimize postoperative complications such as hemorrhage, septal hematoma, and formation of synechiae. Additionally, postoperative packing is thought to stabilize the remaining cartilaginous septum and minimize persistence or recurrence of septal deviation. Despite these theoretic advantages, evidence to support the use of postoperative packing is lacking. Additionally, nasal packing is not an innocuous procedure. The use of nasal packing actually cause these complications such as postop- erative pain, mucosal injury, bleeding, worsening of breathing due to sleep disorders, and postoperative infections. Routine use of anterior nasal packing after septoplasty should be challenged for not presenting proven benefit. As alternatives to traditional packing, septal suturing, septal stapler and fibrin glue have been used recently. The purpose of this article is to summarize the progress of traditional packing to no packing after septoplasty.

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…

Spontaneously Flowing Crystal of Self-Propelled Particles

NASA Astrophysics Data System (ADS)

Briand, Guillaume; Schindler, Michael; Dauchot, Olivier

2018-05-01

We experimentally and numerically study the structure and dynamics of a monodisperse packing of spontaneously aligning self-propelled hard disks. The packings are such that their equilibrium counterparts form perfectly ordered hexagonal structures. Experimentally, we first form a perfect crystal in a hexagonal arena which respects the same crystalline symmetry. Frustration of the hexagonal order, obtained by removing a few particles, leads to the formation of a rapidly diffusing "droplet." Removing more particles, the whole system spontaneously forms a macroscopic sheared flow, while conserving an overall crystalline structure. This flowing crystalline structure, which we call a "rheocrystal," is made possible by the condensation of shear along localized stacking faults. Numerical simulations very well reproduce the experimental observations and allow us to explore the parameter space. They demonstrate that the rheocrystal is induced neither by frustration nor by noise. They further show that larger systems flow faster while still remaining ordered.

27 CFR 24.308 - Bottled or packed wine record.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Bottled or packed wine... BUREAU, DEPARTMENT OF THE TREASURY LIQUORS WINE Records and Reports § 24.308 Bottled or packed wine record. A proprietor who bottles, packs, or receives bottled or packed beverage wine in bond shall...

Close-packed monolayer self-assembly of silica nanospheres assisted by infrared irradiation

NASA Astrophysics Data System (ADS)

Minh, Nguyen Van; Hue, Nguyen Thi; Lien, Nghiem Thi Ha; Hoang, Chu Manh

2018-01-01

In this paper, we report on a fast and cost-effective drop coating technique for the self-assembly of silica nano-spheres from a mono-dispersed colloidal suspension into close-packed monolayer (CMP) on hydrophilic single-crystal silicon substrate. The technique includes the self-assembly of silica nano-spheres on slanted silicon substrate and infrared irradiation during evaporation process of the coated droplet. The influence of the substrate slant angle and infrared irradiation on the formation of silica nano-sphere monolayer is investigated. This achievement is promising for various applications, such as a mask layer for nano-sphere lithography that is employed for producing fundamental elements in photonics, plasmonics, and solar cell. [Figure not available: see fulltext.

The Physics of Protein Crystallization

NASA Technical Reports Server (NTRS)

Vekilov, P. G.; Chernov, A. A.

2002-01-01

This paper covers review of recent research on protein crystal properties, nucleation, growth and perfection. Mechanical properties of crystals built of molecules strongly exceeding the range of molecular forces are very different from conventional ones. Similar scaling is responsible for specificity of phase equilibrium for macromolecular systems of which thermodynamics is discussed. Nucleation and growth peculiarity and similarity in protein solutions as compared to inorganic solutions is addressed. Hypotheses on why and when microgravity (lack of convection) conditions may result in more perfect crystals are discussed.

Defects in crystalline packings of twisted filament bundles. I. Continuum theory of disclinations.

PubMed

Grason, Gregory M

2012-03-01

We develop the theory of the coupling between in-plane order and out-of-plane geometry in twisted, two-dimensionally ordered filament bundles based on the nonlinear continuum elasticity theory of columnar materials. We show that twisted textures of filament backbones necessarily introduce stresses into the cross-sectional packing of bundles and that these stresses are formally equivalent to the geometrically induced stresses generated in thin elastic sheets that are forced to adopt spherical curvature. As in the case of crystalline order on curved membranes, geometrically induced stresses couple elastically to the presence of topological defects in the in-plane order. We derive the effective theory of multiple disclination defects in the cross section of bundle with a fixed twist and show that above a critical degree of twist, one or more fivefold disclinations is favored in the elastic energy ground state. We study the structure and energetics of multidisclination packings based on models of equilibrium and nonequilibrium cross-sectional order.

Engineering solid-state materials. Strategies for modeling and packing control of molecular assemblies into 3-D networks

NASA Astrophysics Data System (ADS)

Videnova-Adrabinska, V.; Etter, M. C.; Ward, M. D.

1993-04-01

The crystal structure and properties of a number of urea cocrystals are studied with regard to symmetry of the hydrogen-bonded molecular assemblies. The logical consequences of hydrogen bonding interactions are followed step-by-step. The problems of aggregate formation, nucleation, and crystal growth are also elucidated. Endeavor is made to envisage the 2-D and 3-D hydrogen bond network in a manageable way by exploiting graph set short hand. Strategies of how to control the symmetry of molecular packing are still to be elaborated. In our strategy, the programmed self-assembly has been based on the principle of molecular recognition of self- and hetero-complementary functional groups. However, the main focus for pre-organizational control has been put on the two-fold axis estimator of the urea molecule.

Hashish Body Packing: A Case Report

PubMed Central

Soriano-Perez, Manuel Jesus; Serrano-Carrillo, Jose Luis; Marin-Montin, Inmaculada; Cruz-Caballero, Alfonso

2009-01-01

A 42-year-old African male was brought by the police to the emergency department under suspicion of drug smuggling by body-packing. Plain abdominal radiograph showed multiple foreign bodies within the gastrointestinal tract. Contrast-enhanced abdominal CT confirmed the findings, and the patient admitted to have swallowed “balls” of hashish. Body-packing is a recognized method of smuggling drugs across international borders. Body packers may present to the emergency department because of drug toxicity, intestinal obstruction, or more commonly, requested by law-enforcement officers for medical confirmation or exclusion of suspected body packing. PMID:19724651

Invited review liquid crystal models of biological materials and silk spinning.

PubMed

Rey, Alejandro D; Herrera-Valencia, Edtson E

2012-06-01

A review of thermodynamic, materials science, and rheological liquid crystal models is presented and applied to a wide range of biological liquid crystals, including helicoidal plywoods, biopolymer solutions, and in vivo liquid crystals. The distinguishing characteristics of liquid crystals (self-assembly, packing, defects, functionalities, processability) are discussed in relation to biological materials and the strong correspondence between different synthetic and biological materials is established. Biological polymer processing based on liquid crystalline precursors includes viscoelastic flow to form and shape fibers. Viscoelastic models for nematic and chiral nematics are reviewed and discussed in terms of key parameters that facilitate understanding and quantitative information from optical textures and rheometers. It is shown that viscoelastic modeling the silk spinning process using liquid crystal theories sheds light on textural transitions in the duct of spiders and silk worms as well as on tactoidal drops and interfacial structures. The range and consistency of the predictions demonstrates that the use of mesoscopic liquid crystal models is another tool to develop the science and biomimetic applications of mesogenic biological soft matter. Copyright © 2011 Wiley Periodicals, Inc.

36 CFR 34.10 - Saddle and pack animals.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 36 Parks, Forests, and Public Property 1 2014-07-01 2014-07-01 false Saddle and pack animals. 34... INTERIOR EL PORTAL ADMINISTRATIVE SITE REGULATIONS § 34.10 Saddle and pack animals. The use of saddle and pack animals is prohibited without a permit from the Superintendent. ...

36 CFR 34.10 - Saddle and pack animals.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 36 Parks, Forests, and Public Property 1 2011-07-01 2011-07-01 false Saddle and pack animals. 34... INTERIOR EL PORTAL ADMINISTRATIVE SITE REGULATIONS § 34.10 Saddle and pack animals. The use of saddle and pack animals is prohibited without a permit from the Superintendent. ...

36 CFR 34.10 - Saddle and pack animals.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 36 Parks, Forests, and Public Property 1 2013-07-01 2013-07-01 false Saddle and pack animals. 34... INTERIOR EL PORTAL ADMINISTRATIVE SITE REGULATIONS § 34.10 Saddle and pack animals. The use of saddle and pack animals is prohibited without a permit from the Superintendent. ...

36 CFR 34.10 - Saddle and pack animals.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 36 Parks, Forests, and Public Property 1 2012-07-01 2012-07-01 false Saddle and pack animals. 34... INTERIOR EL PORTAL ADMINISTRATIVE SITE REGULATIONS § 34.10 Saddle and pack animals. The use of saddle and pack animals is prohibited without a permit from the Superintendent. ...

36 CFR 34.10 - Saddle and pack animals.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 36 Parks, Forests, and Public Property 1 2010-07-01 2010-07-01 false Saddle and pack animals. 34... INTERIOR EL PORTAL ADMINISTRATIVE SITE REGULATIONS § 34.10 Saddle and pack animals. The use of saddle and pack animals is prohibited without a permit from the Superintendent. ...

21 CFR 880.5760 - Chemical cold pack snakebite kit.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Chemical cold pack snakebite kit. 880.5760 Section... Therapeutic Devices § 880.5760 Chemical cold pack snakebite kit. (a) Identification. A chemical cold pack snakebit kit is a device consisting of a chemical cold pack and tourniquet used for first-aid treatment of...

21 CFR 880.5760 - Chemical cold pack snakebite kit.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Chemical cold pack snakebite kit. 880.5760 Section... Therapeutic Devices § 880.5760 Chemical cold pack snakebite kit. (a) Identification. A chemical cold pack snakebit kit is a device consisting of a chemical cold pack and tourniquet used for first-aid treatment of...

21 CFR 880.5760 - Chemical cold pack snakebite kit.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Chemical cold pack snakebite kit. 880.5760 Section... Therapeutic Devices § 880.5760 Chemical cold pack snakebite kit. (a) Identification. A chemical cold pack snakebit kit is a device consisting of a chemical cold pack and tourniquet used for first-aid treatment of...

21 CFR 880.5760 - Chemical cold pack snakebite kit.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Chemical cold pack snakebite kit. 880.5760 Section... Therapeutic Devices § 880.5760 Chemical cold pack snakebite kit. (a) Identification. A chemical cold pack snakebit kit is a device consisting of a chemical cold pack and tourniquet used for first-aid treatment of...

21 CFR 880.5760 - Chemical cold pack snakebite kit.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Chemical cold pack snakebite kit. 880.5760 Section... Therapeutic Devices § 880.5760 Chemical cold pack snakebite kit. (a) Identification. A chemical cold pack snakebit kit is a device consisting of a chemical cold pack and tourniquet used for first-aid treatment of...

Densest local sphere-packing diversity. II. Application to three dimensions

NASA Astrophysics Data System (ADS)

Hopkins, Adam B.; Stillinger, Frank H.; Torquato, Salvatore

2011-01-01

The densest local packings of N three-dimensional identical nonoverlapping spheres within a radius Rmin(N) of a fixed central sphere of the same size are obtained for selected values of N up to N=1054. In the predecessor to this paper [A. B. Hopkins, F. H. Stillinger, and S. Torquato, Phys. Rev. EPLEEE81063-651X10.1103/PhysRevE.81.041305 81, 041305 (2010)], we described our method for finding the putative densest packings of N spheres in d-dimensional Euclidean space Rd and presented those packings in R2 for values of N up to N=348. Here we analyze the properties and characteristics of the densest local packings in R3 and employ knowledge of the Rmin(N), using methods applicable in any d, to construct both a realizability condition for pair correlation functions of sphere packings and an upper bound on the maximal density of infinite sphere packings. In R3, we find wide variability in the densest local packings, including a multitude of packing symmetries such as perfect tetrahedral and imperfect icosahedral symmetry. We compare the densest local packings of N spheres near a central sphere to minimal-energy configurations of N+1 points interacting with short-range repulsive and long-range attractive pair potentials, e.g., 12-6 Lennard-Jones, and find that they are in general completely different, a result that has possible implications for nucleation theory. We also compare the densest local packings to finite subsets of stacking variants of the densest infinite packings in R3 (the Barlow packings) and find that the densest local packings are almost always most similar as measured by a similarity metric, to the subsets of Barlow packings with the smallest number of coordination shells measured about a single central sphere, e.g., a subset of the fcc Barlow packing. Additionally, we observe that the densest local packings are dominated by the dense arrangement of spheres with centers at distance Rmin(N). In particular, we find two “maracas” packings at N=77 and

Novel Crystal Structure C60 Nanowire

NASA Astrophysics Data System (ADS)

Mickelson, William; Aloni, Shaul; Han, Weiqiang; Cumings, John; Zettl, Alex

2003-03-01

We have created insulated C60 nanowire by packing C60 molecules into the interior of insulating boron nitride (BN) nanotubes. For small-diameter BN tubes, the wire consists of a linear chain of C60's. With increasing BN tube inner diameter, novel C60 stacking configurations are obtained (including helical, hollow core, and incommensurate) which are unknown for bulk or thin film forms of C60. C60 in BN nanotubes presents a model system for studying the properties of new dimensionally-constrained "silo" crystal structures.

Lower limb ice application alters ground reaction force during gait initiation

PubMed Central

Muniz, Thiago B.; Moraes, Renato; Guirro, Rinaldo R. J.

2015-01-01

BACKGROUND: Cryotherapy is a widely used technique in physical therapy clinics and sports. However, the effects of cryotherapy on dynamic neuromuscular control are incompletely explained. OBJECTIVES: To evaluate the effects of cryotherapy applied to the calf, ankle and sole of the foot in healthy young adults on ground reaction forces during gait initiation. METHOD: This study evaluated the gait initiation forces, maximum propulsion, braking forces and impulses of 21 women volunteers through a force platform, which provided maximum and minimum ground reaction force values. To assess the effects of cooling, the task - gait initiation - was performed before ice application, immediately after and 30 minutes after removal of the ice pack. Ice was randomly applied on separate days to the calf, ankle and sole of the foot of the participants. RESULTS: It was demonstrated that ice application for 30 minutes to the sole of the foot and calf resulted in significant changes in the vertical force variables, which returned to their pre-application values 30 minutes after the removal of the ice pack. Ice application to the ankle only reduced propulsion impulse. CONCLUSIONS: These results suggest that although caution is necessary when performing activities that require good gait control, the application of ice to the ankle, sole of the foot or calf in 30-minute intervals may be safe even preceding such activities. PMID:25993625

Lower limb ice application alters ground reaction force during gait initiation.

PubMed

Muniz, Thiago B; Moraes, Renato; Guirro, Rinaldo R J

2015-01-01

Cryotherapy is a widely used technique in physical therapy clinics and sports. However, the effects of cryotherapy on dynamic neuromuscular control are incompletely explained. To evaluate the effects of cryotherapy applied to the calf, ankle and sole of the foot in healthy young adults on ground reaction forces during gait initiation. This study evaluated the gait initiation forces, maximum propulsion, braking forces and impulses of 21 women volunteers through a force platform, which provided maximum and minimum ground reaction force values. To assess the effects of cooling, the task--gait initiation--was performed before ice application, immediately after and 30 minutes after removal of the ice pack. Ice was randomly applied on separate days to the calf, ankle and sole of the foot of the participants. It was demonstrated that ice application for 30 minutes to the sole of the foot and calf resulted in significant changes in the vertical force variables, which returned to their pre-application values 30 minutes after the removal of the ice pack. Ice application to the ankle only reduced propulsion impulse. These results suggest that although caution is necessary when performing activities that require good gait control, the application of ice to the ankle, sole of the foot or calf in 30-minute intervals may be safe even preceding such activities.

Simulation of abuse tolerance of lithium-ion battery packs

NASA Astrophysics Data System (ADS)

Spotnitz, Robert M.; Weaver, James; Yeduvaka, Gowri; Doughty, D. H.; Roth, E. P.

A simple approach for using accelerating rate calorimetry data to simulate the thermal abuse resistance of battery packs is described. The thermal abuse tolerance of battery packs is estimated based on the exothermic behavior of a single cell and an energy balance than accounts for radiative, conductive, and convective heat transfer modes of the pack. For the specific example of a notebook computer pack containing eight 18650-size cells, the effects of cell position, heat of reaction, and heat-transfer coefficient are explored. Thermal runaway of the pack is more likely to be induced by thermal runaway of a single cell when that cell is in good contact with other cells and is close to the pack wall.

Geometrical families of mechanically stable granular packings

NASA Astrophysics Data System (ADS)

Gao, Guo-Jie; Blawzdziewicz, Jerzy; O'Hern, Corey S.

2009-12-01

We enumerate and classify nearly all of the possible mechanically stable (MS) packings of bidipserse mixtures of frictionless disks in small sheared systems. We find that MS packings form continuous geometrical families, where each family is defined by its particular network of particle contacts. We also monitor the dynamics of MS packings along geometrical families by applying quasistatic simple shear strain at zero pressure. For small numbers of particles (N<16) , we find that the dynamics is deterministic and highly contracting. That is, if the system is initialized in a MS packing at a given shear strain, it will quickly lock into a periodic orbit at subsequent shear strain, and therefore sample only a very small fraction of the possible MS packings in steady state. In studies with N>16 , we observe an increase in the period and random splittings of the trajectories caused by bifurcations in configuration space. We argue that the ratio of the splitting and contraction rates in large systems will determine the distribution of MS-packing geometrical families visited in steady state. This work is part of our long-term research program to develop a master-equation formalism to describe macroscopic slowly driven granular systems in terms of collections of small subsystems.

Psychrotrophic Clostridium spp. associated with 'blown pack' spoilage of chilled vacuum-packed red meats and dog rolls in gas-impermeable plastic casings.

PubMed

Broda, D M; DeLacy, K M; Bell, R G; Braggins, T J; Cook, R L

1996-04-01

'Blown pack' spoilage of vacuum-packed chilled beef, lamb and venison, and of a cooked meat product, chilled dog rolls packed in an oxygen-impermeable plastic casing, was characterised by sensory, chemical and microbiological analysis. Investigation of the probable causative agents led to the isolation of eight strains of psychrotrophic clostridia. Three strains have been provisionally identified as C. difficile, C. beijerinckii and C. lituseburense; the other five remain unidentified. In inoculation studies only one isolate produced significant amount of gas on meat, causing pack 'blowing'. It is, therefore, possible that 'blown pack' spoilage involves a synergism with one or more other organisms.

New Cu (II), Co(II) and Ni(II) complexes of chalcone derivatives: Synthesis, X-ray crystal structure, electrochemical properties and DFT computational studies

NASA Astrophysics Data System (ADS)

Tabti, Salima; Djedouani, Amel; Aggoun, Djouhra; Warad, Ismail; Rahmouni, Samra; Romdhane, Samir; Fouzi, Hosni

2018-03-01

The reaction of nickel(II), copper(II) and cobalt(II) with 4-hydroxy-3-[(2E)-3-(1H-indol-3-yl)prop-2-enoyl]-6-methyl-2H-pyran-2-one (HL) leads to a series of new complexes: Ni(L)2(NH3), Cu(L)2(DMF)2 and Co(L)2(H2O). The crystal structure of the Cu(L)2(DMF)2 complex have been determined by X-ray diffraction methods. The Cu(II) lying on an inversion centre is coordinated to six oxygen atoms forming an octahedral elongated. Additionally, the electrochemical behavior of the metal complexes were investigated by cyclic voltammetry at a glassy carbon electrode (GC) in CH3CN solutions, showing the quasi-reversible redox process ascribed to the reduction of the MII/MI couples. The X-ray single crystal structure data of the complex was matched excellently with the optimized monomer structure of the desired compound; Hirschfeld surface analysis supported the packed crystal lattice 3D network intermolecular forces. HOMO/LUMO energy level and the global reactivity descriptors quantum parameters are also calculated. The electrophilic and nucleophilic potions in the complex surface are theoretically evaluated by molecular electrostatic potential and Mulliken atomic charges analysis.

Wetting of cholesteric liquid crystals.

PubMed

Silvestre, Nuno M; Figueirinhas Pereira, Maria Carolina; Bernardino, Nelson R; Telo da Gama, Margarida M

2016-02-01

We investigate theoretically the wetting properties of cholesteric liquid crystals at a planar substrate. If the properties of substrate and of the interface are such that the cholesteric layers are not distorted, the wetting properties are similar to those of a nematic liquid crystal. If, on the other hand, the anchoring conditions force the distortion of the liquid crystal layers the wetting properties are altered, the free cholesteric-isotropic interface is non-planar and there is a layer of topological defects close to the substrate. These deformations can either promote or hinder the wetting of the substrate by a cholesteric, depending on the properties of the cholesteric liquid crystal.

Structural characterization of the packings of granular regular polygons.

PubMed

Wang, Chuncheng; Dong, Kejun; Yu, Aibing

2015-12-01

By using a recently developed method for discrete modeling of nonspherical particles, we simulate the random packings of granular regular polygons with three to 11 edges under gravity. The effects of shape and friction on the packing structures are investigated by various structural parameters, including packing fraction, the radial distribution function, coordination number, Voronoi tessellation, and bond-orientational order. We find that packing fraction is generally higher for geometrically nonfrustrated regular polygons, and can be increased by the increase of edge number and decrease of friction. The changes of packing fraction are linked with those of the microstructures, such as the variations of the translational and orientational orders and local configurations. In particular, the free areas of Voronoi tessellations (which are related to local packing fractions) can be described by log-normal distributions for all polygons. The quantitative analyses establish a clearer picture for the packings of regular polygons.

Ultrasound liquid crystal lens

NASA Astrophysics Data System (ADS)

Shimizu, Yuki; Koyama, Daisuke; Fukui, Marina; Emoto, Akira; Nakamura, Kentaro; Matsukawa, Mami

2018-04-01

A variable-focus lens using a combination of liquid crystals and ultrasound is discussed. The lens uses a technique based on ultrasound vibration to control the molecular orientation of the liquid crystal. The lens structure is simple, with no mechanical moving parts and no transparent electrodes, which is helpful for device downsizing; the structure consists of a liquid crystal layer sandwiched between two glass substrates with a piezoelectric ring. The tens-of-kHz ultrasonic resonance flexural vibration used to excite the lens generates an acoustic radiation force on the liquid crystal layer to induce changes in the molecular orientation of the liquid crystal. The orientations of the liquid crystal molecules and the optical characteristics of the lens were investigated under ultrasound excitation. Clear optical images were observed through the lens, and the focal point could be controlled using the input voltage to the piezoelectric ring to give the lens its variable-focus action.

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

PubMed Central

2011-01-01

Background Mapping protein primary sequences to their three dimensional folds referred to as the 'second genetic code' remains an unsolved scientific problem. A crucial part of the problem concerns the geometrical specificity in side chain association leading to densely packed protein cores, a hallmark of correctly folded native structures. Thus, any model of packing within proteins should constitute an indispensable component of protein folding and design. Results In this study an attempt has been made to find, characterize and classify recurring patterns in the packing of side chain atoms within a protein which sustains its native fold. The interaction of side chain atoms within the protein core has been represented as a contact network based on the surface complementarity and overlap between associating side chain surfaces. Some network topologies definitely appear to be preferred and they have been termed 'packing motifs', analogous to super secondary structures in proteins. Study of the distribution of these motifs reveals the ubiquitous presence of typical smaller graphs, which appear to get linked or coalesce to give larger graphs, reminiscent of the nucleation-condensation model in protein folding. One such frequently occurring motif, also envisaged as the unit of clustering, the three residue clique was invariably found in regions of dense packing. Finally, topological measures based on surface contact networks appeared to be effective in discriminating sequences native to a specific fold amongst a set of decoys. Conclusions Out of innumerable topological possibilities, only a finite number of specific packing motifs are actually realized in proteins. This small number of motifs could serve as a basis set in the construction of larger networks. Of these, the triplet clique exhibits distinct preference both in terms of composition and geometry. PMID:21605466

Spatially resolved analysis of short-range structure perturbations in a plastically bent molecular crystal

NASA Astrophysics Data System (ADS)

Panda, Manas K.; Ghosh, Soumyajit; Yasuda, Nobuhiro; Moriwaki, Taro; Mukherjee, Goutam Dev; Reddy, C. Malla; Naumov, Panče

2015-01-01

The exceptional mechanical flexibility observed with certain organic crystals defies the common perception of single crystals as brittle objects. Here, we describe the morphostructural consequences of plastic deformation in crystals of hexachlorobenzene that can be bent mechanically at multiple locations to 360° with retention of macroscopic integrity. This extraordinary plasticity proceeds by segregation of the bent section into flexible layers that slide on top of each other, thereby generating domains with slightly different lattice orientations. Microscopic, spectroscopic and diffraction analyses of the bent crystal showed that the preservation of crystal integrity when stress is applied on the (001) face requires sliding of layers by breaking and re-formation of halogen-halogen interactions. Application of stress on the (100) face, in the direction where π···π interactions dominate the packing, leads to immediate crystal disintegration. Within a broader perspective, this study highlights the yet unrecognized extraordinary malleability of molecular crystals with strongly anisotropic supramolecular interactions.